id string | task_type string | pipeline string | difficulty string | num_hops int64 | question string | context string | reasoning_chain dict | answer string | choices list | modalities list | modality_data list | evidence list | metadata unknown | path_confidence_score float64 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
co_path_00200 | path_traversal | coding_variant | medium | 3 | What is the shortest molecular path from AOPEP to SETX through known protein interactions and pathway memberships? | AOPEP GENE_ANNOTATED_WITH_GO_TERM zinc ion binding -> BRCA1 GENE_ANNOTATED_WITH_GO_TERM zinc ion binding -> SETX PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH BRCA1 | {
"steps": [
{
"hop": 1,
"source_node_id": "AOPEP",
"source_node_type": "GENE",
"source_node_label": "AOPEP",
"edge_relation": "GENE_ANNOTATED_WITH_GO_TERM",
"edge_evidence_type": "IEA:InterPro",
"edge_confidence": 0.6,
"edge_source_db": "GO",
"target_node_id"... | AOPEP -> zinc ion binding -> BRCA1 -> SETX | null | [
"expression",
"intercell_role",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "AOPEP",
"source_db": "UniProt",
"payload": {
"accession": "Q8N6M6",
"sequence": "MDIQLDPARDDLPLMANTSHILVKHYVLDLDVDFESQVIEGTIVLFLEDGNRFKKQNSSIEEACQSESNKACKFGMPEPCHIPVTNARTFSSEMEYNDFAICSKGEKDTSDKDGNHDNQEHASGISSSKYCCD... | [
{
"source_db": "GO",
"source_id": "GO:0008270",
"text": "AOPEP GENE_ANNOTATED_WITH_GO_TERM zinc ion binding",
"confidence": 0.6
},
{
"source_db": "GO",
"source_id": "BRCA1",
"text": "BRCA1 GENE_ANNOTATED_WITH_GO_TERM zinc ion binding",
"confidence": 0.6
},
{
"source_db": ... | {
"gene_a": "AOPEP",
"gene_b": "SETX",
"path_length": 3
} | 0.708999 |
co_path_00201 | path_traversal | coding_variant | easy | 3 | What is the shortest molecular path from BCHE to TUBA4A through known protein interactions and pathway memberships? | BCHE PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH APOE -> MAPT PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH APOE -> MAPT PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH TUBA4A | {
"steps": [
{
"hop": 1,
"source_node_id": "BCHE",
"source_node_type": "GENE",
"source_node_label": "BCHE",
"edge_relation": "PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH",
"edge_evidence_type": "multi-channel",
"edge_confidence": 0.835,
"edge_source_db": "STRING",
"t... | BCHE -> APOE -> MAPT -> TUBA4A | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "BCHE",
"source_db": "UniProt",
"payload": {
"accession": "P06276",
"sequence": "MHSKVTIICIRFLFWFLLLCMLIGKSHTEDDIIIATKNGKVRGMNLTVFGGTVTAFLGIPYAQPPLGRLRFKKPQSLTKWSDIWNATKYANSCCQNIDQSFPGFHGSEMWNPNTDLSEDCLYLNVWIPAPKPKN... | [
{
"source_db": "STRING",
"source_id": "APOE",
"text": "BCHE PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH APOE",
"confidence": 0.835
},
{
"source_db": "STRING",
"source_id": "MAPT",
"text": "MAPT PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH APOE",
"confidence": 0.991
},
{
"source_db": "ST... | {
"gene_a": "BCHE",
"gene_b": "TUBA4A",
"path_length": 3
} | 0.932845 |
co_path_00202 | path_traversal | coding_variant | hard | 4 | What is the shortest molecular path from PDE10A to MSH2 through known protein interactions and pathway memberships? | PDE10A GENE_PARTICIPATES_IN_PATHWAY G alpha (s) signalling events -> ADORA2A GENE_PARTICIPATES_IN_PATHWAY G alpha (s) signalling events -> ADORA2A GENE_ANNOTATED_WITH_GO_TERM negative regulation of neuron apoptotic process -> MSH2 GENE_ANNOTATED_WITH_GO_TERM negative regulation of neuron apoptotic process | {
"steps": [
{
"hop": 1,
"source_node_id": "PDE10A",
"source_node_type": "GENE",
"source_node_label": "PDE10A",
"edge_relation": "GENE_PARTICIPATES_IN_PATHWAY",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "Reactome",
"target_node_i... | PDE10A -> G alpha (s) signalling events -> ADORA2A -> negative regulation of neuron apoptotic process -> MSH2 | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "PDE10A",
"source_db": "UniProt",
"payload": {
"accession": "Q9Y233",
"sequence": "MASLEEPLAPRPQGPLPAAGDEPGCGPGKLRPEPRLSAAGGGSAAGPGPAPEWPGRGRAERAAPPRPPLSSAGRPSPAGGPGALSARGGGCGWVAARAPLALAFSSRVPSSSPSFFYFWPPPPPPPPSFLPS... | [
{
"source_db": "Reactome",
"source_id": "R-HSA-418555",
"text": "PDE10A GENE_PARTICIPATES_IN_PATHWAY G alpha (s) signalling events",
"confidence": 1
},
{
"source_db": "Reactome",
"source_id": "ADORA2A",
"text": "ADORA2A GENE_PARTICIPATES_IN_PATHWAY G alpha (s) signalling events",
... | {
"gene_a": "PDE10A",
"gene_b": "MSH2",
"path_length": 4
} | 0.774597 |
co_path_00203 | path_traversal | coding_variant | medium | 3 | What is the shortest molecular path from ABI1 to KIF5A through known protein interactions and pathway memberships? | ABI1 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH ABL1 -> ABL1 GENE_ANNOTATED_WITH_GO_TERM ATP binding -> KIF5A GENE_ANNOTATED_WITH_GO_TERM ATP binding | {
"steps": [
{
"hop": 1,
"source_node_id": "ABI1",
"source_node_type": "GENE",
"source_node_label": "ABI1",
"edge_relation": "PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH",
"edge_evidence_type": "multi-channel",
"edge_confidence": 0.998,
"edge_source_db": "STRING",
"t... | ABI1 -> ABL1 -> ATP binding -> KIF5A | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ABI1",
"source_db": "UniProt",
"payload": {
"accession": "Q8IZP0",
"sequence": "MAELQMLLEEEIPSGKRALIESYQNLTRVADYCENNYIQATDKRKALEETKAYTTQSLASVAYQINALANNVLQLLDIQASQLRRMESSINHISQTVDIHKEKVARREIGILTTNKNTSRTHKIIAPANMERPV... | [
{
"source_db": "STRING",
"source_id": "ABL1",
"text": "ABI1 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH ABL1",
"confidence": 0.998
},
{
"source_db": "GO",
"source_id": "GO:0005524",
"text": "ABL1 GENE_ANNOTATED_WITH_GO_TERM ATP binding",
"confidence": 0.6
},
{
"source_db": "GO",... | {
"gene_a": "ABI1",
"gene_b": "KIF5A",
"path_length": 3
} | 0.710904 |
co_path_00204 | path_traversal | coding_variant | easy | 2 | What is the shortest molecular path from TUBA4A to SQSTM1 through known protein interactions and pathway memberships? | TUBA4A GENE_ANNOTATED_WITH_GO_TERM protein kinase binding -> SQSTM1 GENE_ANNOTATED_WITH_GO_TERM protein kinase binding | {
"steps": [
{
"hop": 1,
"source_node_id": "TUBA4A",
"source_node_type": "GENE",
"source_node_label": "TUBA4A",
"edge_relation": "GENE_ANNOTATED_WITH_GO_TERM",
"edge_evidence_type": "IPI:ARUK-UCL",
"edge_confidence": 0.6,
"edge_source_db": "GO",
"target_node_i... | TUBA4A -> protein kinase binding -> SQSTM1 | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "TUBA4A",
"source_db": "UniProt",
"payload": {
"accession": "P68366",
"sequence": "MRECISVHVGQAGVQMGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFTTFFCETGAGKHVPRAVFVDLEPTVIDEIRNGPYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDPVLDRIRKLSDQCTGL... | [
{
"source_db": "GO",
"source_id": "GO:0019901",
"text": "TUBA4A GENE_ANNOTATED_WITH_GO_TERM protein kinase binding",
"confidence": 0.6
},
{
"source_db": "GO",
"source_id": "SQSTM1",
"text": "SQSTM1 GENE_ANNOTATED_WITH_GO_TERM protein kinase binding",
"confidence": 0.6
}
] | {
"gene_a": "TUBA4A",
"gene_b": "SQSTM1",
"path_length": 2
} | 0.6 |
co_path_00205 | path_traversal | coding_variant | hard | 4 | What is the shortest molecular path from MLH3 to ALB through known protein interactions and pathway memberships? | MLH3 GENE_ANNOTATED_WITH_GO_TERM ATP binding -> ABCA7 GENE_ANNOTATED_WITH_GO_TERM ATP binding -> ABCA7 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH APOA1 -> ALB PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH APOA1 | {
"steps": [
{
"hop": 1,
"source_node_id": "MLH3",
"source_node_type": "GENE",
"source_node_label": "MLH3",
"edge_relation": "GENE_ANNOTATED_WITH_GO_TERM",
"edge_evidence_type": "IEA:InterPro",
"edge_confidence": 0.6,
"edge_source_db": "GO",
"target_node_id": ... | MLH3 -> ATP binding -> ABCA7 -> APOA1 -> ALB | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "MLH3",
"source_db": "UniProt",
"payload": {
"accession": "Q9UHC1",
"sequence": "MIKCLSVEVQAKLRSGLAISSLGQCVEELALNSIDAEAKCVAVRVNMETFQVQVIDNGFGMGSDDVEKVGNRYFTSKCHSVQDLENPRFYGFRGEALANIADMASAVEISSKKNRTMKTFVKLFQSGKALKACE... | [
{
"source_db": "GO",
"source_id": "GO:0005524",
"text": "MLH3 GENE_ANNOTATED_WITH_GO_TERM ATP binding",
"confidence": 0.6
},
{
"source_db": "GO",
"source_id": "ABCA7",
"text": "ABCA7 GENE_ANNOTATED_WITH_GO_TERM ATP binding",
"confidence": 0.6
},
{
"source_db": "STRING",
... | {
"gene_a": "MLH3",
"gene_b": "ALB",
"path_length": 4
} | 0.772656 |
co_path_00206 | path_traversal | coding_variant | medium | 3 | What is the shortest molecular path from FAP to PALB2 through known protein interactions and pathway memberships? | FAP GENE_ANNOTATED_WITH_GO_TERM protease binding -> BRCA2 GENE_ANNOTATED_WITH_GO_TERM protease binding -> BRCA2 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH PALB2 | {
"steps": [
{
"hop": 1,
"source_node_id": "FAP",
"source_node_type": "GENE",
"source_node_label": "FAP",
"edge_relation": "GENE_ANNOTATED_WITH_GO_TERM",
"edge_evidence_type": "IPI:BHF-UCL",
"edge_confidence": 0.6,
"edge_source_db": "GO",
"target_node_id": "GO... | FAP -> protease binding -> BRCA2 -> PALB2 | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "FAP",
"source_db": "UniProt",
"payload": {
"accession": "Q12884",
"sequence": "MKTWVKIVFGVATSAVLALLVMCIVLRPSRVHNSEENTMRALTLKDILNGTFSYKTFFPNWISGQEYLHQSADNNIVLYNIETGQSYTILSNRTMKSVNASNYGLSPDRQFVYLESDYSKLWRYSYTATYYIYDL... | [
{
"source_db": "GO",
"source_id": "GO:0002020",
"text": "FAP GENE_ANNOTATED_WITH_GO_TERM protease binding",
"confidence": 0.6
},
{
"source_db": "GO",
"source_id": "BRCA2",
"text": "BRCA2 GENE_ANNOTATED_WITH_GO_TERM protease binding",
"confidence": 0.6
},
{
"source_db": "S... | {
"gene_a": "FAP",
"gene_b": "PALB2",
"path_length": 3
} | 0.711141 |
co_path_00207 | path_traversal | coding_variant | medium | 4 | What is the shortest molecular path from HTT to ADM through known protein interactions and pathway memberships? | HTT PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH TP53 -> BRCA1 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH TP53 -> BRCA1 GENE_ANNOTATED_WITH_GO_TERM positive regulation of angiogenesis -> ADM GENE_ANNOTATED_WITH_GO_TERM positive regulation of angiogenesis | {
"steps": [
{
"hop": 1,
"source_node_id": "HTT",
"source_node_type": "GENE",
"source_node_label": "HTT",
"edge_relation": "PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH",
"edge_evidence_type": "multi-channel",
"edge_confidence": 0.998,
"edge_source_db": "STRING",
"tar... | HTT -> TP53 -> BRCA1 -> positive regulation of angiogenesis -> ADM | null | [
"expression",
"intercell_role",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "HTT",
"source_db": "UniProt",
"payload": {
"accession": "P42858",
"sequence": "MATLEKLMKAFESLKSFQQQQQQQQQQQQQQQQQQQQQPPPPPPPPPPPQLPQPPPQAQPLLPQPQPPPPPPPPPPGPAVAEEPLHRPKKELSATKKDRVNHCLTICENIVAQSVRNSPEFQKLLGIAMELFLLC... | [
{
"source_db": "STRING",
"source_id": "TP53",
"text": "HTT PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH TP53",
"confidence": 0.998
},
{
"source_db": "STRING",
"source_id": "BRCA1",
"text": "BRCA1 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH TP53",
"confidence": 0.999
},
{
"source_db": "G... | {
"gene_a": "HTT",
"gene_b": "ADM",
"path_length": 4
} | 0.774015 |
co_path_00208 | path_traversal | coding_variant | medium | 4 | What is the shortest molecular path from PDE10A to ZMYM3 through known protein interactions and pathway memberships? | PDE10A GENE_ANNOTATED_WITH_GO_TERM metal ion binding -> BIRC5 GENE_ANNOTATED_WITH_GO_TERM metal ion binding -> BIRC5 GENE_ANNOTATED_WITH_GO_TERM zinc ion binding -> ZMYM3 GENE_ANNOTATED_WITH_GO_TERM zinc ion binding | {
"steps": [
{
"hop": 1,
"source_node_id": "PDE10A",
"source_node_type": "GENE",
"source_node_label": "PDE10A",
"edge_relation": "GENE_ANNOTATED_WITH_GO_TERM",
"edge_evidence_type": "IEA:UniProtKB-KW",
"edge_confidence": 0.6,
"edge_source_db": "GO",
"target_no... | PDE10A -> metal ion binding -> BIRC5 -> zinc ion binding -> ZMYM3 | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "PDE10A",
"source_db": "UniProt",
"payload": {
"accession": "Q9Y233",
"sequence": "MASLEEPLAPRPQGPLPAAGDEPGCGPGKLRPEPRLSAAGGGSAAGPGPAPEWPGRGRAERAAPPRPPLSSAGRPSPAGGPGALSARGGGCGWVAARAPLALAFSSRVPSSSPSFFYFWPPPPPPPPSFLPS... | [
{
"source_db": "GO",
"source_id": "GO:0046872",
"text": "PDE10A GENE_ANNOTATED_WITH_GO_TERM metal ion binding",
"confidence": 0.6
},
{
"source_db": "GO",
"source_id": "BIRC5",
"text": "BIRC5 GENE_ANNOTATED_WITH_GO_TERM metal ion binding",
"confidence": 0.6
},
{
"source_db... | {
"gene_a": "PDE10A",
"gene_b": "ZMYM3",
"path_length": 4
} | 0.6 |
co_path_00209 | path_traversal | coding_variant | medium | 3 | What is the shortest molecular path from BNIP3 to MET through known protein interactions and pathway memberships? | BNIP3 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH BCL2 -> BCL2 GENE_ANNOTATED_WITH_GO_TERM negative regulation of autophagy -> MET GENE_ANNOTATED_WITH_GO_TERM negative regulation of autophagy | {
"steps": [
{
"hop": 1,
"source_node_id": "BNIP3",
"source_node_type": "GENE",
"source_node_label": "BNIP3",
"edge_relation": "PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH",
"edge_evidence_type": "multi-channel",
"edge_confidence": 0.999,
"edge_source_db": "STRING",
... | BNIP3 -> BCL2 -> negative regulation of autophagy -> MET | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "BNIP3",
"source_db": "UniProt",
"payload": {
"accession": "Q12983",
"sequence": "MSQNGAPGMQEESLQGSWVELHFSNNGNGGSVPASVSIYNGDMEKILLDAQHESGRSSSKSSHCDSPPRSQTPQDTNRASETDTHSIGEKNSSQSEEDDIERRKEVESILKKNSDWIWDWSSRPENIPPKEFL... | [
{
"source_db": "STRING",
"source_id": "BCL2",
"text": "BNIP3 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH BCL2",
"confidence": 0.999
},
{
"source_db": "GO",
"source_id": "GO:0010507",
"text": "BCL2 GENE_ANNOTATED_WITH_GO_TERM negative regulation of autophagy",
"confidence": 0.6
},
{
... | {
"gene_a": "BNIP3",
"gene_b": "MET",
"path_length": 3
} | 0.711141 |
co_path_00210 | path_traversal | coding_variant | easy | 2 | What is the shortest molecular path from JAK2 to ADRB1 through known protein interactions and pathway memberships? | JAK2 GENE_ANNOTATED_WITH_GO_TERM positive regulation of cold-induced thermogenesis -> ADRB1 GENE_ANNOTATED_WITH_GO_TERM positive regulation of cold-induced thermogenesis | {
"steps": [
{
"hop": 1,
"source_node_id": "JAK2",
"source_node_type": "GENE",
"source_node_label": "JAK2",
"edge_relation": "GENE_ANNOTATED_WITH_GO_TERM",
"edge_evidence_type": "ISS:YuBioLab",
"edge_confidence": 0.6,
"edge_source_db": "GO",
"target_node_id": ... | JAK2 -> positive regulation of cold-induced thermogenesis -> ADRB1 | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "JAK2",
"source_db": "UniProt",
"payload": {
"accession": "O60674",
"sequence": "MGMACLTMTEMEGTSTSSIYQNGDISGNANSMKQIDPVLQVYLYHSLGKSEADYLTFPSGEYVAEEICIAASKACGITPVYHNMFALMSETERIWYPPNHVFHIDESTRHNVLYRIRFYFPRWYCSGSNRAYRH... | [
{
"source_db": "GO",
"source_id": "GO:0120162",
"text": "JAK2 GENE_ANNOTATED_WITH_GO_TERM positive regulation of cold-induced thermogenesis",
"confidence": 0.6
},
{
"source_db": "GO",
"source_id": "ADRB1",
"text": "ADRB1 GENE_ANNOTATED_WITH_GO_TERM positive regulation of cold-induced... | {
"gene_a": "JAK2",
"gene_b": "ADRB1",
"path_length": 2
} | 0.6 |
co_path_00211 | path_traversal | coding_variant | easy | 2 | What is the shortest molecular path from FLT3 to ADAM10 through known protein interactions and pathway memberships? | FLT3 GENE_ANNOTATED_WITH_GO_TERM positive regulation of cell population proliferation -> ADAM10 GENE_ANNOTATED_WITH_GO_TERM positive regulation of cell population proliferation | {
"steps": [
{
"hop": 1,
"source_node_id": "FLT3",
"source_node_type": "GENE",
"source_node_label": "FLT3",
"edge_relation": "GENE_ANNOTATED_WITH_GO_TERM",
"edge_evidence_type": "IBA:GO_Central",
"edge_confidence": 0.6,
"edge_source_db": "GO",
"target_node_id"... | FLT3 -> positive regulation of cell population proliferation -> ADAM10 | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "FLT3",
"source_db": "UniProt",
"payload": {
"accession": "P36888",
"sequence": "MPALARDGGQLPLLVVFSAMIFGTITNQDLPVIKCVLINHKNNDSSVGKSSSYPMVSESPEDLGCALRPQSSGTVYEAAAVEVDVSASITLQVLVDAPGNISCLWVFKHSSLNCQPHFDLQNRGVVSMVILKMT... | [
{
"source_db": "GO",
"source_id": "GO:0008284",
"text": "FLT3 GENE_ANNOTATED_WITH_GO_TERM positive regulation of cell population proliferation",
"confidence": 0.6
},
{
"source_db": "GO",
"source_id": "ADAM10",
"text": "ADAM10 GENE_ANNOTATED_WITH_GO_TERM positive regulation of cell po... | {
"gene_a": "FLT3",
"gene_b": "ADAM10",
"path_length": 2
} | 0.6 |
co_path_00212 | path_traversal | coding_variant | hard | 4 | What is the shortest molecular path from CASS4 to AVPR1A through known protein interactions and pathway memberships? | CASS4 GENE_ANNOTATED_WITH_GO_TERM positive regulation of cell migration -> ADRA2A GENE_ANNOTATED_WITH_GO_TERM positive regulation of cell migration -> ADRA2A PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH GNAQ -> AVPR1A PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH GNAQ | {
"steps": [
{
"hop": 1,
"source_node_id": "CASS4",
"source_node_type": "GENE",
"source_node_label": "CASS4",
"edge_relation": "GENE_ANNOTATED_WITH_GO_TERM",
"edge_evidence_type": "IMP:UniProtKB",
"edge_confidence": 0.6,
"edge_source_db": "GO",
"target_node_id... | CASS4 -> positive regulation of cell migration -> ADRA2A -> GNAQ -> AVPR1A | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CASS4",
"source_db": "UniProt",
"payload": {
"accession": "Q9NQ75",
"sequence": "MKGTGIMDCAPKALLARALYDNCPDCSDELAFSRGDILTILEQHVPESEGWWKCLLHGRQGLAPANRLQILTEVAADRPCPPFLRGLEEAPASSEETYQVPTLPRPPTPGPVYEQMRSWAEGPQPPTAQVYEF... | [
{
"source_db": "GO",
"source_id": "GO:0030335",
"text": "CASS4 GENE_ANNOTATED_WITH_GO_TERM positive regulation of cell migration",
"confidence": 0.6
},
{
"source_db": "GO",
"source_id": "ADRA2A",
"text": "ADRA2A GENE_ANNOTATED_WITH_GO_TERM positive regulation of cell migration",
... | {
"gene_a": "CASS4",
"gene_b": "AVPR1A",
"path_length": 4
} | 0.758155 |
co_path_00213 | path_traversal | coding_variant | medium | 4 | What is the shortest molecular path from CFAP410 to CDX2 through known protein interactions and pathway memberships? | CFAP410 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH ALS2 -> ALS2 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH SETX -> SETX GENE_ANNOTATED_WITH_GO_TERM positive regulation of transcription by RNA polymerase II -> CDX2 GENE_ANNOTATED_WITH_GO_TERM positive regulation of transcription by RNA polymerase II | {
"steps": [
{
"hop": 1,
"source_node_id": "CFAP410",
"source_node_type": "GENE",
"source_node_label": "CFAP410",
"edge_relation": "PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH",
"edge_evidence_type": "multi-channel",
"edge_confidence": 0.875,
"edge_source_db": "STRING",
... | CFAP410 -> ALS2 -> SETX -> positive regulation of transcription by RNA polymerase II -> CDX2 | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CFAP410",
"source_db": "UniProt",
"payload": {
"accession": "O43822",
"sequence": "MKLTRKMVLTRAKASELHSVRKLNCWGSRLTDISICQEMPSLEVITLSVNSISTLEPVSRCQRLSELYLRRNRIPSLAELFYLKGLPRLRVLWLAENPCCGTSPHRYRMTVLRTLPRLQKLDNQAVTEEEL... | [
{
"source_db": "STRING",
"source_id": "ALS2",
"text": "CFAP410 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH ALS2",
"confidence": 0.875
},
{
"source_db": "STRING",
"source_id": "SETX",
"text": "ALS2 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH SETX",
"confidence": 0.909
},
{
"source_db": ... | {
"gene_a": "CFAP410",
"gene_b": "CDX2",
"path_length": 4
} | 0.731507 |
co_path_00214 | path_traversal | coding_variant | medium | 3 | What is the shortest molecular path from CDK1 to ADRB1 through known protein interactions and pathway memberships? | BIRC5 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH CDK1 -> BIRC5 GENE_ANNOTATED_WITH_GO_TERM protein heterodimerization activity -> ADRB1 GENE_ANNOTATED_WITH_GO_TERM protein heterodimerization activity | {
"steps": [
{
"hop": 1,
"source_node_id": "CDK1",
"source_node_type": "GENE",
"source_node_label": "CDK1",
"edge_relation": "PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH",
"edge_evidence_type": "multi-channel",
"edge_confidence": 0.997,
"edge_source_db": "STRING",
"t... | CDK1 -> BIRC5 -> protein heterodimerization activity -> ADRB1 | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CDK1",
"source_db": "UniProt",
"payload": {
"accession": "P06493",
"sequence": "MEDYTKIEKIGEGTYGVVYKGRHKTTGQVVAMKKIRLESEEEGVPSTAIREISLLKELRHPNIVSLQDVLMQDSRLYLIFEFLSMDLKKYLDSIPPGQYMDSSLVKSYLYQILQGIVFCHSRRVLHRDLKPQNL... | [
{
"source_db": "STRING",
"source_id": "BIRC5",
"text": "BIRC5 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH CDK1",
"confidence": 0.997
},
{
"source_db": "GO",
"source_id": "GO:0046982",
"text": "BIRC5 GENE_ANNOTATED_WITH_GO_TERM protein heterodimerization activity",
"confidence": 0.6
},... | {
"gene_a": "CDK1",
"gene_b": "ADRB1",
"path_length": 3
} | 0.710667 |
co_path_00215 | path_traversal | coding_variant | medium | 3 | What is the shortest molecular path from LEPR to POLD1 through known protein interactions and pathway memberships? | Single allele VARIANT_IN_GENE LEPR -> Single allele VARIANT_IN_GENE MSH2 -> MSH2 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH POLD1 | {
"steps": [
{
"hop": 1,
"source_node_id": "LEPR",
"source_node_type": "GENE",
"source_node_label": "LEPR",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single allele... | LEPR -> Single allele -> MSH2 -> POLD1 | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "LEPR",
"source_db": "UniProt",
"payload": {
"accession": "P48357",
"sequence": "MICQKFCVVLLHWEFIYVITAFNLSYPITPWRFKLSCMPPNSTYDYFLLPAGLSKNTSNSNGHYETAVEPKFNSSGTHFSNLSKTTFHCCFRSEQDRNCSLCADNIEGKTFVSTVNSLVFQQIDANWNIQCWLK... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE LEPR",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MSH2",
"text": "Single allele VARIANT_IN_GENE MSH2",
"confidence": 1
},
{
"source_db": "STRING",
"source_id... | {
"gene_a": "LEPR",
"gene_b": "POLD1",
"path_length": 3
} | 0.997996 |
co_path_00216 | path_traversal | coding_variant | easy | 2 | What is the shortest molecular path from BRCA1 to MET through known protein interactions and pathway memberships? | BRCA1 GENE_ANNOTATED_WITH_GO_TERM positive regulation of transcription by RNA polymerase II -> MET GENE_ANNOTATED_WITH_GO_TERM positive regulation of transcription by RNA polymerase II | {
"steps": [
{
"hop": 1,
"source_node_id": "BRCA1",
"source_node_type": "GENE",
"source_node_label": "BRCA1",
"edge_relation": "GENE_ANNOTATED_WITH_GO_TERM",
"edge_evidence_type": "IDA:UniProtKB",
"edge_confidence": 0.6,
"edge_source_db": "GO",
"target_node_id... | BRCA1 -> positive regulation of transcription by RNA polymerase II -> MET | null | [
"expression",
"intercell_role",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "BRCA1",
"source_db": "UniProt",
"payload": {
"accession": "P38398",
"sequence": "MDLSALRVEEVQNVINAMQKILECPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRSLQESTRFSQLVEELLKIICAFQLDTGLEYANSYNFAKKENNSPEHLKDEVSIIQSMGYRNR... | [
{
"source_db": "GO",
"source_id": "GO:0045944",
"text": "BRCA1 GENE_ANNOTATED_WITH_GO_TERM positive regulation of transcription by RNA polymerase II",
"confidence": 0.6
},
{
"source_db": "GO",
"source_id": "MET",
"text": "MET GENE_ANNOTATED_WITH_GO_TERM positive regulation of transcr... | {
"gene_a": "BRCA1",
"gene_b": "MET",
"path_length": 2
} | 0.6 |
co_path_00217 | path_traversal | coding_variant | easy | 2 | What is the shortest molecular path from NLRP3 to TARDBP through known protein interactions and pathway memberships? | NLRP3 GENE_ANNOTATED_WITH_GO_TERM DNA-templated transcription -> TARDBP GENE_ANNOTATED_WITH_GO_TERM DNA-templated transcription | {
"steps": [
{
"hop": 1,
"source_node_id": "NLRP3",
"source_node_type": "GENE",
"source_node_label": "NLRP3",
"edge_relation": "GENE_ANNOTATED_WITH_GO_TERM",
"edge_evidence_type": "IEA:UniProtKB-KW",
"edge_confidence": 0.6,
"edge_source_db": "GO",
"target_node... | NLRP3 -> DNA-templated transcription -> TARDBP | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "NLRP3",
"source_db": "UniProt",
"payload": {
"accession": "Q96P20",
"sequence": "MKMASTRCKLARYLEDLEDVDLKKFKMHLEDYPPQKGCIPLPRGQTEKADHVDLATLMIDFNGEEKAWAMAVWIFAAINRRDLYEKAKRDEPKWGSDNARVSNPTVICQEDSIEEEWMGLLEYLSRISICKMK... | [
{
"source_db": "GO",
"source_id": "GO:0006351",
"text": "NLRP3 GENE_ANNOTATED_WITH_GO_TERM DNA-templated transcription",
"confidence": 0.6
},
{
"source_db": "GO",
"source_id": "TARDBP",
"text": "TARDBP GENE_ANNOTATED_WITH_GO_TERM DNA-templated transcription",
"confidence": 0.6
... | {
"gene_a": "NLRP3",
"gene_b": "TARDBP",
"path_length": 2
} | 0.6 |
co_path_00218 | path_traversal | coding_variant | hard | 5 | What is the shortest molecular path from DNMT3A to SPTLC2 through known protein interactions and pathway memberships? | DNMT3A PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH EZH2 -> EZH2 GENE_ENCODES_PROTEIN EZH2 -> EZH2 PROTEIN_PHYSICALLY_INTERACTS_WITH BRCA1 -> BRCA1 PROTEIN_PHYSICALLY_INTERACTS_WITH SPTLC2 -> SPTLC2 GENE_ENCODES_PROTEIN SPTLC2 | {
"steps": [
{
"hop": 1,
"source_node_id": "DNMT3A",
"source_node_type": "GENE",
"source_node_label": "DNMT3A",
"edge_relation": "PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH",
"edge_evidence_type": "multi-channel",
"edge_confidence": 0.999,
"edge_source_db": "STRING",
... | DNMT3A -> EZH2 -> EZH2 -> BRCA1 -> SPTLC2 -> SPTLC2 | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "DNMT3A",
"source_db": "UniProt",
"payload": {
"accession": "Q9Y6K1",
"sequence": "MPAMPSSGPGDTSSSAAEREEDRKDGEEQEEPRGKEERQEPSTTARKVGRPGRKRKHPPVESGDTPKDPAVISKSPSMAQDSGASELLPNGDLEKRSEPQPEEGSPAGGQKGGAPAEGEGAAETLPEASRAV... | [
{
"source_db": "STRING",
"source_id": "EZH2",
"text": "DNMT3A PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH EZH2",
"confidence": 0.999
},
{
"source_db": "bridge",
"source_id": "2146",
"text": "EZH2 GENE_ENCODES_PROTEIN EZH2",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"sou... | {
"gene_a": "DNMT3A",
"gene_b": "SPTLC2",
"path_length": 5
} | 0.918982 |
co_path_00219 | path_traversal | coding_variant | easy | 2 | What is the shortest molecular path from ADRB1 to RET through known protein interactions and pathway memberships? | ADRB1 GENE_ANNOTATED_WITH_GO_TERM positive regulation of MAPK cascade -> RET GENE_ANNOTATED_WITH_GO_TERM positive regulation of MAPK cascade | {
"steps": [
{
"hop": 1,
"source_node_id": "ADRB1",
"source_node_type": "GENE",
"source_node_label": "ADRB1",
"edge_relation": "GENE_ANNOTATED_WITH_GO_TERM",
"edge_evidence_type": "IBA:GO_Central",
"edge_confidence": 0.6,
"edge_source_db": "GO",
"target_node_i... | ADRB1 -> positive regulation of MAPK cascade -> RET | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ADRB1",
"source_db": "UniProt",
"payload": {
"accession": "P08588",
"sequence": "MGAGVLVLGASEPGNLSSAAPLPDGAATAARLLVPASPPASLLPPASESPEPLSQQWTAGMGLLMALIVLLIVAGNVLVIVAIAKTPRLQTLTNLFIMSLASADLVMGLLVVPFGATIVVWGRWEYGSFFCEL... | [
{
"source_db": "GO",
"source_id": "GO:0043410",
"text": "ADRB1 GENE_ANNOTATED_WITH_GO_TERM positive regulation of MAPK cascade",
"confidence": 0.6
},
{
"source_db": "GO",
"source_id": "RET",
"text": "RET GENE_ANNOTATED_WITH_GO_TERM positive regulation of MAPK cascade",
"confidenc... | {
"gene_a": "ADRB1",
"gene_b": "RET",
"path_length": 2
} | 0.6 |
co_path_00220 | path_traversal | coding_variant | easy | 2 | What is the shortest molecular path from TBK1 to BNIP3 through known protein interactions and pathway memberships? | TBK1 GENE_ANNOTATED_WITH_GO_TERM defense response to virus -> BNIP3 GENE_ANNOTATED_WITH_GO_TERM defense response to virus | {
"steps": [
{
"hop": 1,
"source_node_id": "TBK1",
"source_node_type": "GENE",
"source_node_label": "TBK1",
"edge_relation": "GENE_ANNOTATED_WITH_GO_TERM",
"edge_evidence_type": "NAS:ComplexPortal",
"edge_confidence": 0.6,
"edge_source_db": "GO",
"target_node_... | TBK1 -> defense response to virus -> BNIP3 | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "TBK1",
"source_db": "UniProt",
"payload": {
"accession": "Q9UHD2",
"sequence": "MQSTSNHLWLLSDILGQGATANVFRGRHKKTGDLFAIKVFNNISFLRPVDVQMREFEVLKKLNHKNIVKLFAIEEETTTRHKVLIMEFCPCGSLYTVLEEPSNAYGLPESEFLIVLRDVVGGMNHLRENGIVHR... | [
{
"source_db": "GO",
"source_id": "GO:0051607",
"text": "TBK1 GENE_ANNOTATED_WITH_GO_TERM defense response to virus",
"confidence": 0.6
},
{
"source_db": "GO",
"source_id": "BNIP3",
"text": "BNIP3 GENE_ANNOTATED_WITH_GO_TERM defense response to virus",
"confidence": 0.6
}
] | {
"gene_a": "TBK1",
"gene_b": "BNIP3",
"path_length": 2
} | 0.6 |
co_path_00221 | path_traversal | coding_variant | medium | 4 | What is the shortest molecular path from POLD1 to AFP through known protein interactions and pathway memberships? | POLD1 GENE_ANNOTATED_WITH_GO_TERM zinc ion binding -> BIRC5 GENE_ANNOTATED_WITH_GO_TERM zinc ion binding -> BIRC5 GENE_ANNOTATED_WITH_GO_TERM metal ion binding -> AFP GENE_ANNOTATED_WITH_GO_TERM metal ion binding | {
"steps": [
{
"hop": 1,
"source_node_id": "POLD1",
"source_node_type": "GENE",
"source_node_label": "POLD1",
"edge_relation": "GENE_ANNOTATED_WITH_GO_TERM",
"edge_evidence_type": "IEA:UniProtKB-KW",
"edge_confidence": 0.6,
"edge_source_db": "GO",
"target_node... | POLD1 -> zinc ion binding -> BIRC5 -> metal ion binding -> AFP | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "POLD1",
"source_db": "UniProt",
"payload": {
"accession": "P28340",
"sequence": "MDGKRRPGPGPGVPPKRARGGLWDDDDAPRPSQFEEDLALMEEMEAEHRLQEQEEEELQSVLEGVADGQVPPSAIDPRWLRPTPPALDPQTEPLIFQQLEIDHYVGPAQPVPGGPPPSRGSVPVLRAFGVTDE... | [
{
"source_db": "GO",
"source_id": "GO:0008270",
"text": "POLD1 GENE_ANNOTATED_WITH_GO_TERM zinc ion binding",
"confidence": 0.6
},
{
"source_db": "GO",
"source_id": "BIRC5",
"text": "BIRC5 GENE_ANNOTATED_WITH_GO_TERM zinc ion binding",
"confidence": 0.6
},
{
"source_db": ... | {
"gene_a": "POLD1",
"gene_b": "AFP",
"path_length": 4
} | 0.6 |
co_path_00222 | path_traversal | coding_variant | medium | 3 | What is the shortest molecular path from APC to IL17A through known protein interactions and pathway memberships? | APC GENE_ANNOTATED_WITH_GO_TERM protein kinase binding -> CD4 GENE_ANNOTATED_WITH_GO_TERM protein kinase binding -> IL17A PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH CD4 | {
"steps": [
{
"hop": 1,
"source_node_id": "APC",
"source_node_type": "GENE",
"source_node_label": "APC",
"edge_relation": "GENE_ANNOTATED_WITH_GO_TERM",
"edge_evidence_type": "IDA:DisProt",
"edge_confidence": 0.6,
"edge_source_db": "GO",
"target_node_id": "GO... | APC -> protein kinase binding -> CD4 -> IL17A | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "APC",
"source_db": "UniProt",
"payload": {
"accession": "P25054",
"sequence": "MAAASYDQLLKQVEALKMENSNLRQELEDNSNHLTKLETEASNMKEVLKQLQGSIEDEAMASSGQIDLLERLKELNLDSSNFPGVKLRSKMSLRSYGSREGSVSSRSGECSPVPMGSFPRRGFVNGSRESTGYLE... | [
{
"source_db": "GO",
"source_id": "GO:0019901",
"text": "APC GENE_ANNOTATED_WITH_GO_TERM protein kinase binding",
"confidence": 0.6
},
{
"source_db": "GO",
"source_id": "CD4",
"text": "CD4 GENE_ANNOTATED_WITH_GO_TERM protein kinase binding",
"confidence": 0.6
},
{
"source... | {
"gene_a": "APC",
"gene_b": "IL17A",
"path_length": 3
} | 0.704676 |
co_path_00223 | path_traversal | coding_variant | easy | 3 | What is the shortest molecular path from POLD1 to SETX through known protein interactions and pathway memberships? | POLD1 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH MSH6 -> MSH6 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH BRCA1 -> SETX PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH BRCA1 | {
"steps": [
{
"hop": 1,
"source_node_id": "POLD1",
"source_node_type": "GENE",
"source_node_label": "POLD1",
"edge_relation": "PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH",
"edge_evidence_type": "multi-channel",
"edge_confidence": 0.995,
"edge_source_db": "STRING",
... | POLD1 -> MSH6 -> BRCA1 -> SETX | null | [
"expression",
"intercell_role",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "POLD1",
"source_db": "UniProt",
"payload": {
"accession": "P28340",
"sequence": "MDGKRRPGPGPGVPPKRARGGLWDDDDAPRPSQFEEDLALMEEMEAEHRLQEQEEEELQSVLEGVADGQVPPSAIDPRWLRPTPPALDPQTEPLIFQQLEIDHYVGPAQPVPGGPPPSRGSVPVLRAFGVTDE... | [
{
"source_db": "STRING",
"source_id": "MSH6",
"text": "POLD1 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH MSH6",
"confidence": 0.995
},
{
"source_db": "STRING",
"source_id": "BRCA1",
"text": "MSH6 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH BRCA1",
"confidence": 0.996
},
{
"source_db": ... | {
"gene_a": "POLD1",
"gene_b": "SETX",
"path_length": 3
} | 0.993663 |
co_path_00224 | path_traversal | coding_variant | easy | 2 | What is the shortest molecular path from ANG to PFN1 through known protein interactions and pathway memberships? | ANG GENE_ANNOTATED_WITH_GO_TERM actin binding -> PFN1 GENE_ANNOTATED_WITH_GO_TERM actin binding | {
"steps": [
{
"hop": 1,
"source_node_id": "ANG",
"source_node_type": "GENE",
"source_node_label": "ANG",
"edge_relation": "GENE_ANNOTATED_WITH_GO_TERM",
"edge_evidence_type": "IDA:UniProtKB",
"edge_confidence": 0.6,
"edge_source_db": "GO",
"target_node_id": "... | ANG -> actin binding -> PFN1 | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ANG",
"source_db": "UniProt",
"payload": {
"accession": "P03950",
"sequence": "MVMGLGVLLLVFVLGLGLTPPTLAQDNSRYTHFLTQHYDAKPQGRDDRYCESIMRRRGLTSPCKDINTFIHGNKRSIKAICENKNGNPHRENLRISKSSFQVTTCKLHGGSPWPPCQYRATAGFRNVVVACENGL... | [
{
"source_db": "GO",
"source_id": "GO:0003779",
"text": "ANG GENE_ANNOTATED_WITH_GO_TERM actin binding",
"confidence": 0.6
},
{
"source_db": "GO",
"source_id": "PFN1",
"text": "PFN1 GENE_ANNOTATED_WITH_GO_TERM actin binding",
"confidence": 0.6
}
] | {
"gene_a": "ANG",
"gene_b": "PFN1",
"path_length": 2
} | 0.6 |
co_path_00225 | path_traversal | coding_variant | easy | 2 | What is the shortest molecular path from ESR1 to ABL1 through known protein interactions and pathway memberships? | ESR1 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH HSP90AA1 -> ABL1 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH HSP90AA1 | {
"steps": [
{
"hop": 1,
"source_node_id": "ESR1",
"source_node_type": "GENE",
"source_node_label": "ESR1",
"edge_relation": "PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH",
"edge_evidence_type": "multi-channel",
"edge_confidence": 0.999,
"edge_source_db": "STRING",
"t... | ESR1 -> HSP90AA1 -> ABL1 | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ESR1",
"source_db": "UniProt",
"payload": {
"accession": "P03372",
"sequence": "MTMTLHTKASGMALLHQIQGNELEPLNRPQLKIPLERPLGEVYLDSSKPAVYNYPEGAAYEFNAAAAANAQVYGQTGLPYGPGSEAAAFGSNGLGGFPPLNSVSPSPLMLLHPPPQLSPFLQPHGQQVPYYLEN... | [
{
"source_db": "STRING",
"source_id": "HSP90AA1",
"text": "ESR1 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH HSP90AA1",
"confidence": 0.999
},
{
"source_db": "STRING",
"source_id": "ABL1",
"text": "ABL1 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH HSP90AA1",
"confidence": 0.983
}
] | {
"gene_a": "ESR1",
"gene_b": "ABL1",
"path_length": 2
} | 0.990968 |
co_path_00226 | path_traversal | coding_variant | medium | 3 | What is the shortest molecular path from TMPRSS2 to BCL2 through known protein interactions and pathway memberships? | TMPRSS2 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH AR -> AR GENE_ANNOTATED_WITH_GO_TERM positive regulation of cell population proliferation -> BCL2 GENE_ANNOTATED_WITH_GO_TERM positive regulation of cell population proliferation | {
"steps": [
{
"hop": 1,
"source_node_id": "TMPRSS2",
"source_node_type": "GENE",
"source_node_label": "TMPRSS2",
"edge_relation": "PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH",
"edge_evidence_type": "multi-channel",
"edge_confidence": 0.974,
"edge_source_db": "STRING",
... | TMPRSS2 -> AR -> positive regulation of cell population proliferation -> BCL2 | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "TMPRSS2",
"source_db": "UniProt",
"payload": {
"accession": "O15393",
"sequence": "MALNSGSPPAIGPYYENHGYQPENPYPAQPTVVPTVYEVHPAQYYPSPVPQYAPRVLTQASNPVVCTQPKSPSGTVCTSKTKKALCITLTLGTFLVGAALAAGLLWKFMGSKCSNSGIECDSSGTCINPSN... | [
{
"source_db": "STRING",
"source_id": "AR",
"text": "TMPRSS2 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH AR",
"confidence": 0.974
},
{
"source_db": "GO",
"source_id": "GO:0008284",
"text": "AR GENE_ANNOTATED_WITH_GO_TERM positive regulation of cell population proliferation",
"confidence... | {
"gene_a": "TMPRSS2",
"gene_b": "BCL2",
"path_length": 3
} | 0.705159 |
co_path_00227 | path_traversal | coding_variant | medium | 4 | What is the shortest molecular path from CA9 to FLT3 through known protein interactions and pathway memberships? | CA9 GENE_ANNOTATED_WITH_GO_TERM zinc ion binding -> CDKN1A GENE_ANNOTATED_WITH_GO_TERM zinc ion binding -> CEBPA PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH CDKN1A -> CEBPA PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH FLT3 | {
"steps": [
{
"hop": 1,
"source_node_id": "CA9",
"source_node_type": "GENE",
"source_node_label": "CA9",
"edge_relation": "GENE_ANNOTATED_WITH_GO_TERM",
"edge_evidence_type": "IDA:UniProtKB",
"edge_confidence": 0.6,
"edge_source_db": "GO",
"target_node_id": "... | CA9 -> zinc ion binding -> CDKN1A -> CEBPA -> FLT3 | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CA9",
"source_db": "UniProt",
"payload": {
"accession": "Q16790",
"sequence": "MAPLCPSPWLPLLIPAPAPGLTVQLLLSLLLLVPVHPQRLPRMQEDSPLGGGSSGEDDPLGEEDLPSEEDSPREEDPPGEEDLPGEEDLPGEEDLPEVKPKSEEEGSLKLEDLPTVEAPGDPQEPQNNAHRDKEG... | [
{
"source_db": "GO",
"source_id": "GO:0008270",
"text": "CA9 GENE_ANNOTATED_WITH_GO_TERM zinc ion binding",
"confidence": 0.6
},
{
"source_db": "GO",
"source_id": "CDKN1A",
"text": "CDKN1A GENE_ANNOTATED_WITH_GO_TERM zinc ion binding",
"confidence": 0.6
},
{
"source_db": ... | {
"gene_a": "CA9",
"gene_b": "FLT3",
"path_length": 4
} | 0.762267 |
co_path_00228 | path_traversal | coding_variant | medium | 3 | What is the shortest molecular path from PMS2 to SQSTM1 through known protein interactions and pathway memberships? | PMS2 PROTEIN_MEMBER_OF_COMPLEX BLM / BRCA1 / EXO1 / MLH1... -> UBC PROTEIN_MEMBER_OF_COMPLEX BLM / BRCA1 / EXO1 / MLH1... -> SQSTM1 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH UBC | {
"steps": [
{
"hop": 1,
"source_node_id": "PMS2",
"source_node_type": "GENE",
"source_node_label": "PMS2",
"edge_relation": "PROTEIN_MEMBER_OF_COMPLEX",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "OmniPath",
"target_node_id": "Co... | PMS2 -> BLM / BRCA1 / EXO1 / MLH1... -> UBC -> SQSTM1 | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "PMS2",
"source_db": "UniProt",
"payload": {
"accession": "P54278",
"sequence": "MERAESSSTEPAKAIKPIDRKSVHQICSGQVVLSLSTAVKELVENSLDAGATNIDLKLKDYGVDLIEVSDNGCGVEEENFEGLTLKHHTSKIQEFADLTQVETFGFRGEALSSLCALSDVTISTCHASAKVGTR... | [
{
"source_db": "OmniPath",
"source_id": "Compleat:HC6768",
"text": "PMS2 PROTEIN_MEMBER_OF_COMPLEX BLM / BRCA1 / EXO1 / MLH1...",
"confidence": 1
},
{
"source_db": "OmniPath",
"source_id": "UBC",
"text": "UBC PROTEIN_MEMBER_OF_COMPLEX BLM / BRCA1 / EXO1 / MLH1...",
"confidence": ... | {
"gene_a": "PMS2",
"gene_b": "SQSTM1",
"path_length": 3
} | 0.999667 |
co_path_00229 | path_traversal | coding_variant | easy | 2 | What is the shortest molecular path from PINK1 to CDK4 through known protein interactions and pathway memberships? | PINK1 GENE_ANNOTATED_WITH_GO_TERM ATP binding -> CDK4 GENE_ANNOTATED_WITH_GO_TERM ATP binding | {
"steps": [
{
"hop": 1,
"source_node_id": "PINK1",
"source_node_type": "GENE",
"source_node_label": "PINK1",
"edge_relation": "GENE_ANNOTATED_WITH_GO_TERM",
"edge_evidence_type": "IDA:UniProtKB",
"edge_confidence": 0.6,
"edge_source_db": "GO",
"target_node_id... | PINK1 -> ATP binding -> CDK4 | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "PINK1",
"source_db": "UniProt",
"payload": {
"accession": "Q9BXM7",
"sequence": "MAVRQALGRGLQLGRALLLRFTGKPGRAYGLGRPGPAAGCVRGERPGWAAGPGAEPRRVGLGLPNRLRFFRQSVAGLAARLQRQFVVRAWGCAGPCGRAVFLAFGLGLGLIEEKQAESRRAVSACQEIQAIFT... | [
{
"source_db": "GO",
"source_id": "GO:0005524",
"text": "PINK1 GENE_ANNOTATED_WITH_GO_TERM ATP binding",
"confidence": 0.6
},
{
"source_db": "GO",
"source_id": "CDK4",
"text": "CDK4 GENE_ANNOTATED_WITH_GO_TERM ATP binding",
"confidence": 0.6
}
] | {
"gene_a": "PINK1",
"gene_b": "CDK4",
"path_length": 2
} | 0.6 |
co_path_00230 | path_traversal | coding_variant | hard | 4 | What is the shortest molecular path from ABI1 to CA9 through known protein interactions and pathway memberships? | ABI1 GENE_ANNOTATED_WITH_GO_TERM negative regulation of cell population proliferation -> TP53 GENE_ANNOTATED_WITH_GO_TERM negative regulation of cell population proliferation -> TP53 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH HIF1A -> CA9 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH HIF1A | {
"steps": [
{
"hop": 1,
"source_node_id": "ABI1",
"source_node_type": "GENE",
"source_node_label": "ABI1",
"edge_relation": "GENE_ANNOTATED_WITH_GO_TERM",
"edge_evidence_type": "TAS:ProtInc",
"edge_confidence": 0.6,
"edge_source_db": "GO",
"target_node_id": "... | ABI1 -> negative regulation of cell population proliferation -> TP53 -> HIF1A -> CA9 | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ABI1",
"source_db": "UniProt",
"payload": {
"accession": "Q8IZP0",
"sequence": "MAELQMLLEEEIPSGKRALIESYQNLTRVADYCENNYIQATDKRKALEETKAYTTQSLASVAYQINALANNVLQLLDIQASQLRRMESSINHISQTVDIHKEKVARREIGILTTNKNTSRTHKIIAPANMERPV... | [
{
"source_db": "GO",
"source_id": "GO:0008285",
"text": "ABI1 GENE_ANNOTATED_WITH_GO_TERM negative regulation of cell population proliferation",
"confidence": 0.6
},
{
"source_db": "GO",
"source_id": "TP53",
"text": "TP53 GENE_ANNOTATED_WITH_GO_TERM negative regulation of cell popula... | {
"gene_a": "ABI1",
"gene_b": "CA9",
"path_length": 4
} | 0.763326 |
co_path_00231 | path_traversal | coding_variant | easy | 2 | What is the shortest molecular path from VCP to MYC through known protein interactions and pathway memberships? | VCP GENE_ANNOTATED_WITH_GO_TERM ubiquitin protein ligase binding -> MYC GENE_ANNOTATED_WITH_GO_TERM ubiquitin protein ligase binding | {
"steps": [
{
"hop": 1,
"source_node_id": "VCP",
"source_node_type": "GENE",
"source_node_label": "VCP",
"edge_relation": "GENE_ANNOTATED_WITH_GO_TERM",
"edge_evidence_type": "IPI:ParkinsonsUK-UCL",
"edge_confidence": 0.6,
"edge_source_db": "GO",
"target_node... | VCP -> ubiquitin protein ligase binding -> MYC | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "VCP",
"source_db": "UniProt",
"payload": {
"accession": "P55072",
"sequence": "MASGADSKGDDLSTAILKQKNRPNRLIVDEAINEDNSVVSLSQPKMDELQLFRGDTVLLKGKKRREAVCIVLSDDTCSDEKIRMNRVVRNNLRVRLGDVISIQPCPDVKYGKRIHVLPIDDTVEGITGNLFEVYL... | [
{
"source_db": "GO",
"source_id": "GO:0031625",
"text": "VCP GENE_ANNOTATED_WITH_GO_TERM ubiquitin protein ligase binding",
"confidence": 0.6
},
{
"source_db": "GO",
"source_id": "MYC",
"text": "MYC GENE_ANNOTATED_WITH_GO_TERM ubiquitin protein ligase binding",
"confidence": 0.6
... | {
"gene_a": "VCP",
"gene_b": "MYC",
"path_length": 2
} | 0.6 |
co_path_00232 | path_traversal | coding_variant | easy | 2 | What is the shortest molecular path from ACTB to ESR1 through known protein interactions and pathway memberships? | ACTB GENE_ANNOTATED_WITH_GO_TERM protein kinase binding -> ESR1 GENE_ANNOTATED_WITH_GO_TERM protein kinase binding | {
"steps": [
{
"hop": 1,
"source_node_id": "ACTB",
"source_node_type": "GENE",
"source_node_label": "ACTB",
"edge_relation": "GENE_ANNOTATED_WITH_GO_TERM",
"edge_evidence_type": "IPI:ARUK-UCL",
"edge_confidence": 0.6,
"edge_source_db": "GO",
"target_node_id": ... | ACTB -> protein kinase binding -> ESR1 | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ACTB",
"source_db": "UniProt",
"payload": {
"accession": "P60709",
"sequence": "MDDDIAALVVDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMTQIMFETFNTPAMYV... | [
{
"source_db": "GO",
"source_id": "GO:0019901",
"text": "ACTB GENE_ANNOTATED_WITH_GO_TERM protein kinase binding",
"confidence": 0.6
},
{
"source_db": "GO",
"source_id": "ESR1",
"text": "ESR1 GENE_ANNOTATED_WITH_GO_TERM protein kinase binding",
"confidence": 0.6
}
] | {
"gene_a": "ACTB",
"gene_b": "ESR1",
"path_length": 2
} | 0.6 |
co_path_00233 | path_traversal | coding_variant | medium | 3 | What is the shortest molecular path from TP53 to PFN1 through known protein interactions and pathway memberships? | TP53 GENE_PARTICIPATES_IN_PATHWAY Factors involved in megakaryocyte development and platelet production -> ACTB GENE_PARTICIPATES_IN_PATHWAY Factors involved in megakaryocyte development and platelet production -> ACTB PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH PFN1 | {
"steps": [
{
"hop": 1,
"source_node_id": "TP53",
"source_node_type": "GENE",
"source_node_label": "TP53",
"edge_relation": "GENE_PARTICIPATES_IN_PATHWAY",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "Reactome",
"target_node_id": ... | TP53 -> Factors involved in megakaryocyte development and platelet production -> ACTB -> PFN1 | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "TP53",
"source_db": "UniProt",
"payload": {
"accession": "P04637",
"sequence": "MEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPGPDEAPRMPEAAPPVAPAPAAPTPAAPAPAPSWPLSSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMF... | [
{
"source_db": "Reactome",
"source_id": "R-HSA-983231",
"text": "TP53 GENE_PARTICIPATES_IN_PATHWAY Factors involved in megakaryocyte development and platelet production",
"confidence": 1
},
{
"source_db": "Reactome",
"source_id": "ACTB",
"text": "ACTB GENE_PARTICIPATES_IN_PATHWAY Fac... | {
"gene_a": "TP53",
"gene_b": "PFN1",
"path_length": 3
} | 0.999667 |
co_path_00234 | path_traversal | coding_variant | hard | 4 | What is the shortest molecular path from PDE10A to MYC through known protein interactions and pathway memberships? | PDE10A PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH ENPP1 -> BST1 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH ENPP1 -> BST1 GENE_ANNOTATED_WITH_GO_TERM positive regulation of cell population proliferation -> MYC GENE_ANNOTATED_WITH_GO_TERM positive regulation of cell population proliferation | {
"steps": [
{
"hop": 1,
"source_node_id": "PDE10A",
"source_node_type": "GENE",
"source_node_label": "PDE10A",
"edge_relation": "PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH",
"edge_evidence_type": "multi-channel",
"edge_confidence": 0.929,
"edge_source_db": "STRING",
... | PDE10A -> ENPP1 -> BST1 -> positive regulation of cell population proliferation -> MYC | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "PDE10A",
"source_db": "UniProt",
"payload": {
"accession": "Q9Y233",
"sequence": "MASLEEPLAPRPQGPLPAAGDEPGCGPGKLRPEPRLSAAGGGSAAGPGPAPEWPGRGRAERAAPPRPPLSSAGRPSPAGGPGALSARGGGCGWVAARAPLALAFSSRVPSSSPSFFYFWPPPPPPPPSFLPS... | [
{
"source_db": "STRING",
"source_id": "ENPP1",
"text": "PDE10A PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH ENPP1",
"confidence": 0.929
},
{
"source_db": "STRING",
"source_id": "BST1",
"text": "BST1 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH ENPP1",
"confidence": 0.93
},
{
"source_db":... | {
"gene_a": "PDE10A",
"gene_b": "MYC",
"path_length": 4
} | 0.746793 |
co_path_00235 | path_traversal | coding_variant | medium | 4 | What is the shortest molecular path from SFRP4 to ACE through known protein interactions and pathway memberships? | SFRP4 GENE_ANNOTATED_WITH_GO_TERM canonical Wnt signaling pathway -> LRRK2 GENE_ANNOTATED_WITH_GO_TERM canonical Wnt signaling pathway -> LRRK2 GENE_ANNOTATED_WITH_GO_TERM actin binding -> ACE GENE_ANNOTATED_WITH_GO_TERM actin binding | {
"steps": [
{
"hop": 1,
"source_node_id": "SFRP4",
"source_node_type": "GENE",
"source_node_label": "SFRP4",
"edge_relation": "GENE_ANNOTATED_WITH_GO_TERM",
"edge_evidence_type": "IBA:GO_Central",
"edge_confidence": 0.6,
"edge_source_db": "GO",
"target_node_i... | SFRP4 -> canonical Wnt signaling pathway -> LRRK2 -> actin binding -> ACE | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "SFRP4",
"source_db": "UniProt",
"payload": {
"accession": "Q6FHJ7",
"sequence": "MFLSILVALCLWLHLALGVRGAPCEAVRIPMCRHMPWNITRMPNHLHHSTQENAILAIEQYEELVDVNCSAVLRFFLCAMYAPICTLEFLHDPIKPCKSVCQRARDDCEPLMKMYNHSWPESLACDELPVYDR... | [
{
"source_db": "GO",
"source_id": "GO:0060070",
"text": "SFRP4 GENE_ANNOTATED_WITH_GO_TERM canonical Wnt signaling pathway",
"confidence": 0.6
},
{
"source_db": "GO",
"source_id": "LRRK2",
"text": "LRRK2 GENE_ANNOTATED_WITH_GO_TERM canonical Wnt signaling pathway",
"confidence": ... | {
"gene_a": "SFRP4",
"gene_b": "ACE",
"path_length": 4
} | 0.6 |
co_path_00236 | path_traversal | coding_variant | medium | 3 | What is the shortest molecular path from IL22 to TARDBP through known protein interactions and pathway memberships? | IL22 GENE_ANNOTATED_WITH_GO_TERM cytokine activity -> GRN GENE_ANNOTATED_WITH_GO_TERM cytokine activity -> GRN PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH TARDBP | {
"steps": [
{
"hop": 1,
"source_node_id": "IL22",
"source_node_type": "GENE",
"source_node_label": "IL22",
"edge_relation": "GENE_ANNOTATED_WITH_GO_TERM",
"edge_evidence_type": "IBA:GO_Central",
"edge_confidence": 0.6,
"edge_source_db": "GO",
"target_node_id"... | IL22 -> cytokine activity -> GRN -> TARDBP | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "IL22",
"source_db": "UniProt",
"payload": {
"accession": "Q9GZX6",
"sequence": "MAALQKSVSSFLMGTLATSCLLLLALLVQGGAAAPISSHCRLDKSNFQQPYITNRTFMLAKEASLADNNTDVRLIGEKLFHGVSMSERCYLMKQVLNFTLEEVLFPQSDRFQPYMQEVVPFLARLSNRLSTCHI... | [
{
"source_db": "GO",
"source_id": "GO:0005125",
"text": "IL22 GENE_ANNOTATED_WITH_GO_TERM cytokine activity",
"confidence": 0.6
},
{
"source_db": "GO",
"source_id": "GRN",
"text": "GRN GENE_ANNOTATED_WITH_GO_TERM cytokine activity",
"confidence": 0.6
},
{
"source_db": "ST... | {
"gene_a": "IL22",
"gene_b": "TARDBP",
"path_length": 3
} | 0.701277 |
co_path_00237 | path_traversal | coding_variant | medium | 3 | What is the shortest molecular path from HGF to AFF3 through known protein interactions and pathway memberships? | HGF PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH EGFR -> EGFR GENE_ANNOTATED_WITH_GO_TERM double-stranded DNA binding -> AFF3 GENE_ANNOTATED_WITH_GO_TERM double-stranded DNA binding | {
"steps": [
{
"hop": 1,
"source_node_id": "HGF",
"source_node_type": "GENE",
"source_node_label": "HGF",
"edge_relation": "PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH",
"edge_evidence_type": "multi-channel",
"edge_confidence": 0.98,
"edge_source_db": "STRING",
"targ... | HGF -> EGFR -> double-stranded DNA binding -> AFF3 | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "HGF",
"source_db": "UniProt",
"payload": {
"accession": "P14210",
"sequence": "MWVTKLLPALLLQHVLLHLLLLPIAIPYAEGQRKRRNTIHEFKKSAKTTLIKIDPALKIKTKKVNTADQCANRCTRNKGLPFTCKAFVFDKARKQCLWFPFNSMSSGVKKEFGHEFDLYENKDYIRNCIIGKGRS... | [
{
"source_db": "STRING",
"source_id": "EGFR",
"text": "HGF PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH EGFR",
"confidence": 0.98
},
{
"source_db": "GO",
"source_id": "GO:0003690",
"text": "EGFR GENE_ANNOTATED_WITH_GO_TERM double-stranded DNA binding",
"confidence": 0.6
},
{
"sou... | {
"gene_a": "HGF",
"gene_b": "AFF3",
"path_length": 3
} | 0.706604 |
co_path_00238 | path_traversal | coding_variant | easy | 2 | What is the shortest molecular path from CD44 to IL17A through known protein interactions and pathway memberships? | CD44 GENE_ANNOTATED_WITH_GO_TERM inflammatory response -> IL17A GENE_ANNOTATED_WITH_GO_TERM inflammatory response | {
"steps": [
{
"hop": 1,
"source_node_id": "CD44",
"source_node_type": "GENE",
"source_node_label": "CD44",
"edge_relation": "GENE_ANNOTATED_WITH_GO_TERM",
"edge_evidence_type": "IBA:GO_Central",
"edge_confidence": 0.6,
"edge_source_db": "GO",
"target_node_id"... | CD44 -> inflammatory response -> IL17A | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CD44",
"source_db": "UniProt",
"payload": {
"accession": "P16070",
"sequence": "MDKFWWHAAWGLCLVPLSLAQIDLNITCRFAGVFHVEKNGRYSISRTEAADLCKAFNSTLPTMAQMEKALSIGFETCRYGFIEGHVVIPRIHPNSICAANNTGVYILTSNTSQYDTYCFNASAPPEEDCTSVTD... | [
{
"source_db": "GO",
"source_id": "GO:0006954",
"text": "CD44 GENE_ANNOTATED_WITH_GO_TERM inflammatory response",
"confidence": 0.6
},
{
"source_db": "GO",
"source_id": "IL17A",
"text": "IL17A GENE_ANNOTATED_WITH_GO_TERM inflammatory response",
"confidence": 0.6
}
] | {
"gene_a": "CD44",
"gene_b": "IL17A",
"path_length": 2
} | 0.6 |
co_path_00239 | path_traversal | coding_variant | medium | 3 | What is the shortest molecular path from CCND1 to SLC6A2 through known protein interactions and pathway memberships? | CCND1 GENE_ANNOTATED_WITH_GO_TERM protein kinase binding -> ADRA2A GENE_ANNOTATED_WITH_GO_TERM protein kinase binding -> ADRA2A PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH SLC6A2 | {
"steps": [
{
"hop": 1,
"source_node_id": "CCND1",
"source_node_type": "GENE",
"source_node_label": "CCND1",
"edge_relation": "GENE_ANNOTATED_WITH_GO_TERM",
"edge_evidence_type": "IPI:UniProtKB",
"edge_confidence": 0.6,
"edge_source_db": "GO",
"target_node_id... | CCND1 -> protein kinase binding -> ADRA2A -> SLC6A2 | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CCND1",
"source_db": "UniProt",
"payload": {
"accession": "P24385",
"sequence": "MEHQLLCCEVETIRRAYPDANLLNDRVLRAMLKAEETCAPSVSYFKCVQKEVLPSMRKIVATWMLEVCEEQKCEEEVFPLAMNYLDRFLSLEPVKKSRLQLLGATCMFVASKMKETIPLTAEKLCIYTDNSIR... | [
{
"source_db": "GO",
"source_id": "GO:0019901",
"text": "CCND1 GENE_ANNOTATED_WITH_GO_TERM protein kinase binding",
"confidence": 0.6
},
{
"source_db": "GO",
"source_id": "ADRA2A",
"text": "ADRA2A GENE_ANNOTATED_WITH_GO_TERM protein kinase binding",
"confidence": 0.6
},
{
... | {
"gene_a": "CCND1",
"gene_b": "SLC6A2",
"path_length": 3
} | 0.660935 |
co_path_00240 | path_traversal | coding_variant | easy | 2 | What is the shortest molecular path from TARDBP to TP53 through known protein interactions and pathway memberships? | TARDBP GENE_ANNOTATED_WITH_GO_TERM mRNA 3'-UTR binding -> TP53 GENE_ANNOTATED_WITH_GO_TERM mRNA 3'-UTR binding | {
"steps": [
{
"hop": 1,
"source_node_id": "TARDBP",
"source_node_type": "GENE",
"source_node_label": "TARDBP",
"edge_relation": "GENE_ANNOTATED_WITH_GO_TERM",
"edge_evidence_type": "IDA:BHF-UCL",
"edge_confidence": 0.6,
"edge_source_db": "GO",
"target_node_id... | TARDBP -> mRNA 3'-UTR binding -> TP53 | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "TARDBP",
"source_db": "UniProt",
"payload": {
"accession": "Q13148",
"sequence": "MSEYIRVTEDENDEPIEIPSEDDGTVLLSTVTAQFPGACGLRYRNPVSQCMRGVRLVEGILHAPDAGWGNLVYVVNYPKDNKRKMDETDASSAVKVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLM... | [
{
"source_db": "GO",
"source_id": "GO:0003730",
"text": "TARDBP GENE_ANNOTATED_WITH_GO_TERM mRNA 3'-UTR binding",
"confidence": 0.6
},
{
"source_db": "GO",
"source_id": "TP53",
"text": "TP53 GENE_ANNOTATED_WITH_GO_TERM mRNA 3'-UTR binding",
"confidence": 0.6
}
] | {
"gene_a": "TARDBP",
"gene_b": "TP53",
"path_length": 2
} | 0.6 |
co_path_00241 | path_traversal | coding_variant | medium | 3 | What is the shortest molecular path from ADRA2A to IL22 through known protein interactions and pathway memberships? | ADRA2A GENE_ANNOTATED_WITH_GO_TERM protein homodimerization activity -> IL17A GENE_ANNOTATED_WITH_GO_TERM protein homodimerization activity -> IL17A PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH IL22 | {
"steps": [
{
"hop": 1,
"source_node_id": "ADRA2A",
"source_node_type": "GENE",
"source_node_label": "ADRA2A",
"edge_relation": "GENE_ANNOTATED_WITH_GO_TERM",
"edge_evidence_type": "IDA:BHF-UCL",
"edge_confidence": 0.6,
"edge_source_db": "GO",
"target_node_id... | ADRA2A -> protein homodimerization activity -> IL17A -> IL22 | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ADRA2A",
"source_db": "UniProt",
"payload": {
"accession": "P08913",
"sequence": "MFRQEQPLAEGSFAPMGSLQPDAGNASWNGTEAPGGGARATPYSLQVTLTLVCLAGLLMLLTVFGNVLVIIAVFTSRALKAPQNLFLVSLASADILVATLVIPFSLANEVMGYWYFGKAWCEIYLALDVLFC... | [
{
"source_db": "GO",
"source_id": "GO:0042803",
"text": "ADRA2A GENE_ANNOTATED_WITH_GO_TERM protein homodimerization activity",
"confidence": 0.6
},
{
"source_db": "GO",
"source_id": "IL17A",
"text": "IL17A GENE_ANNOTATED_WITH_GO_TERM protein homodimerization activity",
"confiden... | {
"gene_a": "ADRA2A",
"gene_b": "IL22",
"path_length": 3
} | 0.705641 |
co_path_00242 | path_traversal | coding_variant | easy | 2 | What is the shortest molecular path from APH1B to ESR1 through known protein interactions and pathway memberships? | APH1B GENE_PARTICIPATES_IN_PATHWAY Nuclear signaling by ERBB4 -> ESR1 GENE_PARTICIPATES_IN_PATHWAY Nuclear signaling by ERBB4 | {
"steps": [
{
"hop": 1,
"source_node_id": "APH1B",
"source_node_type": "GENE",
"source_node_label": "APH1B",
"edge_relation": "GENE_PARTICIPATES_IN_PATHWAY",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "Reactome",
"target_node_id"... | APH1B -> Nuclear signaling by ERBB4 -> ESR1 | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "APH1B",
"source_db": "UniProt",
"payload": {
"accession": "Q8WW43",
"sequence": "MTAAVFFGCAFIAFGPALALYVFTIATEPLRIIFLIAGAFFWLVSLLISSLVWFMARVIIDNKDGPTQKYLLIFGAFVSVYIQEMFRFAYYKLLKKASEGLKSINPGETAPSMRLLAYVSGLGFGIMSGVFSF... | [
{
"source_db": "Reactome",
"source_id": "R-HSA-1251985",
"text": "APH1B GENE_PARTICIPATES_IN_PATHWAY Nuclear signaling by ERBB4",
"confidence": 1
},
{
"source_db": "Reactome",
"source_id": "ESR1",
"text": "ESR1 GENE_PARTICIPATES_IN_PATHWAY Nuclear signaling by ERBB4",
"confidence... | {
"gene_a": "APH1B",
"gene_b": "ESR1",
"path_length": 2
} | 1 |
co_path_00243 | path_traversal | coding_variant | easy | 2 | What is the shortest molecular path from ACE to AVPR1A through known protein interactions and pathway memberships? | ACE GENE_ANNOTATED_WITH_GO_TERM positive regulation of systemic arterial blood pressure -> AVPR1A GENE_ANNOTATED_WITH_GO_TERM positive regulation of systemic arterial blood pressure | {
"steps": [
{
"hop": 1,
"source_node_id": "ACE",
"source_node_type": "GENE",
"source_node_label": "ACE",
"edge_relation": "GENE_ANNOTATED_WITH_GO_TERM",
"edge_evidence_type": "IBA:GO_Central",
"edge_confidence": 0.6,
"edge_source_db": "GO",
"target_node_id": ... | ACE -> positive regulation of systemic arterial blood pressure -> AVPR1A | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ACE",
"source_db": "UniProt",
"payload": {
"accession": "P12821",
"sequence": "MGAASGRRGPGLLLPLPLLLLLPPQPALALDPGLQPGNFSADEAGAQLFAQSYNSSAEQVLFQSVAASWAHDTNITAENARRQEEAALLSQEFAEAWGQKAKELYEPIWQNFTDPQLRRIIGAVRTLGSANLPLA... | [
{
"source_db": "GO",
"source_id": "GO:0003084",
"text": "ACE GENE_ANNOTATED_WITH_GO_TERM positive regulation of systemic arterial blood pressure",
"confidence": 0.6
},
{
"source_db": "GO",
"source_id": "AVPR1A",
"text": "AVPR1A GENE_ANNOTATED_WITH_GO_TERM positive regulation of syste... | {
"gene_a": "ACE",
"gene_b": "AVPR1A",
"path_length": 2
} | 0.6 |
co_path_00244 | path_traversal | coding_variant | easy | 2 | What is the shortest molecular path from ABI1 to MET through known protein interactions and pathway memberships? | ABI1 GENE_ANNOTATED_WITH_GO_TERM cell surface receptor protein tyrosine kinase signaling pathway -> MET GENE_ANNOTATED_WITH_GO_TERM cell surface receptor protein tyrosine kinase signaling pathway | {
"steps": [
{
"hop": 1,
"source_node_id": "ABI1",
"source_node_type": "GENE",
"source_node_label": "ABI1",
"edge_relation": "GENE_ANNOTATED_WITH_GO_TERM",
"edge_evidence_type": "TAS:ProtInc",
"edge_confidence": 0.6,
"edge_source_db": "GO",
"target_node_id": "... | ABI1 -> cell surface receptor protein tyrosine kinase signaling pathway -> MET | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ABI1",
"source_db": "UniProt",
"payload": {
"accession": "Q8IZP0",
"sequence": "MAELQMLLEEEIPSGKRALIESYQNLTRVADYCENNYIQATDKRKALEETKAYTTQSLASVAYQINALANNVLQLLDIQASQLRRMESSINHISQTVDIHKEKVARREIGILTTNKNTSRTHKIIAPANMERPV... | [
{
"source_db": "GO",
"source_id": "GO:0007169",
"text": "ABI1 GENE_ANNOTATED_WITH_GO_TERM cell surface receptor protein tyrosine kinase signaling pathway",
"confidence": 0.6
},
{
"source_db": "GO",
"source_id": "MET",
"text": "MET GENE_ANNOTATED_WITH_GO_TERM cell surface receptor pro... | {
"gene_a": "ABI1",
"gene_b": "MET",
"path_length": 2
} | 0.6 |
co_path_00245 | path_traversal | coding_variant | medium | 3 | What is the shortest molecular path from CA9 to NRAS through known protein interactions and pathway memberships? | CA9 GENE_ANNOTATED_WITH_GO_TERM zinc ion binding -> BRAF GENE_ANNOTATED_WITH_GO_TERM zinc ion binding -> BRAF PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH NRAS | {
"steps": [
{
"hop": 1,
"source_node_id": "CA9",
"source_node_type": "GENE",
"source_node_label": "CA9",
"edge_relation": "GENE_ANNOTATED_WITH_GO_TERM",
"edge_evidence_type": "IDA:UniProtKB",
"edge_confidence": 0.6,
"edge_source_db": "GO",
"target_node_id": "... | CA9 -> zinc ion binding -> BRAF -> NRAS | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CA9",
"source_db": "UniProt",
"payload": {
"accession": "Q16790",
"sequence": "MAPLCPSPWLPLLIPAPAPGLTVQLLLSLLLLVPVHPQRLPRMQEDSPLGGGSSGEDDPLGEEDLPSEEDSPREEDPPGEEDLPGEEDLPGEEDLPEVKPKSEEEGSLKLEDLPTVEAPGDPQEPQNNAHRDKEG... | [
{
"source_db": "GO",
"source_id": "GO:0008270",
"text": "CA9 GENE_ANNOTATED_WITH_GO_TERM zinc ion binding",
"confidence": 0.6
},
{
"source_db": "GO",
"source_id": "BRAF",
"text": "BRAF GENE_ANNOTATED_WITH_GO_TERM zinc ion binding",
"confidence": 0.6
},
{
"source_db": "STR... | {
"gene_a": "CA9",
"gene_b": "NRAS",
"path_length": 3
} | 0.711141 |
co_codi_00000 | coding_variant | coding_variant | easy | 1 | According to Ensembl VEP, what is the predicted functional consequence of NM_000038.6(APC):c.2441_2442del(p.Asn813_Phe814insTer) in APC? | NM_000038.6(APC):c.2441_2442del(p.Asn813_Phe814insTer) VARIANT_HAS_VEP_CONSEQUENCE APC | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000038.6(APC):c.2441_2442del(p.Asn813_Phe814insTer)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000038.6(APC):c.2441_2442del(p.Asn813_Phe814insTer)",
"edge_relation": "VARIANT_HAS_VEP_CONSEQUENCE",
"edge_evidence_type... | A | [
"A. frameshift_variant",
"B. synonymous_variant",
"C. splice_region_variant",
"D. missense_variant"
] | [
"expression",
"protein_sequence",
"snp_sequence"
] | [
{
"family": "sequence",
"tag": "snp_sequence",
"anchor_node_id": "NM_000038.6(APC):c.2441_2442del(p.Asn813_Phe814insTer)",
"source_db": "Ensembl",
"payload": {
"chrom": "5",
"pos": 112838035,
"ref_allele": "TT",
"alt_allele": "-",
"ref_context": "TGATTATGTTTTTGACACC... | [
{
"source_db": "Ensembl_VEP",
"source_id": "APC",
"text": "NM_000038.6(APC):c.2441_2442del(p.Asn813_Phe814insTer) VARIANT_HAS_VEP_CONSEQUENCE APC",
"confidence": 0.95
}
] | {
"gene": "APC",
"variant": "NM_000038.6(APC):c.2441_2442del(p.Asn813_Phe814insTer)",
"SO_term": "frameshift_variant",
"impact": "HIGH",
"tier": "A"
} | 0.95 |
co_codi_00001 | coding_variant | coding_variant | easy | 1 | According to Ensembl VEP, what is the predicted functional consequence of NM_000038.6(APC):c.3700del(p.Ser1234fs) in APC? | NM_000038.6(APC):c.3700del(p.Ser1234fs) VARIANT_HAS_VEP_CONSEQUENCE APC | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000038.6(APC):c.3700del(p.Ser1234fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000038.6(APC):c.3700del(p.Ser1234fs)",
"edge_relation": "VARIANT_HAS_VEP_CONSEQUENCE",
"edge_evidence_type": "computational_prediction",... | B | [
"A. synonymous_variant",
"B. frameshift_variant",
"C. missense_variant",
"D. splice_region_variant"
] | [
"expression",
"protein_sequence",
"snp_sequence"
] | [
{
"family": "sequence",
"tag": "snp_sequence",
"anchor_node_id": "NM_000038.6(APC):c.3700del(p.Ser1234fs)",
"source_db": "Ensembl",
"payload": {
"chrom": "5",
"pos": 112839294,
"ref_allele": "A",
"alt_allele": "-",
"ref_context": "ATACGTCCACACCTTCATCTAATGCCAAGAGGCAG... | [
{
"source_db": "Ensembl_VEP",
"source_id": "APC",
"text": "NM_000038.6(APC):c.3700del(p.Ser1234fs) VARIANT_HAS_VEP_CONSEQUENCE APC",
"confidence": 0.95
}
] | {
"gene": "APC",
"variant": "NM_000038.6(APC):c.3700del(p.Ser1234fs)",
"SO_term": "frameshift_variant",
"impact": "HIGH",
"tier": "A"
} | 0.95 |
co_codi_00002 | coding_variant | coding_variant | easy | 1 | According to Ensembl VEP, what is the predicted functional consequence of NM_000038.6(APC):c.2851del(p.Tyr951fs) in APC? | NM_000038.6(APC):c.2851del(p.Tyr951fs) VARIANT_HAS_VEP_CONSEQUENCE APC | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000038.6(APC):c.2851del(p.Tyr951fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000038.6(APC):c.2851del(p.Tyr951fs)",
"edge_relation": "VARIANT_HAS_VEP_CONSEQUENCE",
"edge_evidence_type": "computational_prediction",
... | A | [
"A. frameshift_variant",
"B. missense_variant",
"C. synonymous_variant",
"D. splice_region_variant"
] | [
"expression",
"protein_sequence",
"snp_sequence"
] | [
{
"family": "sequence",
"tag": "snp_sequence",
"anchor_node_id": "NM_000038.6(APC):c.2851del(p.Tyr951fs)",
"source_db": "Ensembl",
"payload": {
"chrom": "5",
"pos": 112838445,
"ref_allele": "T",
"alt_allele": "-",
"ref_context": "CTTACAATTTCACTAAGTCGGAAAATTCAAATAGGA... | [
{
"source_db": "Ensembl_VEP",
"source_id": "APC",
"text": "NM_000038.6(APC):c.2851del(p.Tyr951fs) VARIANT_HAS_VEP_CONSEQUENCE APC",
"confidence": 0.95
}
] | {
"gene": "APC",
"variant": "NM_000038.6(APC):c.2851del(p.Tyr951fs)",
"SO_term": "frameshift_variant",
"impact": "HIGH",
"tier": "A"
} | 0.95 |
co_codi_00003 | coding_variant | coding_variant | easy | 1 | According to Ensembl VEP, what is the predicted functional consequence of NM_000038.6(APC):c.7936C>T(p.Gln2646Ter) in APC? | NM_000038.6(APC):c.7936C>T(p.Gln2646Ter) VARIANT_HAS_VEP_CONSEQUENCE APC | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000038.6(APC):c.7936C>T(p.Gln2646Ter)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000038.6(APC):c.7936C>T(p.Gln2646Ter)",
"edge_relation": "VARIANT_HAS_VEP_CONSEQUENCE",
"edge_evidence_type": "computational_prediction... | A | [
"A. stop_gained",
"B. frameshift_variant",
"C. synonymous_variant",
"D. missense_variant"
] | [
"expression",
"protein_sequence",
"snp_sequence"
] | [
{
"family": "sequence",
"tag": "snp_sequence",
"anchor_node_id": "NM_000038.6(APC):c.7936C>T(p.Gln2646Ter)",
"source_db": "Ensembl",
"payload": {
"chrom": "5",
"pos": 112843530,
"ref_allele": "C",
"alt_allele": "T",
"ref_context": "CCGTTTCCTCAGGTGCTACAAATGGTGCTGAATC... | [
{
"source_db": "Ensembl_VEP",
"source_id": "APC",
"text": "NM_000038.6(APC):c.7936C>T(p.Gln2646Ter) VARIANT_HAS_VEP_CONSEQUENCE APC",
"confidence": 0.95
}
] | {
"gene": "APC",
"variant": "NM_000038.6(APC):c.7936C>T(p.Gln2646Ter)",
"SO_term": "stop_gained",
"impact": "HIGH",
"tier": "A"
} | 0.95 |
co_codi_00004 | coding_variant | coding_variant | easy | 1 | According to Ensembl VEP, what is the predicted functional consequence of NM_000038.6(APC):c.1814_1818delinsTAGATGG(p.Asp605fs) in APC? | NM_000038.6(APC):c.1814_1818delinsTAGATGG(p.Asp605fs) VARIANT_HAS_VEP_CONSEQUENCE APC | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000038.6(APC):c.1814_1818delinsTAGATGG(p.Asp605fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000038.6(APC):c.1814_1818delinsTAGATGG(p.Asp605fs)",
"edge_relation": "VARIANT_HAS_VEP_CONSEQUENCE",
"edge_evidence_type":... | C | [
"A. synonymous_variant",
"B. missense_variant",
"C. frameshift_variant",
"D. splice_region_variant"
] | [
"expression",
"protein_sequence",
"snp_sequence"
] | [
{
"family": "sequence",
"tag": "snp_sequence",
"anchor_node_id": "NM_000038.6(APC):c.1814_1818delinsTAGATGG(p.Asp605fs)",
"source_db": "Ensembl",
"payload": {
"chrom": "5",
"pos": 112835021,
"ref_allele": "ATATA",
"alt_allele": "TAGATGG",
"ref_context": "ATTGAGTGCCT... | [
{
"source_db": "Ensembl_VEP",
"source_id": "APC",
"text": "NM_000038.6(APC):c.1814_1818delinsTAGATGG(p.Asp605fs) VARIANT_HAS_VEP_CONSEQUENCE APC",
"confidence": 0.95
}
] | {
"gene": "APC",
"variant": "NM_000038.6(APC):c.1814_1818delinsTAGATGG(p.Asp605fs)",
"SO_term": "frameshift_variant",
"impact": "HIGH",
"tier": "A"
} | 0.95 |
co_codi_00005 | coding_variant | coding_variant | easy | 1 | According to Ensembl VEP, what is the predicted functional consequence of NM_000038.6(APC):c.3448G>T(p.Glu1150Ter) in APC? | NM_000038.6(APC):c.3448G>T(p.Glu1150Ter) VARIANT_HAS_VEP_CONSEQUENCE APC | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000038.6(APC):c.3448G>T(p.Glu1150Ter)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000038.6(APC):c.3448G>T(p.Glu1150Ter)",
"edge_relation": "VARIANT_HAS_VEP_CONSEQUENCE",
"edge_evidence_type": "computational_prediction... | B | [
"A. synonymous_variant",
"B. stop_gained",
"C. missense_variant",
"D. frameshift_variant"
] | [
"expression",
"protein_sequence",
"snp_sequence",
"splice"
] | [
{
"family": "sequence",
"tag": "snp_sequence",
"anchor_node_id": "NM_000038.6(APC):c.3448G>T(p.Glu1150Ter)",
"source_db": "Ensembl",
"payload": {
"chrom": "5",
"pos": 112839042,
"ref_allele": "G",
"alt_allele": "T",
"ref_context": "ATGACTATGAAGATGATAAGCCTACCAATTATAG... | [
{
"source_db": "Ensembl_VEP",
"source_id": "APC",
"text": "NM_000038.6(APC):c.3448G>T(p.Glu1150Ter) VARIANT_HAS_VEP_CONSEQUENCE APC",
"confidence": 0.95
}
] | {
"gene": "APC",
"variant": "NM_000038.6(APC):c.3448G>T(p.Glu1150Ter)",
"SO_term": "stop_gained",
"impact": "HIGH",
"tier": "A"
} | 0.95 |
co_codi_00006 | coding_variant | coding_variant | easy | 1 | According to Ensembl VEP, what is the predicted functional consequence of NM_000038.6(APC):c.383del(p.Arg128fs) in APC? | NM_000038.6(APC):c.383del(p.Arg128fs) VARIANT_HAS_VEP_CONSEQUENCE APC | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000038.6(APC):c.383del(p.Arg128fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000038.6(APC):c.383del(p.Arg128fs)",
"edge_relation": "VARIANT_HAS_VEP_CONSEQUENCE",
"edge_evidence_type": "computational_prediction",
... | C | [
"A. synonymous_variant",
"B. splice_region_variant",
"C. frameshift_variant",
"D. missense_variant"
] | [
"expression",
"protein_sequence",
"snp_sequence"
] | [
{
"family": "sequence",
"tag": "snp_sequence",
"anchor_node_id": "NM_000038.6(APC):c.383del(p.Arg128fs)",
"source_db": "Ensembl",
"payload": {
"chrom": "5",
"pos": 112767351,
"ref_allele": "G",
"alt_allele": "-",
"ref_context": "TCCTGTTCCTATGGGTTCATTTCCAAGAAGAGGGTTT... | [
{
"source_db": "Ensembl_VEP",
"source_id": "APC",
"text": "NM_000038.6(APC):c.383del(p.Arg128fs) VARIANT_HAS_VEP_CONSEQUENCE APC",
"confidence": 0.95
}
] | {
"gene": "APC",
"variant": "NM_000038.6(APC):c.383del(p.Arg128fs)",
"SO_term": "frameshift_variant",
"impact": "HIGH",
"tier": "A"
} | 0.95 |
co_codi_00007 | coding_variant | coding_variant | easy | 1 | According to Ensembl VEP, what is the predicted functional consequence of NM_000038.6(APC):c.3510dup(p.Arg1171fs) in APC? | NM_000038.6(APC):c.3510dup(p.Arg1171fs) VARIANT_HAS_VEP_CONSEQUENCE APC | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000038.6(APC):c.3510dup(p.Arg1171fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000038.6(APC):c.3510dup(p.Arg1171fs)",
"edge_relation": "VARIANT_HAS_VEP_CONSEQUENCE",
"edge_evidence_type": "computational_prediction",... | C | [
"A. synonymous_variant",
"B. splice_region_variant",
"C. frameshift_variant",
"D. missense_variant"
] | [
"expression",
"protein_sequence",
"snp_sequence"
] | [
{
"family": "sequence",
"tag": "snp_sequence",
"anchor_node_id": "NM_000038.6(APC):c.3510dup(p.Arg1171fs)",
"source_db": "Ensembl",
"payload": {
"chrom": "5",
"pos": 112839104,
"ref_allele": "-",
"alt_allele": "A",
"ref_context": "GAAGAAGAAGAGAGACCAACAAATTATAGCATAAA... | [
{
"source_db": "Ensembl_VEP",
"source_id": "APC",
"text": "NM_000038.6(APC):c.3510dup(p.Arg1171fs) VARIANT_HAS_VEP_CONSEQUENCE APC",
"confidence": 0.95
}
] | {
"gene": "APC",
"variant": "NM_000038.6(APC):c.3510dup(p.Arg1171fs)",
"SO_term": "frameshift_variant",
"impact": "HIGH",
"tier": "A"
} | 0.95 |
co_codi_00008 | coding_variant | coding_variant | easy | 1 | According to Ensembl VEP, what is the predicted functional consequence of NM_000038.6(APC):c.3446_3453del(p.Glu1149fs) in APC? | NM_000038.6(APC):c.3446_3453del(p.Glu1149fs) VARIANT_HAS_VEP_CONSEQUENCE APC | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000038.6(APC):c.3446_3453del(p.Glu1149fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000038.6(APC):c.3446_3453del(p.Glu1149fs)",
"edge_relation": "VARIANT_HAS_VEP_CONSEQUENCE",
"edge_evidence_type": "computational_pr... | B | [
"A. missense_variant",
"B. frameshift_variant",
"C. synonymous_variant",
"D. splice_region_variant"
] | [
"expression",
"protein_sequence",
"snp_sequence"
] | [
{
"family": "sequence",
"tag": "snp_sequence",
"anchor_node_id": "NM_000038.6(APC):c.3446_3453del(p.Glu1149fs)",
"source_db": "Ensembl",
"payload": {
"chrom": "5",
"pos": 112839040,
"ref_allele": "AAGAAGAA",
"alt_allele": "-",
"ref_context": "AGATGACTATGAAGATGATAAGC... | [
{
"source_db": "Ensembl_VEP",
"source_id": "APC",
"text": "NM_000038.6(APC):c.3446_3453del(p.Glu1149fs) VARIANT_HAS_VEP_CONSEQUENCE APC",
"confidence": 0.95
}
] | {
"gene": "APC",
"variant": "NM_000038.6(APC):c.3446_3453del(p.Glu1149fs)",
"SO_term": "frameshift_variant",
"impact": "HIGH",
"tier": "A"
} | 0.95 |
co_codi_00009 | coding_variant | coding_variant | medium | 2 | The variant NM_000038.6(APC):c.2309C>A(p.Ser770Ter) causes a stop_gained in gene APC. Which Reactome biological pathway is directly disrupted as a result? | NM_000038.6(APC):c.2309C>A(p.Ser770Ter) VARIANT_HAS_VEP_CONSEQUENCE APC -> APC GENE_PARTICIPATES_IN_PATHWAY Beta-catenin phosphorylation cascade | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000038.6(APC):c.2309C>A(p.Ser770Ter)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000038.6(APC):c.2309C>A(p.Ser770Ter)",
"edge_relation": "VARIANT_HAS_VEP_CONSEQUENCE",
"edge_evidence_type": "computational_prediction",... | A | [
"A. Beta-catenin phosphorylation cascade",
"B. Sensory processing of sound by inner hair cells of the cochlea",
"C. MTOR signalling",
"D. Formation of the non-canonical BAF (ncBAF) complex"
] | [
"expression",
"protein_sequence",
"snp_sequence"
] | [
{
"family": "sequence",
"tag": "snp_sequence",
"anchor_node_id": "NM_000038.6(APC):c.2309C>A(p.Ser770Ter)",
"source_db": "Ensembl",
"payload": {
"chrom": "5",
"pos": 112837903,
"ref_allele": "C",
"alt_allele": "A",
"ref_context": "TGTTAGGAAACAAAAAGCCCTAGAAGCAGAATTAG... | [
{
"source_db": "Ensembl_VEP",
"source_id": "APC",
"text": "NM_000038.6(APC):c.2309C>A(p.Ser770Ter) VARIANT_HAS_VEP_CONSEQUENCE APC",
"confidence": 0.95
},
{
"source_db": "Reactome",
"source_id": "R-HSA-196299",
"text": "APC GENE_PARTICIPATES_IN_PATHWAY Beta-catenin phosphorylation ca... | {
"gene": "APC",
"variant": "NM_000038.6(APC):c.2309C>A(p.Ser770Ter)",
"pathway": "Beta-catenin phosphorylation cascade",
"SO_term": "stop_gained",
"impact": "HIGH",
"tier": "B"
} | 0.974679 |
co_codi_00010 | coding_variant | coding_variant | medium | 2 | The variant NM_000038.6(APC):c.670del(p.Ile224fs) causes a frameshift_variant in gene APC. Which Reactome biological pathway is directly disrupted as a result? | NM_000038.6(APC):c.670del(p.Ile224fs) VARIANT_HAS_VEP_CONSEQUENCE APC -> APC GENE_PARTICIPATES_IN_PATHWAY APC truncation mutants have impaired AXIN binding | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000038.6(APC):c.670del(p.Ile224fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000038.6(APC):c.670del(p.Ile224fs)",
"edge_relation": "VARIANT_HAS_VEP_CONSEQUENCE",
"edge_evidence_type": "computational_prediction",
... | C | [
"A. ERBB2 Activates PTK6 Signaling",
"B. Signaling by GSK3beta mutants",
"C. APC truncation mutants have impaired AXIN binding",
"D. TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain"
] | [
"expression",
"protein_sequence",
"snp_sequence"
] | [
{
"family": "sequence",
"tag": "snp_sequence",
"anchor_node_id": "NM_000038.6(APC):c.670del(p.Ile224fs)",
"source_db": "Ensembl",
"payload": {
"chrom": "5",
"pos": 112792470,
"ref_allele": "A",
"alt_allele": "-",
"ref_context": "TAATTAGGTTTCTTGTTTTATTTTAGCGAAGAATAGC... | [
{
"source_db": "Ensembl_VEP",
"source_id": "APC",
"text": "NM_000038.6(APC):c.670del(p.Ile224fs) VARIANT_HAS_VEP_CONSEQUENCE APC",
"confidence": 0.95
},
{
"source_db": "Reactome",
"source_id": "R-HSA-5467337",
"text": "APC GENE_PARTICIPATES_IN_PATHWAY APC truncation mutants have impa... | {
"gene": "APC",
"variant": "NM_000038.6(APC):c.670del(p.Ile224fs)",
"pathway": "APC truncation mutants have impaired AXIN binding",
"SO_term": "frameshift_variant",
"impact": "HIGH",
"tier": "B"
} | 0.974679 |
co_codi_00011 | coding_variant | coding_variant | medium | 2 | The variant NM_000038.6(APC):c.2537_2543del(p.Arg845_Ser846insTer) causes a frameshift_variant in gene APC. Which Reactome biological pathway is directly disrupted as a result? | NM_000038.6(APC):c.2537_2543del(p.Arg845_Ser846insTer) VARIANT_HAS_VEP_CONSEQUENCE APC -> APC GENE_PARTICIPATES_IN_PATHWAY Apoptotic cleavage of cellular proteins | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000038.6(APC):c.2537_2543del(p.Arg845_Ser846insTer)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000038.6(APC):c.2537_2543del(p.Arg845_Ser846insTer)",
"edge_relation": "VARIANT_HAS_VEP_CONSEQUENCE",
"edge_evidence_type... | C | [
"A. ARMS-mediated activation",
"B. Aspirin ADME",
"C. Apoptotic cleavage of cellular proteins",
"D. NR1H2 & NR1H3 regulate gene expression linked to lipogenesis"
] | [
"expression",
"protein_sequence",
"snp_sequence"
] | [
{
"family": "sequence",
"tag": "snp_sequence",
"anchor_node_id": "NM_000038.6(APC):c.2537_2543del(p.Arg845_Ser846insTer)",
"source_db": "Ensembl",
"payload": {
"chrom": "5",
"pos": 112838131,
"ref_allele": "CTGAAAA",
"alt_allele": "-",
"ref_context": "AGTGTTACCCAGCT... | [
{
"source_db": "Ensembl_VEP",
"source_id": "APC",
"text": "NM_000038.6(APC):c.2537_2543del(p.Arg845_Ser846insTer) VARIANT_HAS_VEP_CONSEQUENCE APC",
"confidence": 0.95
},
{
"source_db": "Reactome",
"source_id": "R-HSA-111465",
"text": "APC GENE_PARTICIPATES_IN_PATHWAY Apoptotic cleava... | {
"gene": "APC",
"variant": "NM_000038.6(APC):c.2537_2543del(p.Arg845_Ser846insTer)",
"pathway": "Apoptotic cleavage of cellular proteins",
"SO_term": "frameshift_variant",
"impact": "HIGH",
"tier": "B"
} | 0.974679 |
co_codi_00012 | coding_variant | coding_variant | medium | 2 | The variant NM_000038.6(APC):c.1380del(p.Glu461fs) causes a frameshift_variant in gene APC. Which Reactome biological pathway is directly disrupted as a result? | NM_000038.6(APC):c.1380del(p.Glu461fs) VARIANT_HAS_VEP_CONSEQUENCE APC -> APC GENE_PARTICIPATES_IN_PATHWAY Ovarian tumor domain proteases | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000038.6(APC):c.1380del(p.Glu461fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000038.6(APC):c.1380del(p.Glu461fs)",
"edge_relation": "VARIANT_HAS_VEP_CONSEQUENCE",
"edge_evidence_type": "computational_prediction",
... | D | [
"A. Activated NTRK2 signals through PLCG1",
"B. HCMV Late Events",
"C. SHC-related events triggered by IGF1R",
"D. Ovarian tumor domain proteases"
] | [
"expression",
"protein_sequence",
"snp_sequence"
] | [
{
"family": "sequence",
"tag": "snp_sequence",
"anchor_node_id": "NM_000038.6(APC):c.1380del(p.Glu461fs)",
"source_db": "Ensembl",
"payload": {
"chrom": "5",
"pos": 112821963,
"ref_allele": "A",
"alt_allele": "-",
"ref_context": "CATCAGATCTGTCCTGCTGTGTGTGTTCTAATGAAA... | [
{
"source_db": "Ensembl_VEP",
"source_id": "APC",
"text": "NM_000038.6(APC):c.1380del(p.Glu461fs) VARIANT_HAS_VEP_CONSEQUENCE APC",
"confidence": 0.95
},
{
"source_db": "Reactome",
"source_id": "R-HSA-5689896",
"text": "APC GENE_PARTICIPATES_IN_PATHWAY Ovarian tumor domain proteases"... | {
"gene": "APC",
"variant": "NM_000038.6(APC):c.1380del(p.Glu461fs)",
"pathway": "Ovarian tumor domain proteases",
"SO_term": "frameshift_variant",
"impact": "HIGH",
"tier": "B"
} | 0.974679 |
co_codi_00013 | coding_variant | coding_variant | medium | 2 | The variant NM_000038.6(APC):c.7918_7919insTTGT(p.Ser2640fs) causes a frameshift_variant in gene APC. Which Reactome biological pathway is directly disrupted as a result? | NM_000038.6(APC):c.7918_7919insTTGT(p.Ser2640fs) VARIANT_HAS_VEP_CONSEQUENCE APC -> APC GENE_PARTICIPATES_IN_PATHWAY APC truncation mutants have impaired AXIN binding | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000038.6(APC):c.7918_7919insTTGT(p.Ser2640fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000038.6(APC):c.7918_7919insTTGT(p.Ser2640fs)",
"edge_relation": "VARIANT_HAS_VEP_CONSEQUENCE",
"edge_evidence_type": "computat... | D | [
"A. Mitotic Prophase",
"B. Ion channel transport",
"C. HDACs deacetylate histones",
"D. APC truncation mutants have impaired AXIN binding"
] | [
"expression",
"protein_sequence",
"snp_sequence"
] | [
{
"family": "sequence",
"tag": "snp_sequence",
"anchor_node_id": "NM_000038.6(APC):c.7918_7919insTTGT(p.Ser2640fs)",
"source_db": "Ensembl",
"payload": {
"chrom": "5",
"pos": 112843513,
"ref_allele": "-",
"alt_allele": "TTGT",
"ref_context": "AAATAGTACTTCTCAGACCGTTT... | [
{
"source_db": "Ensembl_VEP",
"source_id": "APC",
"text": "NM_000038.6(APC):c.7918_7919insTTGT(p.Ser2640fs) VARIANT_HAS_VEP_CONSEQUENCE APC",
"confidence": 0.95
},
{
"source_db": "Reactome",
"source_id": "R-HSA-5467337",
"text": "APC GENE_PARTICIPATES_IN_PATHWAY APC truncation mutant... | {
"gene": "APC",
"variant": "NM_000038.6(APC):c.7918_7919insTTGT(p.Ser2640fs)",
"pathway": "APC truncation mutants have impaired AXIN binding",
"SO_term": "frameshift_variant",
"impact": "HIGH",
"tier": "B"
} | 0.974679 |
co_codi_00014 | coding_variant | coding_variant | medium | 2 | The variant NM_000038.6(APC):c.3870del(p.Gln1291fs) causes a frameshift_variant in gene APC. Which Reactome biological pathway is directly disrupted as a result? | NM_000038.6(APC):c.3870del(p.Gln1291fs) VARIANT_HAS_VEP_CONSEQUENCE APC -> APC GENE_PARTICIPATES_IN_PATHWAY AXIN missense mutants destabilize the destruction complex | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000038.6(APC):c.3870del(p.Gln1291fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000038.6(APC):c.3870del(p.Gln1291fs)",
"edge_relation": "VARIANT_HAS_VEP_CONSEQUENCE",
"edge_evidence_type": "computational_prediction",... | B | [
"A. tamatinib-resistant FLT3 mutants",
"B. AXIN missense mutants destabilize the destruction complex",
"C. Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE)",
"D. STAT5 activation downstream of FLT3 ITD mutants"
] | [
"expression",
"protein_sequence",
"snp_sequence"
] | [
{
"family": "sequence",
"tag": "snp_sequence",
"anchor_node_id": "NM_000038.6(APC):c.3870del(p.Gln1291fs)",
"source_db": "Ensembl",
"payload": {
"chrom": "5",
"pos": 112839464,
"ref_allele": "T",
"alt_allele": "-",
"ref_context": "TGTAGTTCATTATCATCTTTGTCATCAGCTGAAGA... | [
{
"source_db": "Ensembl_VEP",
"source_id": "APC",
"text": "NM_000038.6(APC):c.3870del(p.Gln1291fs) VARIANT_HAS_VEP_CONSEQUENCE APC",
"confidence": 0.95
},
{
"source_db": "Reactome",
"source_id": "R-HSA-5467340",
"text": "APC GENE_PARTICIPATES_IN_PATHWAY AXIN missense mutants destabil... | {
"gene": "APC",
"variant": "NM_000038.6(APC):c.3870del(p.Gln1291fs)",
"pathway": "AXIN missense mutants destabilize the destruction complex",
"SO_term": "frameshift_variant",
"impact": "HIGH",
"tier": "B"
} | 0.974679 |
co_codi_00015 | coding_variant | coding_variant | medium | 2 | The variant NM_000038.6(APC):c.4059dup(p.Phe1354fs) causes a frameshift_variant in gene APC. Which Reactome biological pathway is directly disrupted as a result? | NM_000038.6(APC):c.4059dup(p.Phe1354fs) VARIANT_HAS_VEP_CONSEQUENCE APC -> APC GENE_PARTICIPATES_IN_PATHWAY Disassembly of the destruction complex and recruitment of AXIN to the membrane | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000038.6(APC):c.4059dup(p.Phe1354fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000038.6(APC):c.4059dup(p.Phe1354fs)",
"edge_relation": "VARIANT_HAS_VEP_CONSEQUENCE",
"edge_evidence_type": "computational_prediction",... | A | [
"A. Disassembly of the destruction complex and recruitment of AXIN to the membrane",
"B. Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3",
"C. MDK and PTN in ALK signaling",
"D. GSK3B-mediated proteasomal degradation of PD-L1(CD274)"
] | [
"expression",
"protein_sequence",
"snp_sequence"
] | [
{
"family": "sequence",
"tag": "snp_sequence",
"anchor_node_id": "NM_000038.6(APC):c.4059dup(p.Phe1354fs)",
"source_db": "Ensembl",
"payload": {
"chrom": "5",
"pos": 112839653,
"ref_allele": "-",
"alt_allele": "A",
"ref_context": "CTGCAGGGTTCTAGTTTATCTTCAGAATCAGCCAG... | [
{
"source_db": "Ensembl_VEP",
"source_id": "APC",
"text": "NM_000038.6(APC):c.4059dup(p.Phe1354fs) VARIANT_HAS_VEP_CONSEQUENCE APC",
"confidence": 0.95
},
{
"source_db": "Reactome",
"source_id": "R-HSA-4641262",
"text": "APC GENE_PARTICIPATES_IN_PATHWAY Disassembly of the destruction... | {
"gene": "APC",
"variant": "NM_000038.6(APC):c.4059dup(p.Phe1354fs)",
"pathway": "Disassembly of the destruction complex and recruitment of AXIN to the membrane",
"SO_term": "frameshift_variant",
"impact": "HIGH",
"tier": "B"
} | 0.974679 |
co_codi_00016 | coding_variant | coding_variant | medium | 2 | The variant NM_000038.6(APC):c.5814del(p.Asp1939fs) causes a frameshift_variant in gene APC. Which Reactome biological pathway is directly disrupted as a result? | NM_000038.6(APC):c.5814del(p.Asp1939fs) VARIANT_HAS_VEP_CONSEQUENCE APC -> APC GENE_PARTICIPATES_IN_PATHWAY Ovarian tumor domain proteases | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000038.6(APC):c.5814del(p.Asp1939fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000038.6(APC):c.5814del(p.Asp1939fs)",
"edge_relation": "VARIANT_HAS_VEP_CONSEQUENCE",
"edge_evidence_type": "computational_prediction",... | B | [
"A. Signaling by plasma membrane FGFR1 fusions",
"B. Ovarian tumor domain proteases",
"C. Activated NTRK3 signals through RAS",
"D. MTOR signalling"
] | [
"expression",
"protein_sequence",
"snp_sequence"
] | [
{
"family": "sequence",
"tag": "snp_sequence",
"anchor_node_id": "NM_000038.6(APC):c.5814del(p.Asp1939fs)",
"source_db": "Ensembl",
"payload": {
"chrom": "5",
"pos": 112841408,
"ref_allele": "A",
"alt_allele": "-",
"ref_context": "CAGCCTAAACCCATACTTCAGAAACAATCCACTTT... | [
{
"source_db": "Ensembl_VEP",
"source_id": "APC",
"text": "NM_000038.6(APC):c.5814del(p.Asp1939fs) VARIANT_HAS_VEP_CONSEQUENCE APC",
"confidence": 0.95
},
{
"source_db": "Reactome",
"source_id": "R-HSA-5689896",
"text": "APC GENE_PARTICIPATES_IN_PATHWAY Ovarian tumor domain proteases... | {
"gene": "APC",
"variant": "NM_000038.6(APC):c.5814del(p.Asp1939fs)",
"pathway": "Ovarian tumor domain proteases",
"SO_term": "frameshift_variant",
"impact": "HIGH",
"tier": "B"
} | 0.974679 |
co_codi_00017 | coding_variant | coding_variant | medium | 2 | The variant NM_000038.6(APC):c.7488_7489insA(p.Ser2497fs) causes a frameshift_variant in gene APC. Which Reactome biological pathway is directly disrupted as a result? | NM_000038.6(APC):c.7488_7489insA(p.Ser2497fs) VARIANT_HAS_VEP_CONSEQUENCE APC -> APC GENE_PARTICIPATES_IN_PATHWAY Ovarian tumor domain proteases | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000038.6(APC):c.7488_7489insA(p.Ser2497fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000038.6(APC):c.7488_7489insA(p.Ser2497fs)",
"edge_relation": "VARIANT_HAS_VEP_CONSEQUENCE",
"edge_evidence_type": "computational_... | A | [
"A. Ovarian tumor domain proteases",
"B. Regulation of lipid metabolism by PPARalpha",
"C. RHO GTPases activate KTN1",
"D. Clathrin-mediated endocytosis"
] | [
"expression",
"protein_sequence",
"snp_sequence"
] | [
{
"family": "sequence",
"tag": "snp_sequence",
"anchor_node_id": "NM_000038.6(APC):c.7488_7489insA(p.Ser2497fs)",
"source_db": "Ensembl",
"payload": {
"chrom": "5",
"pos": 112843083,
"ref_allele": "-",
"alt_allele": "A",
"ref_context": "AAACTCCAGTTTTAAGTCCTTCCCTTCCT... | [
{
"source_db": "Ensembl_VEP",
"source_id": "APC",
"text": "NM_000038.6(APC):c.7488_7489insA(p.Ser2497fs) VARIANT_HAS_VEP_CONSEQUENCE APC",
"confidence": 0.95
},
{
"source_db": "Reactome",
"source_id": "R-HSA-5689896",
"text": "APC GENE_PARTICIPATES_IN_PATHWAY Ovarian tumor domain pro... | {
"gene": "APC",
"variant": "NM_000038.6(APC):c.7488_7489insA(p.Ser2497fs)",
"pathway": "Ovarian tumor domain proteases",
"SO_term": "frameshift_variant",
"impact": "HIGH",
"tier": "B"
} | 0.974679 |
co_codi_00018 | coding_variant | coding_variant | medium | 2 | The variant NM_000038.6(APC):c.7387G>T(p.Glu2463Ter) causes a stop_gained in gene APC. Which Reactome biological pathway is directly disrupted as a result? | NM_000038.6(APC):c.7387G>T(p.Glu2463Ter) VARIANT_HAS_VEP_CONSEQUENCE APC -> APC GENE_PARTICIPATES_IN_PATHWAY CTNNB1 T41 mutants aren't phosphorylated | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000038.6(APC):c.7387G>T(p.Glu2463Ter)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000038.6(APC):c.7387G>T(p.Glu2463Ter)",
"edge_relation": "VARIANT_HAS_VEP_CONSEQUENCE",
"edge_evidence_type": "computational_prediction... | B | [
"A. Signaling by FGFR2 in disease",
"B. CTNNB1 T41 mutants aren't phosphorylated",
"C. Homologous DNA Pairing and Strand Exchange",
"D. Regulation of necroptotic cell death"
] | [
"expression",
"protein_sequence",
"snp_sequence"
] | [
{
"family": "sequence",
"tag": "snp_sequence",
"anchor_node_id": "NM_000038.6(APC):c.7387G>T(p.Glu2463Ter)",
"source_db": "Ensembl",
"payload": {
"chrom": "5",
"pos": 112842981,
"ref_allele": "G",
"alt_allele": "T",
"ref_context": "AAGCTCCAAGCCCAACCTTAAGAAGAAAATTGGA... | [
{
"source_db": "Ensembl_VEP",
"source_id": "APC",
"text": "NM_000038.6(APC):c.7387G>T(p.Glu2463Ter) VARIANT_HAS_VEP_CONSEQUENCE APC",
"confidence": 0.95
},
{
"source_db": "Reactome",
"source_id": "R-HSA-5358752",
"text": "APC GENE_PARTICIPATES_IN_PATHWAY CTNNB1 T41 mutants aren't pho... | {
"gene": "APC",
"variant": "NM_000038.6(APC):c.7387G>T(p.Glu2463Ter)",
"pathway": "CTNNB1 T41 mutants aren't phosphorylated",
"SO_term": "stop_gained",
"impact": "HIGH",
"tier": "B"
} | 0.974679 |
co_codi_00019 | coding_variant | coding_variant | medium | 2 | The variant NM_000038.6(APC):c.2944del(p.Ser982fs) causes a frameshift_variant in gene APC. Which Reactome biological pathway is directly disrupted as a result? | NM_000038.6(APC):c.2944del(p.Ser982fs) VARIANT_HAS_VEP_CONSEQUENCE APC -> APC GENE_PARTICIPATES_IN_PATHWAY CTNNB1 T41 mutants aren't phosphorylated | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000038.6(APC):c.2944del(p.Ser982fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000038.6(APC):c.2944del(p.Ser982fs)",
"edge_relation": "VARIANT_HAS_VEP_CONSEQUENCE",
"edge_evidence_type": "computational_prediction",
... | A | [
"A. CTNNB1 T41 mutants aren't phosphorylated",
"B. Prefoldin mediated transfer of substrate to CCT/TriC",
"C. TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain",
"D. ESR-mediated signaling"
] | [
"expression",
"protein_sequence",
"snp_sequence"
] | [
{
"family": "sequence",
"tag": "snp_sequence",
"anchor_node_id": "NM_000038.6(APC):c.2944del(p.Ser982fs)",
"source_db": "Ensembl",
"payload": {
"chrom": "5",
"pos": 112838538,
"ref_allele": "T",
"alt_allele": "-",
"ref_context": "ATAGTGTCAGTAGTAGTGATGGTTATGGTAAAAGAG... | [
{
"source_db": "Ensembl_VEP",
"source_id": "APC",
"text": "NM_000038.6(APC):c.2944del(p.Ser982fs) VARIANT_HAS_VEP_CONSEQUENCE APC",
"confidence": 0.95
},
{
"source_db": "Reactome",
"source_id": "R-HSA-5358752",
"text": "APC GENE_PARTICIPATES_IN_PATHWAY CTNNB1 T41 mutants aren't phosp... | {
"gene": "APC",
"variant": "NM_000038.6(APC):c.2944del(p.Ser982fs)",
"pathway": "CTNNB1 T41 mutants aren't phosphorylated",
"SO_term": "frameshift_variant",
"impact": "HIGH",
"tier": "B"
} | 0.974679 |
co_codi_00020 | coding_variant | coding_variant | medium | 2 | The variant NM_000038.6(APC):c.5814del(p.Asp1939fs) causes a frameshift_variant in gene APC. Which Reactome biological pathway is directly disrupted as a result? | NM_000038.6(APC):c.5814del(p.Asp1939fs) VARIANT_HAS_VEP_CONSEQUENCE APC -> APC GENE_PARTICIPATES_IN_PATHWAY Truncations of AMER1 destabilize the destruction complex | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000038.6(APC):c.5814del(p.Asp1939fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000038.6(APC):c.5814del(p.Asp1939fs)",
"edge_relation": "VARIANT_HAS_VEP_CONSEQUENCE",
"edge_evidence_type": "computational_prediction",... | B | [
"A. Signaling by BRAF and RAF1 fusions",
"B. Truncations of AMER1 destabilize the destruction complex",
"C. Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha",
"D. Defective DNA double strand break response due to BRCA1 loss of function"
] | [
"expression",
"protein_sequence",
"snp_sequence"
] | [
{
"family": "sequence",
"tag": "snp_sequence",
"anchor_node_id": "NM_000038.6(APC):c.5814del(p.Asp1939fs)",
"source_db": "Ensembl",
"payload": {
"chrom": "5",
"pos": 112841408,
"ref_allele": "A",
"alt_allele": "-",
"ref_context": "CAGCCTAAACCCATACTTCAGAAACAATCCACTTT... | [
{
"source_db": "Ensembl_VEP",
"source_id": "APC",
"text": "NM_000038.6(APC):c.5814del(p.Asp1939fs) VARIANT_HAS_VEP_CONSEQUENCE APC",
"confidence": 0.95
},
{
"source_db": "Reactome",
"source_id": "R-HSA-5467348",
"text": "APC GENE_PARTICIPATES_IN_PATHWAY Truncations of AMER1 destabili... | {
"gene": "APC",
"variant": "NM_000038.6(APC):c.5814del(p.Asp1939fs)",
"pathway": "Truncations of AMER1 destabilize the destruction complex",
"SO_term": "frameshift_variant",
"impact": "HIGH",
"tier": "B"
} | 0.974679 |
co_codi_00021 | coding_variant | coding_variant | medium | 2 | The variant NM_000038.6(APC):c.4189G>T(p.Glu1397Ter) causes a stop_gained in gene APC. Which Reactome biological pathway is directly disrupted as a result? | NM_000038.6(APC):c.4189G>T(p.Glu1397Ter) VARIANT_HAS_VEP_CONSEQUENCE APC -> APC GENE_PARTICIPATES_IN_PATHWAY Disassembly of the destruction complex and recruitment of AXIN to the membrane | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000038.6(APC):c.4189G>T(p.Glu1397Ter)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000038.6(APC):c.4189G>T(p.Glu1397Ter)",
"edge_relation": "VARIANT_HAS_VEP_CONSEQUENCE",
"edge_evidence_type": "computational_prediction... | A | [
"A. Disassembly of the destruction complex and recruitment of AXIN to the membrane",
"B. The role of GTSE1 in G2/M progression after G2 checkpoint",
"C. Noncanonical activation of NOTCH3",
"D. PI3K events in ERBB2 signaling"
] | [
"expression",
"protein_sequence",
"snp_sequence",
"splice"
] | [
{
"family": "sequence",
"tag": "snp_sequence",
"anchor_node_id": "NM_000038.6(APC):c.4189G>T(p.Glu1397Ter)",
"source_db": "Ensembl",
"payload": {
"chrom": "5",
"pos": 112839783,
"ref_allele": "G",
"alt_allele": "T",
"ref_context": "CCCCACTCATGTTTAGCAGATGTACTTCTGTCAG... | [
{
"source_db": "Ensembl_VEP",
"source_id": "APC",
"text": "NM_000038.6(APC):c.4189G>T(p.Glu1397Ter) VARIANT_HAS_VEP_CONSEQUENCE APC",
"confidence": 0.95
},
{
"source_db": "Reactome",
"source_id": "R-HSA-4641262",
"text": "APC GENE_PARTICIPATES_IN_PATHWAY Disassembly of the destructio... | {
"gene": "APC",
"variant": "NM_000038.6(APC):c.4189G>T(p.Glu1397Ter)",
"pathway": "Disassembly of the destruction complex and recruitment of AXIN to the membrane",
"SO_term": "stop_gained",
"impact": "HIGH",
"tier": "B"
} | 0.974679 |
co_codi_00022 | coding_variant | coding_variant | medium | 2 | The variant NM_000038.6(APC):c.3587dup(p.Phe1197fs) causes a frameshift_variant in gene APC. Which Reactome biological pathway is directly disrupted as a result? | NM_000038.6(APC):c.3587dup(p.Phe1197fs) VARIANT_HAS_VEP_CONSEQUENCE APC -> APC GENE_PARTICIPATES_IN_PATHWAY CTNNB1 S45 mutants aren't phosphorylated | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000038.6(APC):c.3587dup(p.Phe1197fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000038.6(APC):c.3587dup(p.Phe1197fs)",
"edge_relation": "VARIANT_HAS_VEP_CONSEQUENCE",
"edge_evidence_type": "computational_prediction",... | A | [
"A. CTNNB1 S45 mutants aren't phosphorylated",
"B. Activated NTRK2 signals through CDK5",
"C. Pexophagy",
"D. Signaling by BRAF and RAF1 fusions"
] | [
"expression",
"protein_sequence",
"snp_sequence"
] | [
{
"family": "sequence",
"tag": "snp_sequence",
"anchor_node_id": "NM_000038.6(APC):c.3587dup(p.Phe1197fs)",
"source_db": "Ensembl",
"payload": {
"chrom": "5",
"pos": 112839181,
"ref_allele": "-",
"alt_allele": "C",
"ref_context": "TAGTTTAAAATATGCCACAGATATTCCTTCATCAC... | [
{
"source_db": "Ensembl_VEP",
"source_id": "APC",
"text": "NM_000038.6(APC):c.3587dup(p.Phe1197fs) VARIANT_HAS_VEP_CONSEQUENCE APC",
"confidence": 0.95
},
{
"source_db": "Reactome",
"source_id": "R-HSA-5358751",
"text": "APC GENE_PARTICIPATES_IN_PATHWAY CTNNB1 S45 mutants aren't phos... | {
"gene": "APC",
"variant": "NM_000038.6(APC):c.3587dup(p.Phe1197fs)",
"pathway": "CTNNB1 S45 mutants aren't phosphorylated",
"SO_term": "frameshift_variant",
"impact": "HIGH",
"tier": "B"
} | 0.974679 |
co_codi_00023 | coding_variant | coding_variant | medium | 2 | The variant NM_000038.6(APC):c.2546_2552del(p.Asp849fs) causes a frameshift_variant in gene APC. Which Reactome biological pathway is directly disrupted as a result? | NM_000038.6(APC):c.2546_2552del(p.Asp849fs) VARIANT_HAS_VEP_CONSEQUENCE APC -> APC GENE_PARTICIPATES_IN_PATHWAY CTNNB1 S33 mutants aren't phosphorylated | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000038.6(APC):c.2546_2552del(p.Asp849fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000038.6(APC):c.2546_2552del(p.Asp849fs)",
"edge_relation": "VARIANT_HAS_VEP_CONSEQUENCE",
"edge_evidence_type": "computational_pred... | A | [
"A. CTNNB1 S33 mutants aren't phosphorylated",
"B. HDR through Homologous Recombination (HRR)",
"C. PINK1-PRKN Mediated Mitophagy",
"D. SHC-mediated cascade:FGFR4"
] | [
"expression",
"protein_sequence",
"snp_sequence"
] | [
{
"family": "sequence",
"tag": "snp_sequence",
"anchor_node_id": "NM_000038.6(APC):c.2546_2552del(p.Asp849fs)",
"source_db": "Ensembl",
"payload": {
"chrom": "5",
"pos": 112838140,
"ref_allele": "ATAGAAG",
"alt_allele": "-",
"ref_context": "CAGCTCCTCTTCATCAAGAGGAAGC... | [
{
"source_db": "Ensembl_VEP",
"source_id": "APC",
"text": "NM_000038.6(APC):c.2546_2552del(p.Asp849fs) VARIANT_HAS_VEP_CONSEQUENCE APC",
"confidence": 0.95
},
{
"source_db": "Reactome",
"source_id": "R-HSA-5358747",
"text": "APC GENE_PARTICIPATES_IN_PATHWAY CTNNB1 S33 mutants aren't ... | {
"gene": "APC",
"variant": "NM_000038.6(APC):c.2546_2552del(p.Asp849fs)",
"pathway": "CTNNB1 S33 mutants aren't phosphorylated",
"SO_term": "frameshift_variant",
"impact": "HIGH",
"tier": "B"
} | 0.974679 |
co_codi_00024 | coding_variant | coding_variant | medium | 2 | The variant NM_000038.6(APC):c.160del(p.Ser54fs) causes a frameshift_variant in gene APC. Which Reactome biological pathway is directly disrupted as a result? | NM_000038.6(APC):c.160del(p.Ser54fs) VARIANT_HAS_VEP_CONSEQUENCE APC -> APC GENE_PARTICIPATES_IN_PATHWAY Degradation of beta-catenin by the destruction complex | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000038.6(APC):c.160del(p.Ser54fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000038.6(APC):c.160del(p.Ser54fs)",
"edge_relation": "VARIANT_HAS_VEP_CONSEQUENCE",
"edge_evidence_type": "computational_prediction",
... | A | [
"A. Degradation of beta-catenin by the destruction complex",
"B. Activated point mutants of FGFR2",
"C. Hh mutants are degraded by ERAD",
"D. RUNX3 regulates CDKN1A transcription"
] | [
"expression",
"protein_sequence",
"snp_sequence"
] | [
{
"family": "sequence",
"tag": "snp_sequence",
"anchor_node_id": "NM_000038.6(APC):c.160del(p.Ser54fs)",
"source_db": "Ensembl",
"payload": {
"chrom": "5",
"pos": 112766350,
"ref_allele": "A",
"alt_allele": "-",
"ref_context": "TTAATATATTGTGTTCTTTTTAACAGGAAGTACTTAAA... | [
{
"source_db": "Ensembl_VEP",
"source_id": "APC",
"text": "NM_000038.6(APC):c.160del(p.Ser54fs) VARIANT_HAS_VEP_CONSEQUENCE APC",
"confidence": 0.95
},
{
"source_db": "Reactome",
"source_id": "R-HSA-195253",
"text": "APC GENE_PARTICIPATES_IN_PATHWAY Degradation of beta-catenin by the... | {
"gene": "APC",
"variant": "NM_000038.6(APC):c.160del(p.Ser54fs)",
"pathway": "Degradation of beta-catenin by the destruction complex",
"SO_term": "frameshift_variant",
"impact": "HIGH",
"tier": "B"
} | 0.974679 |
co_codi_00025 | coding_variant | coding_variant | hard | 3 | The variant NM_000038.6(APC):c.1847del(p.Leu616fs) causes a frameshift_variant in the coding sequence of gene APC. Which protein product is directly altered by this variant? | NM_000038.6(APC):c.1847del(p.Leu616fs) VARIANT_HAS_VEP_CONSEQUENCE APC -> APC GENE_HAS_TRANSCRIPT APC-209 -> APC-209 TRANSCRIPT_ENCODES_PROTEIN ENSP00000426541 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000038.6(APC):c.1847del(p.Leu616fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000038.6(APC):c.1847del(p.Leu616fs)",
"edge_relation": "VARIANT_HAS_VEP_CONSEQUENCE",
"edge_evidence_type": "computational_prediction",
... | A | [
"A. ENSP00000426541",
"B. RBMS1",
"C. PARP2",
"D. ENSP00000505258"
] | [
"expression",
"protein_sequence",
"snp_sequence"
] | [
{
"family": "sequence",
"tag": "snp_sequence",
"anchor_node_id": "NM_000038.6(APC):c.1847del(p.Leu616fs)",
"source_db": "Ensembl",
"payload": {
"chrom": "5",
"pos": 112835054,
"ref_allele": "T",
"alt_allele": "-",
"ref_context": "CACTGAGAATAAAGCTGATATATGTGCTGTAGATGG... | [
{
"source_db": "Ensembl_VEP",
"source_id": "APC",
"text": "NM_000038.6(APC):c.1847del(p.Leu616fs) VARIANT_HAS_VEP_CONSEQUENCE APC",
"confidence": 0.95
},
{
"source_db": "Ensembl",
"source_id": "ENST00000509732",
"text": "APC GENE_HAS_TRANSCRIPT APC-209",
"confidence": 1
},
{
... | {
"gene": "APC",
"variant": "NM_000038.6(APC):c.1847del(p.Leu616fs)",
"protein": "ENSP00000426541",
"SO_term": "frameshift_variant",
"impact": "HIGH",
"tier": "C"
} | 0.983048 |
co_codi_00026 | coding_variant | coding_variant | hard | 3 | The variant NM_000038.6(APC):c.1981del(p.Cys661fs) causes a frameshift_variant in the coding sequence of gene APC. Which protein product is directly altered by this variant? | NM_000038.6(APC):c.1981del(p.Cys661fs) VARIANT_HAS_VEP_CONSEQUENCE APC -> APC GENE_HAS_TRANSCRIPT APC-209 -> APC-209 TRANSCRIPT_ENCODES_PROTEIN ENSP00000426541 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000038.6(APC):c.1981del(p.Cys661fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000038.6(APC):c.1981del(p.Cys661fs)",
"edge_relation": "VARIANT_HAS_VEP_CONSEQUENCE",
"edge_evidence_type": "computational_prediction",
... | C | [
"A. ITGA1_ITGB1",
"B. ENSP00000508097",
"C. ENSP00000426541",
"D. ENSP00000445628"
] | [
"expression",
"protein_sequence",
"snp_sequence"
] | [
{
"family": "sequence",
"tag": "snp_sequence",
"anchor_node_id": "NM_000038.6(APC):c.1981del(p.Cys661fs)",
"source_db": "Ensembl",
"payload": {
"chrom": "5",
"pos": 112837575,
"ref_allele": "T",
"alt_allele": "-",
"ref_context": "ATTTTGTGATCTCTTGATTTTATTTCAGGCAAATCC... | [
{
"source_db": "Ensembl_VEP",
"source_id": "APC",
"text": "NM_000038.6(APC):c.1981del(p.Cys661fs) VARIANT_HAS_VEP_CONSEQUENCE APC",
"confidence": 0.95
},
{
"source_db": "Ensembl",
"source_id": "ENST00000509732",
"text": "APC GENE_HAS_TRANSCRIPT APC-209",
"confidence": 1
},
{
... | {
"gene": "APC",
"variant": "NM_000038.6(APC):c.1981del(p.Cys661fs)",
"protein": "ENSP00000426541",
"SO_term": "frameshift_variant",
"impact": "HIGH",
"tier": "C"
} | 0.983048 |
co_codi_00027 | coding_variant | coding_variant | hard | 3 | The variant NM_000038.6(APC):c.1653del(p.Leu551fs) causes a frameshift_variant in the coding sequence of gene APC. Which protein product is directly altered by this variant? | NM_000038.6(APC):c.1653del(p.Leu551fs) VARIANT_HAS_VEP_CONSEQUENCE APC -> APC GENE_HAS_TRANSCRIPT APC-209 -> APC-209 TRANSCRIPT_ENCODES_PROTEIN ENSP00000426541 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000038.6(APC):c.1653del(p.Leu551fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000038.6(APC):c.1653del(p.Leu551fs)",
"edge_relation": "VARIANT_HAS_VEP_CONSEQUENCE",
"edge_evidence_type": "computational_prediction",
... | D | [
"A. GLA",
"B. ENSP00000347942",
"C. PALLD",
"D. ENSP00000426541"
] | [
"expression",
"protein_sequence",
"snp_sequence"
] | [
{
"family": "sequence",
"tag": "snp_sequence",
"anchor_node_id": "NM_000038.6(APC):c.1653del(p.Leu551fs)",
"source_db": "Ensembl",
"payload": {
"chrom": "5",
"pos": 112828882,
"ref_allele": "G",
"alt_allele": "-",
"ref_context": "AATCTAAAATTGATTAATTTGCAGGTTATTGCGAGT... | [
{
"source_db": "Ensembl_VEP",
"source_id": "APC",
"text": "NM_000038.6(APC):c.1653del(p.Leu551fs) VARIANT_HAS_VEP_CONSEQUENCE APC",
"confidence": 0.95
},
{
"source_db": "Ensembl",
"source_id": "ENST00000509732",
"text": "APC GENE_HAS_TRANSCRIPT APC-209",
"confidence": 1
},
{
... | {
"gene": "APC",
"variant": "NM_000038.6(APC):c.1653del(p.Leu551fs)",
"protein": "ENSP00000426541",
"SO_term": "frameshift_variant",
"impact": "HIGH",
"tier": "C"
} | 0.983048 |
co_codi_00028 | coding_variant | coding_variant | hard | 3 | The variant NM_000038.6(APC):c.5202del(p.Ser1737fs) causes a frameshift_variant in the coding sequence of gene APC. Which protein product is directly altered by this variant? | NM_000038.6(APC):c.5202del(p.Ser1737fs) VARIANT_HAS_VEP_CONSEQUENCE APC -> APC GENE_HAS_TRANSCRIPT APC-209 -> APC-209 TRANSCRIPT_ENCODES_PROTEIN ENSP00000426541 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000038.6(APC):c.5202del(p.Ser1737fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000038.6(APC):c.5202del(p.Ser1737fs)",
"edge_relation": "VARIANT_HAS_VEP_CONSEQUENCE",
"edge_evidence_type": "computational_prediction",... | D | [
"A. MED26",
"B. SYNJ1",
"C. ENSP00000718056",
"D. ENSP00000426541"
] | [
"expression",
"protein_sequence",
"snp_sequence"
] | [
{
"family": "sequence",
"tag": "snp_sequence",
"anchor_node_id": "NM_000038.6(APC):c.5202del(p.Ser1737fs)",
"source_db": "Ensembl",
"payload": {
"chrom": "5",
"pos": 112840796,
"ref_allele": "A",
"alt_allele": "-",
"ref_context": "GCAGAGGAAGGTGATATTCTTGCAGAATGCATTAA... | [
{
"source_db": "Ensembl_VEP",
"source_id": "APC",
"text": "NM_000038.6(APC):c.5202del(p.Ser1737fs) VARIANT_HAS_VEP_CONSEQUENCE APC",
"confidence": 0.95
},
{
"source_db": "Ensembl",
"source_id": "ENST00000509732",
"text": "APC GENE_HAS_TRANSCRIPT APC-209",
"confidence": 1
},
{... | {
"gene": "APC",
"variant": "NM_000038.6(APC):c.5202del(p.Ser1737fs)",
"protein": "ENSP00000426541",
"SO_term": "frameshift_variant",
"impact": "HIGH",
"tier": "C"
} | 0.983048 |
co_codi_00029 | coding_variant | coding_variant | hard | 3 | The variant NM_000038.6(APC):c.4019_4020dup(p.Ser1341fs) causes a frameshift_variant in the coding sequence of gene APC. Which protein product is directly altered by this variant? | NM_000038.6(APC):c.4019_4020dup(p.Ser1341fs) VARIANT_HAS_VEP_CONSEQUENCE APC -> APC GENE_HAS_TRANSCRIPT APC-209 -> APC-209 TRANSCRIPT_ENCODES_PROTEIN ENSP00000426541 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000038.6(APC):c.4019_4020dup(p.Ser1341fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000038.6(APC):c.4019_4020dup(p.Ser1341fs)",
"edge_relation": "VARIANT_HAS_VEP_CONSEQUENCE",
"edge_evidence_type": "computational_pr... | C | [
"A. ENSP00000411105",
"B. SERPINF1",
"C. ENSP00000426541",
"D. ENSP00000714615"
] | [
"expression",
"protein_sequence",
"snp_sequence"
] | [
{
"family": "sequence",
"tag": "snp_sequence",
"anchor_node_id": "NM_000038.6(APC):c.4019_4020dup(p.Ser1341fs)",
"source_db": "Ensembl",
"payload": {
"chrom": "5",
"pos": 112839613,
"ref_allele": "-",
"alt_allele": "CT",
"ref_context": "TCCAGCAGTGTCACAGCACCCTAGAACCA... | [
{
"source_db": "Ensembl_VEP",
"source_id": "APC",
"text": "NM_000038.6(APC):c.4019_4020dup(p.Ser1341fs) VARIANT_HAS_VEP_CONSEQUENCE APC",
"confidence": 0.95
},
{
"source_db": "Ensembl",
"source_id": "ENST00000509732",
"text": "APC GENE_HAS_TRANSCRIPT APC-209",
"confidence": 1
}... | {
"gene": "APC",
"variant": "NM_000038.6(APC):c.4019_4020dup(p.Ser1341fs)",
"protein": "ENSP00000426541",
"SO_term": "frameshift_variant",
"impact": "HIGH",
"tier": "C"
} | 0.983048 |
co_codi_00030 | coding_variant | coding_variant | hard | 3 | The variant NM_000038.6(APC):c.2700_2701del(p.Gln901fs) causes a frameshift_variant in gene APC. APC functionally interacts with CTNNB1. Which disease is CTNNB1 directly associated with? | NM_000038.6(APC):c.2700_2701del(p.Gln901fs) VARIANT_HAS_VEP_CONSEQUENCE APC -> APC PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH CTNNB1 -> CTNNB1 GENE_ASSOCIATED_WITH_DISEASE gallbladder cancer | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000038.6(APC):c.2700_2701del(p.Gln901fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000038.6(APC):c.2700_2701del(p.Gln901fs)",
"edge_relation": "VARIANT_HAS_VEP_CONSEQUENCE",
"edge_evidence_type": "computational_pred... | B | [
"A. excessive hair growth",
"B. gallbladder cancer",
"C. inherited oocyte maturation defect",
"D. syndromic X-linked intellectual disability Lubs type"
] | [
"expression",
"protein_sequence",
"protein_structure",
"snp_sequence"
] | [
{
"family": "sequence",
"tag": "snp_sequence",
"anchor_node_id": "NM_000038.6(APC):c.2700_2701del(p.Gln901fs)",
"source_db": "Ensembl",
"payload": {
"chrom": "5",
"pos": 112838294,
"ref_allele": "TC",
"alt_allele": "-",
"ref_context": "GCAGCCCAGATTGCCAAAGTCATGGAAGAA... | [
{
"source_db": "Ensembl_VEP",
"source_id": "APC",
"text": "NM_000038.6(APC):c.2700_2701del(p.Gln901fs) VARIANT_HAS_VEP_CONSEQUENCE APC",
"confidence": 0.95
},
{
"source_db": "STRING",
"source_id": "CTNNB1",
"text": "APC PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH CTNNB1",
"confidence": ... | {
"gene_a": "APC",
"gene_b": "CTNNB1",
"variant": "NM_000038.6(APC):c.2700_2701del(p.Gln901fs)",
"disease": "gallbladder cancer",
"SO_term": "frameshift_variant",
"tier": "D"
} | 0.687701 |
co_codi_00031 | coding_variant | coding_variant | hard | 3 | The variant NM_000038.6(APC):c.2945del(p.Pro981_Ser982insTer) causes a frameshift_variant in gene APC. APC functionally interacts with AXIN2. Which disease is AXIN2 directly associated with? | NM_000038.6(APC):c.2945del(p.Pro981_Ser982insTer) VARIANT_HAS_VEP_CONSEQUENCE APC -> APC PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH AXIN2 -> AXIN2 GENE_ASSOCIATED_WITH_DISEASE female breast carcinoma | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000038.6(APC):c.2945del(p.Pro981_Ser982insTer)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000038.6(APC):c.2945del(p.Pro981_Ser982insTer)",
"edge_relation": "VARIANT_HAS_VEP_CONSEQUENCE",
"edge_evidence_type": "comput... | A | [
"A. female breast carcinoma",
"B. eczematous inflammatory disorders",
"C. Hashimoto thyroiditis",
"D. nemaline myopathy"
] | [
"expression",
"protein_sequence",
"protein_structure",
"snp_sequence"
] | [
{
"family": "sequence",
"tag": "snp_sequence",
"anchor_node_id": "NM_000038.6(APC):c.2945del(p.Pro981_Ser982insTer)",
"source_db": "Ensembl",
"payload": {
"chrom": "5",
"pos": 112838539,
"ref_allele": "C",
"alt_allele": "-",
"ref_context": "TAGTGTCAGTAGTAGTGATGGTTAT... | [
{
"source_db": "Ensembl_VEP",
"source_id": "APC",
"text": "NM_000038.6(APC):c.2945del(p.Pro981_Ser982insTer) VARIANT_HAS_VEP_CONSEQUENCE APC",
"confidence": 0.95
},
{
"source_db": "STRING",
"source_id": "AXIN2",
"text": "APC PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH AXIN2",
"confidenc... | {
"gene_a": "APC",
"gene_b": "AXIN2",
"variant": "NM_000038.6(APC):c.2945del(p.Pro981_Ser982insTer)",
"disease": "female breast carcinoma",
"SO_term": "frameshift_variant",
"tier": "D"
} | 0.640746 |
co_codi_00032 | coding_variant | coding_variant | hard | 3 | The variant NM_000038.6(APC):c.1984del(p.Leu662fs) causes a frameshift_variant in gene APC. APC functionally interacts with AXIN2. Which disease is AXIN2 directly associated with? | NM_000038.6(APC):c.1984del(p.Leu662fs) VARIANT_HAS_VEP_CONSEQUENCE APC -> APC PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH AXIN2 -> AXIN2 GENE_ASSOCIATED_WITH_DISEASE oligodontia-cancer predisposition syndrome | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000038.6(APC):c.1984del(p.Leu662fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000038.6(APC):c.1984del(p.Leu662fs)",
"edge_relation": "VARIANT_HAS_VEP_CONSEQUENCE",
"edge_evidence_type": "computational_prediction",
... | B | [
"A. thorax anomalies",
"B. oligodontia-cancer predisposition syndrome",
"C. vaginal bleeding",
"D. acute leukemia"
] | [
"expression",
"protein_sequence",
"protein_structure",
"snp_sequence"
] | [
{
"family": "sequence",
"tag": "snp_sequence",
"anchor_node_id": "NM_000038.6(APC):c.1984del(p.Leu662fs)",
"source_db": "Ensembl",
"payload": {
"chrom": "5",
"pos": 112837578,
"ref_allele": "C",
"alt_allele": "-",
"ref_context": "TTGTGATCTCTTGATTTTATTTCAGGCAAATCCTAA... | [
{
"source_db": "Ensembl_VEP",
"source_id": "APC",
"text": "NM_000038.6(APC):c.1984del(p.Leu662fs) VARIANT_HAS_VEP_CONSEQUENCE APC",
"confidence": 0.95
},
{
"source_db": "STRING",
"source_id": "AXIN2",
"text": "APC PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH AXIN2",
"confidence": 0.999
... | {
"gene_a": "APC",
"gene_b": "AXIN2",
"variant": "NM_000038.6(APC):c.1984del(p.Leu662fs)",
"disease": "oligodontia-cancer predisposition syndrome",
"SO_term": "frameshift_variant",
"tier": "D"
} | 0.98272 |
co_codi_00033 | coding_variant | coding_variant | hard | 3 | The variant NM_000038.6(APC):c.642del(p.Gln215fs) causes a frameshift_variant in gene APC. APC functionally interacts with AXIN2. Which disease is AXIN2 directly associated with? | NM_000038.6(APC):c.642del(p.Gln215fs) VARIANT_HAS_VEP_CONSEQUENCE APC -> APC PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH AXIN2 -> AXIN2 GENE_ASSOCIATED_WITH_DISEASE AXIN2-related attenuated familial adenomatous polyposis | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000038.6(APC):c.642del(p.Gln215fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000038.6(APC):c.642del(p.Gln215fs)",
"edge_relation": "VARIANT_HAS_VEP_CONSEQUENCE",
"edge_evidence_type": "computational_prediction",
... | A | [
"A. AXIN2-related attenuated familial adenomatous polyposis",
"B. gastrointestinal disease",
"C. Orofaciodigital syndrome type 2",
"D. lichen planus, oral"
] | [
"expression",
"protein_sequence",
"protein_structure",
"snp_sequence"
] | [
{
"family": "sequence",
"tag": "snp_sequence",
"anchor_node_id": "NM_000038.6(APC):c.642del(p.Gln215fs)",
"source_db": "Ensembl",
"payload": {
"chrom": "5",
"pos": 112780900,
"ref_allele": "A",
"alt_allele": "-",
"ref_context": "GTTGCGATGGAAGAACAACTAGGTACCTGCCAGGATA... | [
{
"source_db": "Ensembl_VEP",
"source_id": "APC",
"text": "NM_000038.6(APC):c.642del(p.Gln215fs) VARIANT_HAS_VEP_CONSEQUENCE APC",
"confidence": 0.95
},
{
"source_db": "STRING",
"source_id": "AXIN2",
"text": "APC PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH AXIN2",
"confidence": 0.999
... | {
"gene_a": "APC",
"gene_b": "AXIN2",
"variant": "NM_000038.6(APC):c.642del(p.Gln215fs)",
"disease": "AXIN2-related attenuated familial adenomatous polyposis",
"SO_term": "frameshift_variant",
"tier": "D"
} | 0.834787 |
co_codi_00034 | coding_variant | coding_variant | hard | 3 | The variant NM_000038.6(APC):c.674_689del(p.Glu225fs) causes a frameshift_variant in gene APC. APC functionally interacts with CTNNB1. Which disease is CTNNB1 directly associated with? | NM_000038.6(APC):c.674_689del(p.Glu225fs) VARIANT_HAS_VEP_CONSEQUENCE APC -> APC PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH CTNNB1 -> CTNNB1 GENE_ASSOCIATED_WITH_DISEASE osteopathia striata with cranial sclerosis | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000038.6(APC):c.674_689del(p.Glu225fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000038.6(APC):c.674_689del(p.Glu225fs)",
"edge_relation": "VARIANT_HAS_VEP_CONSEQUENCE",
"edge_evidence_type": "computational_predicti... | A | [
"A. osteopathia striata with cranial sclerosis",
"B. Abnormal esophagus morphology",
"C. Cerebro-facio-articular syndrome",
"D. amyloid-beta toxicity"
] | [
"expression",
"protein_sequence",
"protein_structure",
"snp_sequence"
] | [
{
"family": "sequence",
"tag": "snp_sequence",
"anchor_node_id": "NM_000038.6(APC):c.674_689del(p.Glu225fs)",
"source_db": "Ensembl",
"payload": {
"chrom": "5",
"pos": 112792474,
"ref_allele": "AAAAGGACATACTTCG",
"alt_allele": "-",
"ref_context": "TAGGTTTCTTGTTTTATT... | [
{
"source_db": "Ensembl_VEP",
"source_id": "APC",
"text": "NM_000038.6(APC):c.674_689del(p.Glu225fs) VARIANT_HAS_VEP_CONSEQUENCE APC",
"confidence": 0.95
},
{
"source_db": "STRING",
"source_id": "CTNNB1",
"text": "APC PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH CTNNB1",
"confidence": 0.... | {
"gene_a": "APC",
"gene_b": "CTNNB1",
"variant": "NM_000038.6(APC):c.674_689del(p.Glu225fs)",
"disease": "osteopathia striata with cranial sclerosis",
"SO_term": "frameshift_variant",
"tier": "D"
} | 0.712735 |
co_codi_00035 | coding_variant | coding_variant | hard | 3 | The variant NM_000038.6(APC):c.1051G>T(p.Gly351Ter) causes a stop_gained in gene APC. APC functionally interacts with CTNNB1. Which disease is CTNNB1 directly associated with? | NM_000038.6(APC):c.1051G>T(p.Gly351Ter) VARIANT_HAS_VEP_CONSEQUENCE APC -> APC PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH CTNNB1 -> CTNNB1 GENE_ASSOCIATED_WITH_DISEASE pilocytic astrocytoma | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000038.6(APC):c.1051G>T(p.Gly351Ter)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000038.6(APC):c.1051G>T(p.Gly351Ter)",
"edge_relation": "VARIANT_HAS_VEP_CONSEQUENCE",
"edge_evidence_type": "computational_prediction",... | B | [
"A. autosomal recessive ataxia, Beauce type",
"B. pilocytic astrocytoma",
"C. MIX",
"D. decubitus ulcer"
] | [
"expression",
"protein_sequence",
"protein_structure",
"snp_sequence"
] | [
{
"family": "sequence",
"tag": "snp_sequence",
"anchor_node_id": "NM_000038.6(APC):c.1051G>T(p.Gly351Ter)",
"source_db": "Ensembl",
"payload": {
"chrom": "5",
"pos": 112819083,
"ref_allele": "G",
"alt_allele": "T",
"ref_context": "TGCTAGCTATGTCTAGCTCCCAAGACAGCTGTATA... | [
{
"source_db": "Ensembl_VEP",
"source_id": "APC",
"text": "NM_000038.6(APC):c.1051G>T(p.Gly351Ter) VARIANT_HAS_VEP_CONSEQUENCE APC",
"confidence": 0.95
},
{
"source_db": "STRING",
"source_id": "CTNNB1",
"text": "APC PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH CTNNB1",
"confidence": 0.99... | {
"gene_a": "APC",
"gene_b": "CTNNB1",
"variant": "NM_000038.6(APC):c.1051G>T(p.Gly351Ter)",
"disease": "pilocytic astrocytoma",
"SO_term": "stop_gained",
"tier": "D"
} | 0.705468 |
co_codi_00036 | coding_variant | coding_variant | hard | 3 | The variant NM_000038.6(APC):c.2550_2562dup(p.Glu855fs) causes a frameshift_variant in gene APC. APC functionally interacts with AXIN2. Which disease is AXIN2 directly associated with? | NM_000038.6(APC):c.2550_2562dup(p.Glu855fs) VARIANT_HAS_VEP_CONSEQUENCE APC -> APC PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH AXIN2 -> AXIN2 GENE_ASSOCIATED_WITH_DISEASE oligodontia-cancer predisposition syndrome | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000038.6(APC):c.2550_2562dup(p.Glu855fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000038.6(APC):c.2550_2562dup(p.Glu855fs)",
"edge_relation": "VARIANT_HAS_VEP_CONSEQUENCE",
"edge_evidence_type": "computational_pred... | C | [
"A. presbyopia",
"B. skin sarcoma",
"C. oligodontia-cancer predisposition syndrome",
"D. celiac disease"
] | [
"expression",
"protein_sequence",
"protein_structure",
"snp_sequence"
] | [
{
"family": "sequence",
"tag": "snp_sequence",
"anchor_node_id": "NM_000038.6(APC):c.2550_2562dup(p.Glu855fs)",
"source_db": "Ensembl",
"payload": {
"chrom": "5",
"pos": 112838144,
"ref_allele": "-",
"alt_allele": "AAGTTTGGAGAGA",
"ref_context": "TCCTCTTCATCAAGAGGAA... | [
{
"source_db": "Ensembl_VEP",
"source_id": "APC",
"text": "NM_000038.6(APC):c.2550_2562dup(p.Glu855fs) VARIANT_HAS_VEP_CONSEQUENCE APC",
"confidence": 0.95
},
{
"source_db": "STRING",
"source_id": "AXIN2",
"text": "APC PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH AXIN2",
"confidence": 0.... | {
"gene_a": "APC",
"gene_b": "AXIN2",
"variant": "NM_000038.6(APC):c.2550_2562dup(p.Glu855fs)",
"disease": "oligodontia-cancer predisposition syndrome",
"SO_term": "frameshift_variant",
"tier": "D"
} | 0.98272 |
co_codi_00037 | coding_variant | coding_variant | hard | 3 | The variant NM_000038.6(APC):c.3287_3288del(p.Gln1096fs) causes a frameshift_variant in gene APC. APC functionally interacts with AXIN2. Which disease is AXIN2 directly associated with? | NM_000038.6(APC):c.3287_3288del(p.Gln1096fs) VARIANT_HAS_VEP_CONSEQUENCE APC -> APC PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH AXIN2 -> AXIN2 GENE_ASSOCIATED_WITH_DISEASE conjunctival intraepithelial neoplasm | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000038.6(APC):c.3287_3288del(p.Gln1096fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000038.6(APC):c.3287_3288del(p.Gln1096fs)",
"edge_relation": "VARIANT_HAS_VEP_CONSEQUENCE",
"edge_evidence_type": "computational_pr... | A | [
"A. conjunctival intraepithelial neoplasm",
"B. acute kidney injury",
"C. urethra transitional cell carcinoma",
"D. adult neuronal ceroid lipofuscinosis"
] | [
"expression",
"protein_sequence",
"protein_structure",
"snp_sequence"
] | [
{
"family": "sequence",
"tag": "snp_sequence",
"anchor_node_id": "NM_000038.6(APC):c.3287_3288del(p.Gln1096fs)",
"source_db": "Ensembl",
"payload": {
"chrom": "5",
"pos": 112838881,
"ref_allele": "AG",
"alt_allele": "-",
"ref_context": "TGAGAGCACTGATGATAAACACCTCAAGT... | [
{
"source_db": "Ensembl_VEP",
"source_id": "APC",
"text": "NM_000038.6(APC):c.3287_3288del(p.Gln1096fs) VARIANT_HAS_VEP_CONSEQUENCE APC",
"confidence": 0.95
},
{
"source_db": "STRING",
"source_id": "AXIN2",
"text": "APC PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH AXIN2",
"confidence": 0... | {
"gene_a": "APC",
"gene_b": "AXIN2",
"variant": "NM_000038.6(APC):c.3287_3288del(p.Gln1096fs)",
"disease": "conjunctival intraepithelial neoplasm",
"SO_term": "frameshift_variant",
"tier": "D"
} | 0.559744 |
co_codi_00038 | coding_variant | coding_variant | hard | 3 | The variant NM_000038.6(APC):c.902del(p.Pro301fs) causes a frameshift_variant in gene APC. APC functionally interacts with AXIN2. Which disease is AXIN2 directly associated with? | NM_000038.6(APC):c.902del(p.Pro301fs) VARIANT_HAS_VEP_CONSEQUENCE APC -> APC PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH AXIN2 -> AXIN2 GENE_ASSOCIATED_WITH_DISEASE thyroid tumor | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000038.6(APC):c.902del(p.Pro301fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000038.6(APC):c.902del(p.Pro301fs)",
"edge_relation": "VARIANT_HAS_VEP_CONSEQUENCE",
"edge_evidence_type": "computational_prediction",
... | B | [
"A. familial melanoma",
"B. thyroid tumor",
"C. Kufor-Rakeb syndrome",
"D. T-B+Severe combined immunodeficiency"
] | [
"expression",
"protein_sequence",
"protein_structure",
"snp_sequence"
] | [
{
"family": "sequence",
"tag": "snp_sequence",
"anchor_node_id": "NM_000038.6(APC):c.902del(p.Pro301fs)",
"source_db": "Ensembl",
"payload": {
"chrom": "5",
"pos": 112815562,
"ref_allele": "C",
"alt_allele": "-",
"ref_context": "GGACCATGAAACAGCCAGTGTTTTGAGTTCTAGTAGC... | [
{
"source_db": "Ensembl_VEP",
"source_id": "APC",
"text": "NM_000038.6(APC):c.902del(p.Pro301fs) VARIANT_HAS_VEP_CONSEQUENCE APC",
"confidence": 0.95
},
{
"source_db": "STRING",
"source_id": "AXIN2",
"text": "APC PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH AXIN2",
"confidence": 0.999
... | {
"gene_a": "APC",
"gene_b": "AXIN2",
"variant": "NM_000038.6(APC):c.902del(p.Pro301fs)",
"disease": "thyroid tumor",
"SO_term": "frameshift_variant",
"tier": "D"
} | 0.559744 |
co_codi_00039 | coding_variant | coding_variant | hard | 3 | The variant NM_000038.6(APC):c.3363del(p.Asn1122fs) causes a frameshift_variant in gene APC. APC functionally interacts with AXIN2. Which disease is AXIN2 directly associated with? | NM_000038.6(APC):c.3363del(p.Asn1122fs) VARIANT_HAS_VEP_CONSEQUENCE APC -> APC PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH AXIN2 -> AXIN2 GENE_ASSOCIATED_WITH_DISEASE mucosal melanoma | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000038.6(APC):c.3363del(p.Asn1122fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000038.6(APC):c.3363del(p.Asn1122fs)",
"edge_relation": "VARIANT_HAS_VEP_CONSEQUENCE",
"edge_evidence_type": "computational_prediction",... | C | [
"A. Urinary incontinence",
"B. Infarcted brain tissue",
"C. mucosal melanoma",
"D. umbilical nodule tumor"
] | [
"expression",
"protein_sequence",
"protein_structure",
"snp_sequence"
] | [
{
"family": "sequence",
"tag": "snp_sequence",
"anchor_node_id": "NM_000038.6(APC):c.3363del(p.Asn1122fs)",
"source_db": "Ensembl",
"payload": {
"chrom": "5",
"pos": 112838957,
"ref_allele": "T",
"alt_allele": "-",
"ref_context": "CGGGGAGCCAATGGTTCAGAAACAAATCGAGTGGG... | [
{
"source_db": "Ensembl_VEP",
"source_id": "APC",
"text": "NM_000038.6(APC):c.3363del(p.Asn1122fs) VARIANT_HAS_VEP_CONSEQUENCE APC",
"confidence": 0.95
},
{
"source_db": "STRING",
"source_id": "AXIN2",
"text": "APC PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH AXIN2",
"confidence": 0.999
... | {
"gene_a": "APC",
"gene_b": "AXIN2",
"variant": "NM_000038.6(APC):c.3363del(p.Asn1122fs)",
"disease": "mucosal melanoma",
"SO_term": "frameshift_variant",
"tier": "D"
} | 0.559744 |
co_codi_00040 | coding_variant | coding_variant | hard | 3 | The variant NM_000038.6(APC):c.4091del(p.Ser1364fs) causes a frameshift_variant in gene APC. APC functionally interacts with CTNNB1. Which disease is CTNNB1 directly associated with? | NM_000038.6(APC):c.4091del(p.Ser1364fs) VARIANT_HAS_VEP_CONSEQUENCE APC -> APC PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH CTNNB1 -> CTNNB1 GENE_ASSOCIATED_WITH_DISEASE synovial sarcoma | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000038.6(APC):c.4091del(p.Ser1364fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000038.6(APC):c.4091del(p.Ser1364fs)",
"edge_relation": "VARIANT_HAS_VEP_CONSEQUENCE",
"edge_evidence_type": "computational_prediction",... | A | [
"A. synovial sarcoma",
"B. Age-related cataract",
"C. hormone",
"D. familial restrictive cardiomyopathy"
] | [
"expression",
"protein_sequence",
"protein_structure",
"snp_sequence"
] | [
{
"family": "sequence",
"tag": "snp_sequence",
"anchor_node_id": "NM_000038.6(APC):c.4091del(p.Ser1364fs)",
"source_db": "Ensembl",
"payload": {
"chrom": "5",
"pos": 112839685,
"ref_allele": "G",
"alt_allele": "-",
"ref_context": "CAGGCACAAAGCTGTTGAATTTTCTTCAGGAGCGA... | [
{
"source_db": "Ensembl_VEP",
"source_id": "APC",
"text": "NM_000038.6(APC):c.4091del(p.Ser1364fs) VARIANT_HAS_VEP_CONSEQUENCE APC",
"confidence": 0.95
},
{
"source_db": "STRING",
"source_id": "CTNNB1",
"text": "APC PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH CTNNB1",
"confidence": 0.99... | {
"gene_a": "APC",
"gene_b": "CTNNB1",
"variant": "NM_000038.6(APC):c.4091del(p.Ser1364fs)",
"disease": "synovial sarcoma",
"SO_term": "frameshift_variant",
"tier": "D"
} | 0.646877 |
co_codi_00041 | coding_variant | coding_variant | hard | 3 | The variant NM_000038.6(APC):c.3793del(p.Glu1265fs) causes a frameshift_variant in gene APC. APC functionally interacts with CTNNB1. Which disease is CTNNB1 directly associated with? | NM_000038.6(APC):c.3793del(p.Glu1265fs) VARIANT_HAS_VEP_CONSEQUENCE APC -> APC PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH CTNNB1 -> CTNNB1 GENE_ASSOCIATED_WITH_DISEASE listeriosis | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000038.6(APC):c.3793del(p.Glu1265fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000038.6(APC):c.3793del(p.Glu1265fs)",
"edge_relation": "VARIANT_HAS_VEP_CONSEQUENCE",
"edge_evidence_type": "computational_prediction",... | B | [
"A. bilateral striopallidodentate calcinosis",
"B. listeriosis",
"C. appendix adenoma",
"D. Baraitser-Winter cerebrofrontofacial syndrome"
] | [
"expression",
"protein_sequence",
"protein_structure",
"snp_sequence"
] | [
{
"family": "sequence",
"tag": "snp_sequence",
"anchor_node_id": "NM_000038.6(APC):c.3793del(p.Glu1265fs)",
"source_db": "Ensembl",
"payload": {
"chrom": "5",
"pos": 112839387,
"ref_allele": "G",
"alt_allele": "-",
"ref_context": "CTTGCAAAGTTTCTTCTATTAACCAAGAAACAATA... | [
{
"source_db": "Ensembl_VEP",
"source_id": "APC",
"text": "NM_000038.6(APC):c.3793del(p.Glu1265fs) VARIANT_HAS_VEP_CONSEQUENCE APC",
"confidence": 0.95
},
{
"source_db": "STRING",
"source_id": "CTNNB1",
"text": "APC PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH CTNNB1",
"confidence": 0.99... | {
"gene_a": "APC",
"gene_b": "CTNNB1",
"variant": "NM_000038.6(APC):c.3793del(p.Glu1265fs)",
"disease": "listeriosis",
"SO_term": "frameshift_variant",
"tier": "D"
} | 0.805734 |
co_codi_00042 | coding_variant | coding_variant | hard | 3 | The variant NM_000038.6(APC):c.2237dup(p.Ser747fs) causes a frameshift_variant in gene APC. APC functionally interacts with AXIN2. Which disease is AXIN2 directly associated with? | NM_000038.6(APC):c.2237dup(p.Ser747fs) VARIANT_HAS_VEP_CONSEQUENCE APC -> APC PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH AXIN2 -> AXIN2 GENE_ASSOCIATED_WITH_DISEASE gallbladder carcinoma | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000038.6(APC):c.2237dup(p.Ser747fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000038.6(APC):c.2237dup(p.Ser747fs)",
"edge_relation": "VARIANT_HAS_VEP_CONSEQUENCE",
"edge_evidence_type": "computational_prediction",
... | D | [
"A. Dias-Logan syndrome",
"B. esophagitis",
"C. Spinocerebellar atrophy",
"D. gallbladder carcinoma"
] | [
"expression",
"protein_sequence",
"protein_structure",
"snp_sequence"
] | [
{
"family": "sequence",
"tag": "snp_sequence",
"anchor_node_id": "NM_000038.6(APC):c.2237dup(p.Ser747fs)",
"source_db": "Ensembl",
"payload": {
"chrom": "5",
"pos": 112837831,
"ref_allele": "-",
"alt_allele": "G",
"ref_context": "CATGGCAAATAGGCCTGCGAAGTACAAGGATGCCAA... | [
{
"source_db": "Ensembl_VEP",
"source_id": "APC",
"text": "NM_000038.6(APC):c.2237dup(p.Ser747fs) VARIANT_HAS_VEP_CONSEQUENCE APC",
"confidence": 0.95
},
{
"source_db": "STRING",
"source_id": "AXIN2",
"text": "APC PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH AXIN2",
"confidence": 0.999
... | {
"gene_a": "APC",
"gene_b": "AXIN2",
"variant": "NM_000038.6(APC):c.2237dup(p.Ser747fs)",
"disease": "gallbladder carcinoma",
"SO_term": "frameshift_variant",
"tier": "D"
} | 0.559744 |
co_codi_00043 | coding_variant | coding_variant | hard | 3 | The variant NM_000038.6(APC):c.2677delinsAA(p.Glu893fs) causes a frameshift_variant in gene APC. APC functionally interacts with AXIN2. Which disease is AXIN2 directly associated with? | NM_000038.6(APC):c.2677delinsAA(p.Glu893fs) VARIANT_HAS_VEP_CONSEQUENCE APC -> APC PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH AXIN2 -> AXIN2 GENE_ASSOCIATED_WITH_DISEASE tooth agenesis | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000038.6(APC):c.2677delinsAA(p.Glu893fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000038.6(APC):c.2677delinsAA(p.Glu893fs)",
"edge_relation": "VARIANT_HAS_VEP_CONSEQUENCE",
"edge_evidence_type": "computational_pred... | A | [
"A. tooth agenesis",
"B. LEOPARD syndrome 1",
"C. familial ovarian cancer",
"D. fingertip paraesthesia"
] | [
"expression",
"protein_sequence",
"protein_structure",
"snp_sequence"
] | [
{
"family": "sequence",
"tag": "snp_sequence",
"anchor_node_id": "NM_000038.6(APC):c.2677delinsAA(p.Glu893fs)",
"source_db": "Ensembl",
"payload": {
"chrom": "5",
"pos": 112838271,
"ref_allele": "G",
"alt_allele": "AA",
"ref_context": "GAGGTTTGCAGATCTCCACCACTGCAGCCC... | [
{
"source_db": "Ensembl_VEP",
"source_id": "APC",
"text": "NM_000038.6(APC):c.2677delinsAA(p.Glu893fs) VARIANT_HAS_VEP_CONSEQUENCE APC",
"confidence": 0.95
},
{
"source_db": "STRING",
"source_id": "AXIN2",
"text": "APC PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH AXIN2",
"confidence": 0.... | {
"gene_a": "APC",
"gene_b": "AXIN2",
"variant": "NM_000038.6(APC):c.2677delinsAA(p.Glu893fs)",
"disease": "tooth agenesis",
"SO_term": "frameshift_variant",
"tier": "D"
} | 0.750278 |
co_codi_00044 | coding_variant | coding_variant | hard | 3 | The variant NM_000038.6(APC):c.1674_1680del(p.Asn558fs) causes a frameshift_variant in gene APC. APC functionally interacts with AXIN2. Which disease is AXIN2 directly associated with? | NM_000038.6(APC):c.1674_1680del(p.Asn558fs) VARIANT_HAS_VEP_CONSEQUENCE APC -> APC PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH AXIN2 -> AXIN2 GENE_ASSOCIATED_WITH_DISEASE oligodontia-cancer predisposition syndrome | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000038.6(APC):c.1674_1680del(p.Asn558fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000038.6(APC):c.1674_1680del(p.Asn558fs)",
"edge_relation": "VARIANT_HAS_VEP_CONSEQUENCE",
"edge_evidence_type": "computational_pred... | B | [
"A. teratoma with malignant transformation",
"B. oligodontia-cancer predisposition syndrome",
"C. MB",
"D. Lower limb muscle weakness"
] | [
"expression",
"protein_sequence",
"protein_structure",
"snp_sequence"
] | [
{
"family": "sequence",
"tag": "snp_sequence",
"anchor_node_id": "NM_000038.6(APC):c.1674_1680del(p.Asn558fs)",
"source_db": "Ensembl",
"payload": {
"chrom": "5",
"pos": 112828903,
"ref_allele": "TAGTAAA",
"alt_allele": "-",
"ref_context": "CAGGTTATTGCGAGTGTTTTGAGGA... | [
{
"source_db": "Ensembl_VEP",
"source_id": "APC",
"text": "NM_000038.6(APC):c.1674_1680del(p.Asn558fs) VARIANT_HAS_VEP_CONSEQUENCE APC",
"confidence": 0.95
},
{
"source_db": "STRING",
"source_id": "AXIN2",
"text": "APC PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH AXIN2",
"confidence": 0.... | {
"gene_a": "APC",
"gene_b": "AXIN2",
"variant": "NM_000038.6(APC):c.1674_1680del(p.Asn558fs)",
"disease": "oligodontia-cancer predisposition syndrome",
"SO_term": "frameshift_variant",
"tier": "D"
} | 0.98272 |
co_codi_00045 | coding_variant | coding_variant | hard | 3 | The variant NM_000038.6(APC):c.3640_3643del(p.Ser1214fs) causes a frameshift_variant in gene APC. APC functionally interacts with CTNNB1. Which disease is CTNNB1 directly associated with? | NM_000038.6(APC):c.3640_3643del(p.Ser1214fs) VARIANT_HAS_VEP_CONSEQUENCE APC -> APC PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH CTNNB1 -> CTNNB1 GENE_ASSOCIATED_WITH_DISEASE exudative vitreoretinopathy | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000038.6(APC):c.3640_3643del(p.Ser1214fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000038.6(APC):c.3640_3643del(p.Ser1214fs)",
"edge_relation": "VARIANT_HAS_VEP_CONSEQUENCE",
"edge_evidence_type": "computational_pr... | A | [
"A. exudative vitreoretinopathy",
"B. _Full",
"C. Filoviridae infectious disease",
"D. embryonal rhabdomyosarcoma"
] | [
"expression",
"protein_sequence",
"protein_structure",
"snp_sequence"
] | [
{
"family": "sequence",
"tag": "snp_sequence",
"anchor_node_id": "NM_000038.6(APC):c.3640_3643del(p.Ser1214fs)",
"source_db": "Ensembl",
"payload": {
"chrom": "5",
"pos": 112839234,
"ref_allele": "AGCA",
"alt_allele": "-",
"ref_context": "TCTCAAAGAGTTCATCTGGACAAAGCA... | [
{
"source_db": "Ensembl_VEP",
"source_id": "APC",
"text": "NM_000038.6(APC):c.3640_3643del(p.Ser1214fs) VARIANT_HAS_VEP_CONSEQUENCE APC",
"confidence": 0.95
},
{
"source_db": "STRING",
"source_id": "CTNNB1",
"text": "APC PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH CTNNB1",
"confidence":... | {
"gene_a": "APC",
"gene_b": "CTNNB1",
"variant": "NM_000038.6(APC):c.3640_3643del(p.Ser1214fs)",
"disease": "exudative vitreoretinopathy",
"SO_term": "frameshift_variant",
"tier": "D"
} | 0.98272 |
co_codi_00046 | coding_variant | coding_variant | hard | 3 | The variant NM_000038.6(APC):c.6783_6786dup(p.Glu2263Ter) causes a frameshift_variant in gene APC. APC functionally interacts with AXIN2. Which disease is AXIN2 directly associated with? | NM_000038.6(APC):c.6783_6786dup(p.Glu2263Ter) VARIANT_HAS_VEP_CONSEQUENCE APC -> APC PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH AXIN2 -> AXIN2 GENE_ASSOCIATED_WITH_DISEASE kidney Wilms tumor | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000038.6(APC):c.6783_6786dup(p.Glu2263Ter)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000038.6(APC):c.6783_6786dup(p.Glu2263Ter)",
"edge_relation": "VARIANT_HAS_VEP_CONSEQUENCE",
"edge_evidence_type": "computational_... | A | [
"A. kidney Wilms tumor",
"B. conjunctival cancer",
"C. Epstein-Barr virus-associated lymphoproliferative disorder",
"D. gastrointestinal stromal tumor"
] | [
"expression",
"protein_sequence",
"protein_structure",
"snp_sequence"
] | [
{
"family": "sequence",
"tag": "snp_sequence",
"anchor_node_id": "NM_000038.6(APC):c.6783_6786dup(p.Glu2263Ter)",
"source_db": "Ensembl",
"payload": {
"chrom": "5",
"pos": 112842377,
"ref_allele": "-",
"alt_allele": "TAGT",
"ref_context": "CCTGTTTCTAAAAAAGGCCCACCCCT... | [
{
"source_db": "Ensembl_VEP",
"source_id": "APC",
"text": "NM_000038.6(APC):c.6783_6786dup(p.Glu2263Ter) VARIANT_HAS_VEP_CONSEQUENCE APC",
"confidence": 0.95
},
{
"source_db": "STRING",
"source_id": "AXIN2",
"text": "APC PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH AXIN2",
"confidence": ... | {
"gene_a": "APC",
"gene_b": "AXIN2",
"variant": "NM_000038.6(APC):c.6783_6786dup(p.Glu2263Ter)",
"disease": "kidney Wilms tumor",
"SO_term": "frameshift_variant",
"tier": "D"
} | 0.559744 |
co_codi_00047 | coding_variant | coding_variant | hard | 3 | The variant NM_000038.6(APC):c.1051G>T(p.Gly351Ter) causes a stop_gained in gene APC. APC functionally interacts with CTNNB1. Which disease is CTNNB1 directly associated with? | NM_000038.6(APC):c.1051G>T(p.Gly351Ter) VARIANT_HAS_VEP_CONSEQUENCE APC -> APC PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH CTNNB1 -> CTNNB1 GENE_ASSOCIATED_WITH_DISEASE autosomal dominant polycystic liver disease | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000038.6(APC):c.1051G>T(p.Gly351Ter)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000038.6(APC):c.1051G>T(p.Gly351Ter)",
"edge_relation": "VARIANT_HAS_VEP_CONSEQUENCE",
"edge_evidence_type": "computational_prediction",... | C | [
"A. spectrum",
"B. TDP",
"C. autosomal dominant polycystic liver disease",
"D. chromosome 1p36 deletion syndrome"
] | [
"expression",
"protein_sequence",
"protein_structure",
"snp_sequence"
] | [
{
"family": "sequence",
"tag": "snp_sequence",
"anchor_node_id": "NM_000038.6(APC):c.1051G>T(p.Gly351Ter)",
"source_db": "Ensembl",
"payload": {
"chrom": "5",
"pos": 112819083,
"ref_allele": "G",
"alt_allele": "T",
"ref_context": "TGCTAGCTATGTCTAGCTCCCAAGACAGCTGTATA... | [
{
"source_db": "Ensembl_VEP",
"source_id": "APC",
"text": "NM_000038.6(APC):c.1051G>T(p.Gly351Ter) VARIANT_HAS_VEP_CONSEQUENCE APC",
"confidence": 0.95
},
{
"source_db": "STRING",
"source_id": "CTNNB1",
"text": "APC PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH CTNNB1",
"confidence": 0.99... | {
"gene_a": "APC",
"gene_b": "CTNNB1",
"variant": "NM_000038.6(APC):c.1051G>T(p.Gly351Ter)",
"disease": "autosomal dominant polycystic liver disease",
"SO_term": "stop_gained",
"tier": "D"
} | 0.674531 |
co_codi_00048 | coding_variant | coding_variant | hard | 3 | The variant NM_000038.6(APC):c.1315_1316dup(p.Ala440fs) causes a frameshift_variant in gene APC. APC functionally interacts with AXIN2. Which disease is AXIN2 directly associated with? | NM_000038.6(APC):c.1315_1316dup(p.Ala440fs) VARIANT_HAS_VEP_CONSEQUENCE APC -> APC PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH AXIN2 -> AXIN2 GENE_ASSOCIATED_WITH_DISEASE extraosseous osteosarcoma | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000038.6(APC):c.1315_1316dup(p.Ala440fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000038.6(APC):c.1315_1316dup(p.Ala440fs)",
"edge_relation": "VARIANT_HAS_VEP_CONSEQUENCE",
"edge_evidence_type": "computational_pred... | D | [
"A. respiratory system disorder",
"B. papillary hidradenoma",
"C. infantile neuronal ceroid lipofuscinosis",
"D. extraosseous osteosarcoma"
] | [
"expression",
"protein_sequence",
"protein_structure",
"snp_sequence"
] | [
{
"family": "sequence",
"tag": "snp_sequence",
"anchor_node_id": "NM_000038.6(APC):c.1315_1316dup(p.Ala440fs)",
"source_db": "Ensembl",
"payload": {
"chrom": "5",
"pos": 112821898,
"ref_allele": "-",
"alt_allele": "CC",
"ref_context": "CTCTTCAAATAACAAAGCATTATGGTTTAT... | [
{
"source_db": "Ensembl_VEP",
"source_id": "APC",
"text": "NM_000038.6(APC):c.1315_1316dup(p.Ala440fs) VARIANT_HAS_VEP_CONSEQUENCE APC",
"confidence": 0.95
},
{
"source_db": "STRING",
"source_id": "AXIN2",
"text": "APC PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH AXIN2",
"confidence": 0.... | {
"gene_a": "APC",
"gene_b": "AXIN2",
"variant": "NM_000038.6(APC):c.1315_1316dup(p.Ala440fs)",
"disease": "extraosseous osteosarcoma",
"SO_term": "frameshift_variant",
"tier": "D"
} | 0.640746 |
co_codi_00049 | coding_variant | coding_variant | hard | 3 | The variant NM_000038.6(APC):c.2898dup(p.Val967fs) causes a frameshift_variant in gene APC. APC functionally interacts with AXIN2. Which disease is AXIN2 directly associated with? | NM_000038.6(APC):c.2898dup(p.Val967fs) VARIANT_HAS_VEP_CONSEQUENCE APC -> APC PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH AXIN2 -> AXIN2 GENE_ASSOCIATED_WITH_DISEASE myotonic syndrome | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000038.6(APC):c.2898dup(p.Val967fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000038.6(APC):c.2898dup(p.Val967fs)",
"edge_relation": "VARIANT_HAS_VEP_CONSEQUENCE",
"edge_evidence_type": "computational_prediction",
... | B | [
"A. leptin deficiency",
"B. myotonic syndrome",
"C. nervous system cancer",
"D. bacterial zoonotic disease"
] | [
"expression",
"protein_sequence",
"protein_structure",
"snp_sequence"
] | [
{
"family": "sequence",
"tag": "snp_sequence",
"anchor_node_id": "NM_000038.6(APC):c.2898dup(p.Val967fs)",
"source_db": "Ensembl",
"payload": {
"chrom": "5",
"pos": 112838492,
"ref_allele": "-",
"alt_allele": "T",
"ref_context": "CCTTATGCCAAATTAGAATACAAGAGATCTTCAAAT... | [
{
"source_db": "Ensembl_VEP",
"source_id": "APC",
"text": "NM_000038.6(APC):c.2898dup(p.Val967fs) VARIANT_HAS_VEP_CONSEQUENCE APC",
"confidence": 0.95
},
{
"source_db": "STRING",
"source_id": "AXIN2",
"text": "APC PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH AXIN2",
"confidence": 0.999
... | {
"gene_a": "APC",
"gene_b": "AXIN2",
"variant": "NM_000038.6(APC):c.2898dup(p.Val967fs)",
"disease": "myotonic syndrome",
"SO_term": "frameshift_variant",
"tier": "D"
} | 0.616025 |
co_codi_00050 | coding_variant | coding_variant | hard | 3 | The variant NM_000038.6(APC):c.141del(p.Lys49fs) causes a frameshift_variant in gene APC. APC functionally interacts with CTNNB1. Which disease is CTNNB1 directly associated with? | NM_000038.6(APC):c.141del(p.Lys49fs) VARIANT_HAS_VEP_CONSEQUENCE APC -> APC PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH CTNNB1 -> CTNNB1 GENE_ASSOCIATED_WITH_DISEASE CTNNB1-related neurodevelopmental disorder and/or vitreoretinopathy | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000038.6(APC):c.141del(p.Lys49fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000038.6(APC):c.141del(p.Lys49fs)",
"edge_relation": "VARIANT_HAS_VEP_CONSEQUENCE",
"edge_evidence_type": "computational_prediction",
... | D | [
"A. Beckwith-Wiedemann syndromes",
"B. Primary progressive non fluent aphasia",
"C. trismus",
"D. CTNNB1-related neurodevelopmental disorder and/or vitreoretinopathy"
] | [
"expression",
"protein_sequence",
"protein_structure",
"snp_sequence"
] | [
{
"family": "sequence",
"tag": "snp_sequence",
"anchor_node_id": "NM_000038.6(APC):c.141del(p.Lys49fs)",
"source_db": "Ensembl",
"payload": {
"chrom": "5",
"pos": 112766331,
"ref_allele": "A",
"alt_allele": "-",
"ref_context": "AGTTATTTAGAATTTCATGTTAATATATTGTGTTCTTT... | [
{
"source_db": "Ensembl_VEP",
"source_id": "APC",
"text": "NM_000038.6(APC):c.141del(p.Lys49fs) VARIANT_HAS_VEP_CONSEQUENCE APC",
"confidence": 0.95
},
{
"source_db": "STRING",
"source_id": "CTNNB1",
"text": "APC PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH CTNNB1",
"confidence": 0.999
... | {
"gene_a": "APC",
"gene_b": "CTNNB1",
"variant": "NM_000038.6(APC):c.141del(p.Lys49fs)",
"disease": "CTNNB1-related neurodevelopmental disorder and/or vitreoretinopathy",
"SO_term": "frameshift_variant",
"tier": "D"
} | 0.705233 |
co_codi_00051 | coding_variant | coding_variant | hard | 3 | The variant NM_000038.6(APC):c.3999del(p.Lys1333fs) causes a frameshift_variant in gene APC. APC functionally interacts with CTNNB1. Which disease is CTNNB1 directly associated with? | NM_000038.6(APC):c.3999del(p.Lys1333fs) VARIANT_HAS_VEP_CONSEQUENCE APC -> APC PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH CTNNB1 -> CTNNB1 GENE_ASSOCIATED_WITH_DISEASE parathyroid gland adenoma | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000038.6(APC):c.3999del(p.Lys1333fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000038.6(APC):c.3999del(p.Lys1333fs)",
"edge_relation": "VARIANT_HAS_VEP_CONSEQUENCE",
"edge_evidence_type": "computational_prediction",... | A | [
"A. parathyroid gland adenoma",
"B. Chest pain",
"C. heart disorder",
"D. ischemic necrosis"
] | [
"expression",
"protein_sequence",
"protein_structure",
"snp_sequence"
] | [
{
"family": "sequence",
"tag": "snp_sequence",
"anchor_node_id": "NM_000038.6(APC):c.3999del(p.Lys1333fs)",
"source_db": "Ensembl",
"payload": {
"chrom": "5",
"pos": 112839593,
"ref_allele": "A",
"alt_allele": "-",
"ref_context": "GAAGATCCTGTGAGCGAAGTTCCAGCAGTGTCACA... | [
{
"source_db": "Ensembl_VEP",
"source_id": "APC",
"text": "NM_000038.6(APC):c.3999del(p.Lys1333fs) VARIANT_HAS_VEP_CONSEQUENCE APC",
"confidence": 0.95
},
{
"source_db": "STRING",
"source_id": "CTNNB1",
"text": "APC PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH CTNNB1",
"confidence": 0.99... | {
"gene_a": "APC",
"gene_b": "CTNNB1",
"variant": "NM_000038.6(APC):c.3999del(p.Lys1333fs)",
"disease": "parathyroid gland adenoma",
"SO_term": "frameshift_variant",
"tier": "D"
} | 0.645314 |
co_codi_00052 | coding_variant | coding_variant | hard | 3 | The variant NM_000038.6(APC):c.1365del(p.Lys455fs) causes a frameshift_variant in gene APC. APC functionally interacts with CTNNB1. Which disease is CTNNB1 directly associated with? | NM_000038.6(APC):c.1365del(p.Lys455fs) VARIANT_HAS_VEP_CONSEQUENCE APC -> APC PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH CTNNB1 -> CTNNB1 GENE_ASSOCIATED_WITH_DISEASE salivary gland adenoid cystic carcinoma | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000038.6(APC):c.1365del(p.Lys455fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000038.6(APC):c.1365del(p.Lys455fs)",
"edge_relation": "VARIANT_HAS_VEP_CONSEQUENCE",
"edge_evidence_type": "computational_prediction",
... | A | [
"A. salivary gland adenoid cystic carcinoma",
"B. hereditary macular dystrophy",
"C. goiter",
"D. FL"
] | [
"expression",
"protein_sequence",
"protein_structure",
"snp_sequence"
] | [
{
"family": "sequence",
"tag": "snp_sequence",
"anchor_node_id": "NM_000038.6(APC):c.1365del(p.Lys455fs)",
"source_db": "Ensembl",
"payload": {
"chrom": "5",
"pos": 112821948,
"ref_allele": "A",
"alt_allele": "-",
"ref_context": "CCAGCTCCTGTTGAACATCAGATCTGTCCTGCTGTG... | [
{
"source_db": "Ensembl_VEP",
"source_id": "APC",
"text": "NM_000038.6(APC):c.1365del(p.Lys455fs) VARIANT_HAS_VEP_CONSEQUENCE APC",
"confidence": 0.95
},
{
"source_db": "STRING",
"source_id": "CTNNB1",
"text": "APC PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH CTNNB1",
"confidence": 0.999... | {
"gene_a": "APC",
"gene_b": "CTNNB1",
"variant": "NM_000038.6(APC):c.1365del(p.Lys455fs)",
"disease": "salivary gland adenoid cystic carcinoma",
"SO_term": "frameshift_variant",
"tier": "D"
} | 0.642167 |
co_mech_00000 | mechanistic_explanation | coding_variant | medium | 4 | Explain the molecular mechanism by which NM_000546.6(TP53):c.470T>G (p.Val157Gly) affects the p75NTR recruits signalling complexes pathway, citing each molecular step. | NM_000546.6(TP53):c.470T>G (p.Val157Gly) VARIANT_IN_GENE TP53 -> TP53 GENE_PARTICIPATES_IN_PATHWAY Signaling by ALK fusions and activated point mutants -> SQSTM1 GENE_PARTICIPATES_IN_PATHWAY Signaling by ALK fusions and activated point mutants -> SQSTM1 GENE_PARTICIPATES_IN_PATHWAY p75NTR recruits signalling complexes | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000546.6(TP53):c.470T>G (p.Val157Gly)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000546.6(TP53):c.470T>G (p.Val157Gly)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1... | NM_000546.6(TP53):c.470T>G (p.Val157Gly) VARIANT_IN_GENE TP53 -> TP53 GENE_PARTICIPATES_IN_PATHWAY Signaling by ALK fusions and activated point mutants -> SQSTM1 GENE_PARTICIPATES_IN_PATHWAY Signaling by ALK fusions and activated point mutants -> SQSTM1 GENE_PARTICIPATES_IN_PATHWAY p75NTR recruits signalling complexes | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "TP53",
"source_db": "UniProt",
"payload": {
"accession": "P04637",
"sequence": "MEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPGPDEAPRMPEAAPPVAPAPAAPTPAAPAPAPSWPLSSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMF... | [
{
"source_db": "ClinVar",
"source_id": "TP53",
"text": "NM_000546.6(TP53):c.470T>G (p.Val157Gly) VARIANT_IN_GENE TP53",
"confidence": 1
},
{
"source_db": "Reactome",
"source_id": "R-HSA-9725370",
"text": "TP53 GENE_PARTICIPATES_IN_PATHWAY Signaling by ALK fusions and activated point ... | {
"variant": "NM_000546.6(TP53):c.470T>G (p.Val157Gly)",
"pathway": "p75NTR recruits signalling complexes"
} | 1 |
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