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_dise_00171 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in MSH6 are classified as Pathogenic or Likely Pathogenic for chromosome 16q22 deletion syndrome? | Single allele VARIANT_IN_GENE MSH6 -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE chromosome 16q22 deletion syndrome | {
"steps": [
{
"hop": 1,
"source_node_id": "MSH6",
"source_node_type": "GENE",
"source_node_label": "MSH6",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single allele... | Single allele | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "MSH6",
"source_db": "UniProt",
"payload": {
"accession": "P52701",
"sequence": "MSRQSTLYSFFPKSPALSDANKASARASREGGRAAAAPGASPSPGGDAAWSEAGPGPRPLARSASPPKAKNLNGGLRRSVAPAAPTSCDFSPGDLVWAKMEGYPWWPCLVYNHPFDGTFIREKGKSVRVHVQFF... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE MSH6",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0013798",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE chromosome 16q22 deletion syndrome",
"confiden... | {
"gene": "MSH6",
"disease": "chromosome 16q22 deletion syndrome",
"pathogenic_variants": [
"Single allele"
]
} | 0.83666 |
co_dise_00172 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in MSH6 are classified as Pathogenic or Likely Pathogenic for Sotos syndrome? | Single allele VARIANT_IN_GENE MSH6 -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE Sotos syndrome | {
"steps": [
{
"hop": 1,
"source_node_id": "MSH6",
"source_node_type": "GENE",
"source_node_label": "MSH6",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single allele... | Single allele | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "MSH6",
"source_db": "UniProt",
"payload": {
"accession": "P52701",
"sequence": "MSRQSTLYSFFPKSPALSDANKASARASREGGRAAAAPGASPSPGGDAAWSEAGPGPRPLARSASPPKAKNLNGGLRRSVAPAAPTSCDFSPGDLVWAKMEGYPWWPCLVYNHPFDGTFIREKGKSVRVHVQFF... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE MSH6",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0019349",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE Sotos syndrome",
"confidence": 0.7
}
] | {
"gene": "MSH6",
"disease": "Sotos syndrome",
"pathogenic_variants": [
"Single allele"
]
} | 0.83666 |
co_dise_00173 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in BDNF are classified as Pathogenic or Likely Pathogenic for Inborn genetic diseases? | NM_001709.5(BDNF):c.502G>T (p.Glu168Ter) VARIANT_IN_GENE BDNF -> NM_001709.5(BDNF):c.502G>T (p.Glu168Ter) VARIANT_HAS_CLINICAL_SIGNIFICANCE Inborn genetic diseases | {
"steps": [
{
"hop": 1,
"source_node_id": "BDNF",
"source_node_type": "GENE",
"source_node_label": "BDNF",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_001709.5(B... | NM_001709.5(BDNF):c.502G>T (p.Glu168Ter) | null | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "BDNF",
"source_db": "UniProt",
"payload": {
"accession": "P23560",
"sequence": "MTILFLTMVISYFGCMKAAPMKEANIRGQGGLAYPGVRTHGTLESVNGPKAGSRGLTSLADTFEHVIEELLDEDQKVRPNEENNKDADLYTSRVMLSSQVPLEPPLLFLLEEYKNYLDAANMSMRVRRHSDPAR... | [
{
"source_db": "ClinVar",
"source_id": "NM_001709.5(BDNF):c.502G>T (p.Glu168Ter)",
"text": "NM_001709.5(BDNF):c.502G>T (p.Glu168Ter) VARIANT_IN_GENE BDNF",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:inborn_genetic_diseases",
"text": "NM_001709.5(BDNF):c.502G>T... | {
"gene": "BDNF",
"disease": "Inborn genetic diseases",
"pathogenic_variants": [
"NM_001709.5(BDNF):c.502G>T (p.Glu168Ter)"
]
} | 0.83666 |
co_dise_00174 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in KMT2D are classified as Pathogenic or Likely Pathogenic for familial adenomatous polyposis 1? | Single allele VARIANT_IN_GENE KMT2D -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE familial adenomatous polyposis 1 | {
"steps": [
{
"hop": 1,
"source_node_id": "KMT2D",
"source_node_type": "GENE",
"source_node_label": "KMT2D",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single alle... | Single allele | null | [
"expression",
"protein_sequence"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "KMT2D",
"source_db": "UniProt",
"payload": {
"accession": "O14686",
"sequence": "MDSQKLAGEDKDSEPAADGPAASEDPSATESDLPNPHVGEVSVLSSGSPRLQETPQDCSGGPVRRCALCNCGEPSLHGQRELRRFELPFDWPRCPVVSPGGSPGPNEAVLPSEDLSQIGFPEGLTPAHLGEPG... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE KMT2D",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0021056",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE familial adenomatous polyposis 1",
"confidenc... | {
"gene": "KMT2D",
"disease": "familial adenomatous polyposis 1",
"pathogenic_variants": [
"Single allele"
]
} | 0.83666 |
co_dise_00175 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in AOPEP are classified as Pathogenic or Likely Pathogenic for Fanconi anemia complementation group C? | NM_000136.3(FANCC):c.1002del (p.Phe335fs) VARIANT_IN_GENE AOPEP -> NM_000136.3(FANCC):c.1002del (p.Phe335fs) VARIANT_HAS_CLINICAL_SIGNIFICANCE Fanconi anemia complementation group C | {
"steps": [
{
"hop": 1,
"source_node_id": "AOPEP",
"source_node_type": "GENE",
"source_node_label": "AOPEP",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_000136.3... | NM_000136.3(FANCC):c.571del (p.Ile191fs); NM_000136.3(FANCC):c.844-1G>A; NM_000136.3(FANCC):c.1653dup (p.Lys552Ter); NM_000136.3(FANCC):c.1002del (p.Phe335fs); NM_000136.3(FANCC):c.883dup (p.Asp295fs) | null | [
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "AOPEP",
"source_db": "UniProt",
"payload": {
"accession": "Q8N6M6",
"sequence": "MDIQLDPARDDLPLMANTSHILVKHYVLDLDVDFESQVIEGTIVLFLEDGNRFKKQNSSIEEACQSESNKACKFGMPEPCHIPVTNARTFSSEMEYNDFAICSKGEKDTSDKDGNHDNQEHASGISSSKYCCD... | [
{
"source_db": "ClinVar",
"source_id": "NM_000136.3(FANCC):c.1002del (p.Phe335fs)",
"text": "NM_000136.3(FANCC):c.1002del (p.Phe335fs) VARIANT_IN_GENE AOPEP",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0009213",
"text": "NM_000136.3(FANCC):c.1002del (p.Phe335fs)... | {
"gene": "AOPEP",
"disease": "Fanconi anemia complementation group C",
"pathogenic_variants": [
"NM_000136.3(FANCC):c.571del (p.Ile191fs)",
"NM_000136.3(FANCC):c.844-1G>A",
"NM_000136.3(FANCC):c.1653dup (p.Lys552Ter)",
"NM_000136.3(FANCC):c.1002del (p.Phe335fs)",
"NM_000136.3(FANCC):c.883dup ... | 0.83666 |
co_dise_00176 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in CTNNB1 are classified as Pathogenic or Likely Pathogenic for autosomal dominant polycystic liver disease? | NM_001904.4(CTNNB1):c.2189G>A (p.Gly730Asp) VARIANT_IN_GENE CTNNB1 -> NM_001904.4(CTNNB1):c.2189G>A (p.Gly730Asp) VARIANT_HAS_CLINICAL_SIGNIFICANCE autosomal dominant polycystic liver disease | {
"steps": [
{
"hop": 1,
"source_node_id": "CTNNB1",
"source_node_type": "GENE",
"source_node_label": "CTNNB1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_001904... | NM_001904.4(CTNNB1):c.2189G>A (p.Gly730Asp) | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CTNNB1",
"source_db": "UniProt",
"payload": {
"accession": "P35222",
"sequence": "MATQADLMELDMAMEPDRKAAVSHWQQQSYLDSGIHSGATTTAPSLSGKGNPEEEDVDTSQVLYEWEQGFSQSFTQEQVADIDGQYAMTRAQRVRAAMFPETLDEGMQIPSTQFDAAHPTNVQRLAEPSQML... | [
{
"source_db": "ClinVar",
"source_id": "NM_001904.4(CTNNB1):c.2189G>A (p.Gly730Asp)",
"text": "NM_001904.4(CTNNB1):c.2189G>A (p.Gly730Asp) VARIANT_IN_GENE CTNNB1",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0000447",
"text": "NM_001904.4(CTNNB1):c.2189G>A (p.Gly... | {
"gene": "CTNNB1",
"disease": "autosomal dominant polycystic liver disease",
"pathogenic_variants": [
"NM_001904.4(CTNNB1):c.2189G>A (p.Gly730Asp)"
]
} | 0.707107 |
co_dise_00177 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in CDKN2A are classified as Pathogenic or Likely Pathogenic for Hereditary nonpolyposis colorectal neoplasms? | Single allele VARIANT_IN_GENE CDKN2A -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE Hereditary nonpolyposis colorectal neoplasms | {
"steps": [
{
"hop": 1,
"source_node_id": "CDKN2A",
"source_node_type": "GENE",
"source_node_label": "CDKN2A",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single al... | Single allele | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CDKN2A",
"source_db": "UniProt",
"payload": {
"accession": "Q8N726",
"sequence": "MVRRFLVTLRIRRACGPPRVRVFVVHIPRLTGEWAAPGAPAAVALVLMLLRSQRLGQQPLPRRPGHDDGQRPSGGAAAAPRRGAQLRRPRHSHPTRARRCPGGLPGHAGGAAPGRGAAGRARCLGPSARGPG... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE CDKN2A",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:hereditary_nonpolyposis_colorectal_neoplasms",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE Hereditar... | {
"gene": "CDKN2A",
"disease": "Hereditary nonpolyposis colorectal neoplasms",
"pathogenic_variants": [
"Single allele"
]
} | 0.83666 |
co_dise_00178 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in ACVR1 are classified as Pathogenic or Likely Pathogenic for Delayed speech and language development? | Single allele VARIANT_IN_GENE ACVR1 -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE Delayed speech and language development | {
"steps": [
{
"hop": 1,
"source_node_id": "ACVR1",
"source_node_type": "GENE",
"source_node_label": "ACVR1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single alle... | Single allele | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ACVR1",
"source_db": "UniProt",
"payload": {
"accession": "Q04771",
"sequence": "MVDGVMILPVLIMIALPSPSMEDEKPKVNPKLYMCVCEGLSCGNEDHCEGQQCFSSLSINDGFHVYQKGCFQVYEQGKMTCKTPPSPGQAVECCQGDWCNRNITAQLPTKGKSFPGTQNFHLEVGLIILSVVF... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE ACVR1",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:delayed_speech_and_language_development",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE Delayed speech ... | {
"gene": "ACVR1",
"disease": "Delayed speech and language development",
"pathogenic_variants": [
"Single allele"
]
} | 0.707107 |
co_dise_00179 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in CHCHD10 are classified as Pathogenic or Likely Pathogenic for 16q24.3 microdeletion syndrome? | Single allele VARIANT_IN_GENE CHCHD10 -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE 16q24.3 microdeletion syndrome | {
"steps": [
{
"hop": 1,
"source_node_id": "CHCHD10",
"source_node_type": "GENE",
"source_node_label": "CHCHD10",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single ... | Single allele | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CHCHD10",
"source_db": "UniProt",
"payload": {
"accession": "Q8WYQ3",
"sequence": "MPRGSRSAASRPASRPAAPSAHPPAHPPPSAAAPAPAPSGQPGLMAQMATTAAGVAVGSAVGHVMGSALTGAFSGGSSEPSQPAVQQAPTPAAPQPLQMGPCAYEIRQFLDCSTTQSDLSLCEGFSEALKQ... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE CHCHD10",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0016838",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE 16q24.3 microdeletion syndrome",
"confidenc... | {
"gene": "CHCHD10",
"disease": "16q24.3 microdeletion syndrome",
"pathogenic_variants": [
"Single allele"
]
} | 0.707107 |
co_dise_00180 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in ADORA2A are classified as Pathogenic or Likely Pathogenic for Kleefstra syndrome 2? | Single allele VARIANT_IN_GENE ADORA2A -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE Kleefstra syndrome 2 | {
"steps": [
{
"hop": 1,
"source_node_id": "ADORA2A",
"source_node_type": "GENE",
"source_node_label": "ADORA2A",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single ... | Single allele | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ADORA2A",
"source_db": "UniProt",
"payload": {
"accession": "P29274",
"sequence": "MPIMGSSVYITVELAIAVLAILGNVLVCWAVWLNSNLQNVTNYFVVSLAAADIAVGVLAIPFAITISTGFCAACHGCLFIACFVLVLTQSSIFSLLAIAIDRYIAIRIPLRYNGLVTGTRAKGIIAICWVL... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE ADORA2A",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0054701",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE Kleefstra syndrome 2",
"confidence": 0.7
... | {
"gene": "ADORA2A",
"disease": "Kleefstra syndrome 2",
"pathogenic_variants": [
"Single allele"
]
} | 0.83666 |
co_dise_00181 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in MSH6 are classified as Pathogenic or Likely Pathogenic for 8p inverted duplication/deletion syndrome? | Single allele VARIANT_IN_GENE MSH6 -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE 8p inverted duplication/deletion syndrome | {
"steps": [
{
"hop": 1,
"source_node_id": "MSH6",
"source_node_type": "GENE",
"source_node_label": "MSH6",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single allele... | Single allele | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "MSH6",
"source_db": "UniProt",
"payload": {
"accession": "P52701",
"sequence": "MSRQSTLYSFFPKSPALSDANKASARASREGGRAAAAPGASPSPGGDAAWSEAGPGPRPLARSASPPKAKNLNGGLRRSVAPAAPTSCDFSPGDLVWAKMEGYPWWPCLVYNHPFDGTFIREKGKSVRVHVQFF... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE MSH6",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0019876",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE 8p inverted duplication/deletion syndrome",
"c... | {
"gene": "MSH6",
"disease": "8p inverted duplication/deletion syndrome",
"pathogenic_variants": [
"Single allele"
]
} | 0.707107 |
co_dise_00182 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in PALB2 are classified as Pathogenic or Likely Pathogenic for breast-ovarian cancer, familial, susceptibility to, 5? | NM_024675.4(PALB2):c.2659_2660del (p.Ile887fs) VARIANT_IN_GENE PALB2 -> NM_024675.4(PALB2):c.2659_2660del (p.Ile887fs) VARIANT_HAS_CLINICAL_SIGNIFICANCE breast-ovarian cancer, familial, susceptibility to, 5 | {
"steps": [
{
"hop": 1,
"source_node_id": "PALB2",
"source_node_type": "GENE",
"source_node_label": "PALB2",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_024675.4... | NC_000016.10:g.(?_23619184)_(23619333_?)del; NM_024675.4(PALB2):c.84del (p.Glu27_Tyr28insTer); NM_024675.4(PALB2):c.1025del (p.Asn342fs); NM_024675.4(PALB2):c.2979del (p.Phe994fs); NM_024675.4(PALB2):c.2472T>A (p.Cys824Ter) | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "PALB2",
"source_db": "UniProt",
"payload": {
"accession": "Q86YC2",
"sequence": "MDEPPGKPLSCEEKEKLKEKLAFLKREYSKTLARLQRAQRAEKIKHSIKKTVEEQDCLSQQDLSPQLKHSEPKNKICVYDKLHIKTHLDEETGEKTSITLDVGPESFNPGDGPGGLPIQRTDDTQEHFPHRVS... | [
{
"source_db": "ClinVar",
"source_id": "NM_024675.4(PALB2):c.2659_2660del (p.Ile887fs)",
"text": "NM_024675.4(PALB2):c.2659_2660del (p.Ile887fs) VARIANT_IN_GENE PALB2",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0957530",
"text": "NM_024675.4(PALB2):c.2659_2660d... | {
"gene": "PALB2",
"disease": "breast-ovarian cancer, familial, susceptibility to, 5",
"pathogenic_variants": [
"NC_000016.10:g.(?_23619184)_(23619333_?)del",
"NM_024675.4(PALB2):c.84del (p.Glu27_Tyr28insTer)",
"NM_024675.4(PALB2):c.1025del (p.Asn342fs)",
"NM_024675.4(PALB2):c.2979del (p.Phe994fs)... | 0.83666 |
co_dise_00183 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in CFAP410 are classified as Pathogenic or Likely Pathogenic for strabismus? | Single allele VARIANT_IN_GENE CFAP410 -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE strabismus | {
"steps": [
{
"hop": 1,
"source_node_id": "CFAP410",
"source_node_type": "GENE",
"source_node_label": "CFAP410",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single ... | Single allele | null | [
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CFAP410",
"source_db": "UniProt",
"payload": {
"accession": "O43822",
"sequence": "MKLTRKMVLTRAKASELHSVRKLNCWGSRLTDISICQEMPSLEVITLSVNSISTLEPVSRCQRLSELYLRRNRIPSLAELFYLKGLPRLRVLWLAENPCCGTSPHRYRMTVLRTLPRLQKLDNQAVTEEEL... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE CFAP410",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0003432",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE strabismus",
"confidence": 0.5
}
] | {
"gene": "CFAP410",
"disease": "strabismus",
"pathogenic_variants": [
"Single allele"
]
} | 0.707107 |
co_dise_00184 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in APC are classified as Pathogenic or Likely Pathogenic for familial adenomatous polyposis 1? | NM_000038.6(APC):c.6739del (p.Ser2247fs) VARIANT_IN_GENE APC -> NM_000038.6(APC):c.6739del (p.Ser2247fs) VARIANT_HAS_CLINICAL_SIGNIFICANCE familial adenomatous polyposis 1 | {
"steps": [
{
"hop": 1,
"source_node_id": "APC",
"source_node_type": "GENE",
"source_node_label": "APC",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_000038.6(APC... | NM_000038.6(APC):c.685del (p.Leu229fs); NM_000038.6(APC):c.6851_6853delinsTC (p.Pro2284fs); NM_000038.6(APC):c.6943C>T (p.Gln2315Ter); NM_000038.6(APC):c.1548+2T>A; NM_000038.6(APC):c.6248_6249del (p.Ile2083fs) | null | [
"expression",
"protein_sequence"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "APC",
"source_db": "UniProt",
"payload": {
"accession": "P25054",
"sequence": "MAAASYDQLLKQVEALKMENSNLRQELEDNSNHLTKLETEASNMKEVLKQLQGSIEDEAMASSGQIDLLERLKELNLDSSNFPGVKLRSKMSLRSYGSREGSVSSRSGECSPVPMGSFPRRGFVNGSRESTGYLE... | [
{
"source_db": "ClinVar",
"source_id": "NM_000038.6(APC):c.6739del (p.Ser2247fs)",
"text": "NM_000038.6(APC):c.6739del (p.Ser2247fs) VARIANT_IN_GENE APC",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0021056",
"text": "NM_000038.6(APC):c.6739del (p.Ser2247fs) VARI... | {
"gene": "APC",
"disease": "familial adenomatous polyposis 1",
"pathogenic_variants": [
"NM_000038.6(APC):c.685del (p.Leu229fs)",
"NM_000038.6(APC):c.6851_6853delinsTC (p.Pro2284fs)",
"NM_000038.6(APC):c.6943C>T (p.Gln2315Ter)",
"NM_000038.6(APC):c.1548+2T>A",
"NM_000038.6(APC):c.6248_6249del... | 0.921954 |
co_dise_00185 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in KMT2C are classified as Pathogenic or Likely Pathogenic for 16q24.3 microdeletion syndrome? | Single allele VARIANT_IN_GENE KMT2C -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE 16q24.3 microdeletion syndrome | {
"steps": [
{
"hop": 1,
"source_node_id": "KMT2C",
"source_node_type": "GENE",
"source_node_label": "KMT2C",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single alle... | Single allele | null | [
"expression",
"protein_sequence"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "KMT2C",
"source_db": "UniProt",
"payload": {
"accession": "Q8NEZ4",
"sequence": "MSSEEDKSVEQPQPPPPPPEEPGAPAPSPAAADKRPRGRPRKDGASPFQRARKKPRSRGKTAVEDEDSMDGLETTETETIVETEIKEQSAEEDAEAEVDNSKQLIPTLQRSVSEESANSLVSVGVEAKISEQL... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE KMT2C",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0016838",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE 16q24.3 microdeletion syndrome",
"confidence"... | {
"gene": "KMT2C",
"disease": "16q24.3 microdeletion syndrome",
"pathogenic_variants": [
"Single allele"
]
} | 0.707107 |
co_dise_00186 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in PMS2 are classified as Pathogenic or Likely Pathogenic for Seizure? | Single allele VARIANT_IN_GENE PMS2 -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE Seizure | {
"steps": [
{
"hop": 1,
"source_node_id": "PMS2",
"source_node_type": "GENE",
"source_node_label": "PMS2",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single allele... | Single allele | 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": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE PMS2",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:seizure",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE Seizure",
"confidence": 0.5
}
] | {
"gene": "PMS2",
"disease": "Seizure",
"pathogenic_variants": [
"Single allele"
]
} | 0.707107 |
co_dise_00187 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in NOTCH1 are classified as Pathogenic or Likely Pathogenic for T-cell acute lymphoblastic leukemia? | Single allele VARIANT_IN_GENE NOTCH1 -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE T-cell acute lymphoblastic leukemia | {
"steps": [
{
"hop": 1,
"source_node_id": "NOTCH1",
"source_node_type": "GENE",
"source_node_label": "NOTCH1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single al... | Single allele | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "NOTCH1",
"source_db": "UniProt",
"payload": {
"accession": "P46531",
"sequence": "MPPLLAPLLCLALLPALAARGPRCSQPGETCLNGGKCEAANGTEACVCGGAFVGPRCQDPNPCLSTPCKNAGTCHVVDRRGVADYACSCALGFSGPLCLTPLDNACLTNPCRNGGTCDLLTLTEYKCRCPPG... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE NOTCH1",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0004963",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE T-cell acute lymphoblastic leukemia",
"confi... | {
"gene": "NOTCH1",
"disease": "T-cell acute lymphoblastic leukemia",
"pathogenic_variants": [
"Single allele"
]
} | 0.707107 |
co_dise_00188 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in TP53 are classified as Pathogenic or Likely Pathogenic for DiGeorge syndrome? | Single allele VARIANT_IN_GENE TP53 -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE DiGeorge syndrome | {
"steps": [
{
"hop": 1,
"source_node_id": "TP53",
"source_node_type": "GENE",
"source_node_label": "TP53",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single allele... | Single allele | 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": "Single allele",
"text": "Single allele VARIANT_IN_GENE TP53",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0008564",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE DiGeorge syndrome",
"confidence": 0.5
}
] | {
"gene": "TP53",
"disease": "DiGeorge syndrome",
"pathogenic_variants": [
"Single allele"
]
} | 0.707107 |
co_dise_00189 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in CD274 are classified as Pathogenic or Likely Pathogenic for Renal transitional cell carcinoma? | Single allele VARIANT_IN_GENE CD274 -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE Renal transitional cell carcinoma | {
"steps": [
{
"hop": 1,
"source_node_id": "CD274",
"source_node_type": "GENE",
"source_node_label": "CD274",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single alle... | Single allele | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CD274",
"source_db": "UniProt",
"payload": {
"accession": "Q9NZQ7",
"sequence": "MRIFAVFIFMTYWHLLNAFTVTVPKDLYVVEYGSNMTIECKFPVEKQLDLAALIVYWEMEDKNIIQFVHGEEDLKVQHSSYRQRARLLKDQLSLGNAALQITDVKLQDAGVYRCMISYGGADYKRITVKVNAP... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE CD274",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:renal_transitional_cell_carcinoma",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE Renal transitional ce... | {
"gene": "CD274",
"disease": "Renal transitional cell carcinoma",
"pathogenic_variants": [
"Single allele"
]
} | 0.707107 |
co_dise_00190 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in PMS2 are classified as Pathogenic or Likely Pathogenic for polydactyly? | Single allele VARIANT_IN_GENE PMS2 -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE polydactyly | {
"steps": [
{
"hop": 1,
"source_node_id": "PMS2",
"source_node_type": "GENE",
"source_node_label": "PMS2",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single allele... | Single allele | 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": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE PMS2",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0021003",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE polydactyly",
"confidence": 0.5
}
] | {
"gene": "PMS2",
"disease": "polydactyly",
"pathogenic_variants": [
"Single allele"
]
} | 0.707107 |
co_dise_00191 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in KIF5A are classified as Pathogenic or Likely Pathogenic for hereditary spastic paraplegia 10? | NM_004984.4(KIF5A):c.728G>A (p.Gly243Glu) VARIANT_IN_GENE KIF5A -> NM_004984.4(KIF5A):c.728G>A (p.Gly243Glu) VARIANT_HAS_CLINICAL_SIGNIFICANCE hereditary spastic paraplegia 10 | {
"steps": [
{
"hop": 1,
"source_node_id": "KIF5A",
"source_node_type": "GENE",
"source_node_label": "KIF5A",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_004984.4... | NM_004984.4(KIF5A):c.1233dup (p.Glu412fs); NM_004984.4(KIF5A):c.737G>T (p.Gly246Val); NM_004984.4(KIF5A):c.854C>T (p.Thr285Ile); NM_004984.4(KIF5A):c.765C>G (p.Ile255Met); NM_004984.4(KIF5A):c.728G>A (p.Gly243Glu) | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "KIF5A",
"source_db": "UniProt",
"payload": {
"accession": "Q12840",
"sequence": "MAETNNECSIKVLCRFRPLNQAEILRGDKFIPIFQGDDSVVIGGKPYVFDRVFPPNTTQEQVYHACAMQIVKDVLAGYNGTIFAYGQTSSGKTHTMEGKLHDPQLMGIIPRIARDIFNHIYSMDENLEFHIKV... | [
{
"source_db": "ClinVar",
"source_id": "NM_004984.4(KIF5A):c.728G>A (p.Gly243Glu)",
"text": "NM_004984.4(KIF5A):c.728G>A (p.Gly243Glu) VARIANT_IN_GENE KIF5A",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0011408",
"text": "NM_004984.4(KIF5A):c.728G>A (p.Gly243Glu)... | {
"gene": "KIF5A",
"disease": "hereditary spastic paraplegia 10",
"pathogenic_variants": [
"NM_004984.4(KIF5A):c.1233dup (p.Glu412fs)",
"NM_004984.4(KIF5A):c.737G>T (p.Gly246Val)",
"NM_004984.4(KIF5A):c.854C>T (p.Thr285Ile)",
"NM_004984.4(KIF5A):c.765C>G (p.Ile255Met)",
"NM_004984.4(KIF5A):c.7... | 0.83666 |
co_dise_00192 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in PRPH are classified as Pathogenic or Likely Pathogenic for amyotrophic lateral sclerosis type 1? | NM_006262.4(PRPH):c.607-1G>A VARIANT_IN_GENE PRPH -> NM_006262.4(PRPH):c.607-1G>A VARIANT_HAS_CLINICAL_SIGNIFICANCE amyotrophic lateral sclerosis type 1 | {
"steps": [
{
"hop": 1,
"source_node_id": "PRPH",
"source_node_type": "GENE",
"source_node_label": "PRPH",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_006262.4(P... | NM_006262.4(PRPH):c.745C>T (p.Gln249Ter); NM_006262.4(PRPH):c.919C>T (p.Gln307Ter); NM_006262.4(PRPH):c.607-1G>A | null | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "PRPH",
"source_db": "UniProt",
"payload": {
"accession": "P41219",
"sequence": "MSHHPSGLRAGFSSTSYRRTFGPPPSLSPGAFSYSSSSRFSSSRLLGSASPSSSVRLGSFRSPRAGAGALLRLPSERLDFSMAEALNQEFLATRSNEKQELQELNDRFANFIEKVRFLEQQNAALRGELSQARG... | [
{
"source_db": "ClinVar",
"source_id": "NM_006262.4(PRPH):c.607-1G>A",
"text": "NM_006262.4(PRPH):c.607-1G>A VARIANT_IN_GENE PRPH",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0007103",
"text": "NM_006262.4(PRPH):c.607-1G>A VARIANT_HAS_CLINICAL_SIGNIFICANCE amyot... | {
"gene": "PRPH",
"disease": "amyotrophic lateral sclerosis type 1",
"pathogenic_variants": [
"NM_006262.4(PRPH):c.745C>T (p.Gln249Ter)",
"NM_006262.4(PRPH):c.919C>T (p.Gln307Ter)",
"NM_006262.4(PRPH):c.607-1G>A"
]
} | 0.83666 |
co_dise_00193 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in ATM are classified as Pathogenic or Likely Pathogenic for T-cell acute lymphoblastic leukemia? | Single allele VARIANT_IN_GENE ATM -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE T-cell acute lymphoblastic leukemia | {
"steps": [
{
"hop": 1,
"source_node_id": "ATM",
"source_node_type": "GENE",
"source_node_label": "ATM",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single allele",... | Single allele | null | [
"expression",
"protein_sequence"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ATM",
"source_db": "UniProt",
"payload": {
"accession": "Q13315",
"sequence": "MSLVLNDLLICCRQLEHDRATERKKEVEKFKRLIRDPETIKHLDRHSDSKQGKYLNWDAVFRFLQKYIQKETECLRIAKPNVSASTQASRQKKMQEISSLVKYFIKCANRRAPRLKCQELLNYIMDTVKDSSNGA... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE ATM",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0004963",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE T-cell acute lymphoblastic leukemia",
"confiden... | {
"gene": "ATM",
"disease": "T-cell acute lymphoblastic leukemia",
"pathogenic_variants": [
"Single allele"
]
} | 0.707107 |
co_dise_00194 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in CSF3R are classified as Pathogenic or Likely Pathogenic for hereditary neutrophilia? | NM_000760.4(CSF3R):c.843+2T>C VARIANT_IN_GENE CSF3R -> NM_000760.4(CSF3R):c.843+2T>C VARIANT_HAS_CLINICAL_SIGNIFICANCE hereditary neutrophilia | {
"steps": [
{
"hop": 1,
"source_node_id": "CSF3R",
"source_node_type": "GENE",
"source_node_label": "CSF3R",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_000760.4... | NM_000760.4(CSF3R):c.843+2T>C; NM_000760.4(CSF3R):c.1919C>A (p.Thr640Asn) | null | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CSF3R",
"source_db": "UniProt",
"payload": {
"accession": "Q99062",
"sequence": "MARLGNCSLTWAALIILLLPGSLEECGHISVSAPIVHLGDPITASCIIKQNCSHLDPEPQILWRLGAELQPGGRQQRLSDGTQESIITLPHLNHTQAFLSCCLNWGNSLQILDQVELRAGYPPAIPHNLSCLM... | [
{
"source_db": "ClinVar",
"source_id": "NM_000760.4(CSF3R):c.843+2T>C",
"text": "NM_000760.4(CSF3R):c.843+2T>C VARIANT_IN_GENE CSF3R",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0008092",
"text": "NM_000760.4(CSF3R):c.843+2T>C VARIANT_HAS_CLINICAL_SIGNIFICANCE h... | {
"gene": "CSF3R",
"disease": "hereditary neutrophilia",
"pathogenic_variants": [
"NM_000760.4(CSF3R):c.843+2T>C",
"NM_000760.4(CSF3R):c.1919C>A (p.Thr640Asn)"
]
} | 0.921954 |
co_dise_00195 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in AURKA are classified as Pathogenic or Likely Pathogenic for See cases? | GRCh38/hg38 20q13.2-13.32(chr20:54594888-58190583)x1 VARIANT_IN_GENE AURKA -> GRCh38/hg38 20q13.2-13.32(chr20:54594888-58190583)x1 VARIANT_HAS_CLINICAL_SIGNIFICANCE See cases | {
"steps": [
{
"hop": 1,
"source_node_id": "AURKA",
"source_node_type": "GENE",
"source_node_label": "AURKA",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "GRCh38/hg38... | GRCh38/hg38 20q13.2-13.32(chr20:54594888-58190583)x1 | null | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "AURKA",
"source_db": "UniProt",
"payload": {
"accession": "O14965",
"sequence": "MDRSKENCISGPVKATAPVGGPKRVLVTQQFPCQNPLPVNSGQAQRVLCPSNSSQRIPLQAQKLVSSHKPVQNQKQKQLQATSVPHPVSRPLNNTQKSKQPLPSAPENNPEEELASKQKNEESKKRQWALEDF... | [
{
"source_db": "ClinVar",
"source_id": "GRCh38/hg38 20q13.2-13.32(chr20:54594888-58190583)x1",
"text": "GRCh38/hg38 20q13.2-13.32(chr20:54594888-58190583)x1 VARIANT_IN_GENE AURKA",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:see_cases",
"text": "GRCh38/hg38 20q... | {
"gene": "AURKA",
"disease": "See cases",
"pathogenic_variants": [
"GRCh38/hg38 20q13.2-13.32(chr20:54594888-58190583)x1"
]
} | 0.707107 |
co_dise_00196 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in APC are classified as Pathogenic or Likely Pathogenic for Renal transitional cell carcinoma? | Single allele VARIANT_IN_GENE APC -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE Renal transitional cell carcinoma | {
"steps": [
{
"hop": 1,
"source_node_id": "APC",
"source_node_type": "GENE",
"source_node_label": "APC",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single allele",... | Single allele | null | [
"expression",
"protein_sequence"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "APC",
"source_db": "UniProt",
"payload": {
"accession": "P25054",
"sequence": "MAAASYDQLLKQVEALKMENSNLRQELEDNSNHLTKLETEASNMKEVLKQLQGSIEDEAMASSGQIDLLERLKELNLDSSNFPGVKLRSKMSLRSYGSREGSVSSRSGECSPVPMGSFPRRGFVNGSRESTGYLE... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE APC",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:renal_transitional_cell_carcinoma",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE Renal transitional cell... | {
"gene": "APC",
"disease": "Renal transitional cell carcinoma",
"pathogenic_variants": [
"Single allele"
]
} | 0.707107 |
co_dise_00197 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in ASXL1 are classified as Pathogenic or Likely Pathogenic for not specified? | GRCh37/hg19 20q11.21(chr20:31013426-31031739)x1 VARIANT_IN_GENE ASXL1 -> GRCh37/hg19 20q11.21(chr20:31013426-31031739)x1 VARIANT_HAS_CLINICAL_SIGNIFICANCE not specified | {
"steps": [
{
"hop": 1,
"source_node_id": "ASXL1",
"source_node_type": "GENE",
"source_node_label": "ASXL1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "GRCh37/hg19... | GRCh37/hg19 20q11.21(chr20:31013426-31031739)x1 | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ASXL1",
"source_db": "UniProt",
"payload": {
"accession": "Q8IXJ9",
"sequence": "MKDKQKKKKERTWAEAARLVLENYSDAPMTPKQILQVIEAEGLKEMRSGTSPLACLNAMLHSNSRGGEGLFYKLPGRISLFTLKKDALQWSRHPATVEGEEPEDTADVESCGSNEASTVSGENDVSLDETSSN... | [
{
"source_db": "ClinVar",
"source_id": "GRCh37/hg19 20q11.21(chr20:31013426-31031739)x1",
"text": "GRCh37/hg19 20q11.21(chr20:31013426-31031739)x1 VARIANT_IN_GENE ASXL1",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:not_specified",
"text": "GRCh37/hg19 20q11.21(... | {
"gene": "ASXL1",
"disease": "not specified",
"pathogenic_variants": [
"GRCh37/hg19 20q11.21(chr20:31013426-31031739)x1"
]
} | 0.83666 |
co_dise_00198 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in ABL1 are classified as Pathogenic or Likely Pathogenic for Delayed speech and language development? | Single allele VARIANT_IN_GENE ABL1 -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE Delayed speech and language development | {
"steps": [
{
"hop": 1,
"source_node_id": "ABL1",
"source_node_type": "GENE",
"source_node_label": "ABL1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single allele... | Single allele | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ABL1",
"source_db": "UniProt",
"payload": {
"accession": "P00519",
"sequence": "MLEICLKLVGCKSKKGLSSSSSCYLEEALQRPVASDFEPQGLSEAARWNSKENLLAGPSENDPNLFVALYDFVASGDNTLSITKGEKLRVLGYNHNGEWCEAQTKNGQGWVPSNYITPVNSLEKHSWYHGPVSR... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE ABL1",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:delayed_speech_and_language_development",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE Delayed speech a... | {
"gene": "ABL1",
"disease": "Delayed speech and language development",
"pathogenic_variants": [
"Single allele"
]
} | 0.707107 |
co_dise_00199 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in MSH2 are classified as Pathogenic or Likely Pathogenic for bilateral polymicrogyria? | Single allele VARIANT_IN_GENE MSH2 -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE bilateral polymicrogyria | {
"steps": [
{
"hop": 1,
"source_node_id": "MSH2",
"source_node_type": "GENE",
"source_node_label": "MSH2",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single allele... | Single allele | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "MSH2",
"source_db": "UniProt",
"payload": {
"accession": "P43246",
"sequence": "MAVQPKETLQLESAAEVGFVRFFQGMPEKPTTTVRLFDRGDFYTAHGEDALLAAREVFKTQGVIKYMGPAGAKNLQSVVLSKMNFESFVKDLLLVRQYRVEVYKNRAGNKASKENDWYLAYKASPGNLSQFEDI... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE MSH2",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0017091",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE bilateral polymicrogyria",
"confidence": 0.7
... | {
"gene": "MSH2",
"disease": "bilateral polymicrogyria",
"pathogenic_variants": [
"Single allele"
]
} | 0.83666 |
co_dise_00200 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in CDKN2A are classified as Pathogenic or Likely Pathogenic for autosomal recessive juvenile Parkinson disease 2? | Single allele VARIANT_IN_GENE CDKN2A -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE autosomal recessive juvenile Parkinson disease 2 | {
"steps": [
{
"hop": 1,
"source_node_id": "CDKN2A",
"source_node_type": "GENE",
"source_node_label": "CDKN2A",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single al... | Single allele | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CDKN2A",
"source_db": "UniProt",
"payload": {
"accession": "Q8N726",
"sequence": "MVRRFLVTLRIRRACGPPRVRVFVVHIPRLTGEWAAPGAPAAVALVLMLLRSQRLGQQPLPRRPGHDDGQRPSGGAAAAPRRGAQLRRPRHSHPTRARRCPGGLPGHAGGAAPGRGAAGRARCLGPSARGPG... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE CDKN2A",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0010820",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE autosomal recessive juvenile Parkinson disease 2... | {
"gene": "CDKN2A",
"disease": "autosomal recessive juvenile Parkinson disease 2",
"pathogenic_variants": [
"Single allele"
]
} | 0.83666 |
co_dise_00201 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in RAD51C are classified as Pathogenic or Likely Pathogenic for Fanconi anemia complementation group O? | NC_000017.11:g.(?_58720736)_(58720822_?)dup VARIANT_IN_GENE RAD51C -> NC_000017.11:g.(?_58720736)_(58720822_?)dup VARIANT_HAS_CLINICAL_SIGNIFICANCE Fanconi anemia complementation group O | {
"steps": [
{
"hop": 1,
"source_node_id": "RAD51C",
"source_node_type": "GENE",
"source_node_label": "RAD51C",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NC_000017... | NC_000017.10:g.(56780691_56787219)_(56801462_56809844)del; NM_058216.3(RAD51C):c.471dup (p.Ile158fs); NM_058216.3(RAD51C):c.728del (p.Gly243fs); NM_058216.3(RAD51C):c.559_563dup (p.Lys188fs); NM_058216.3(RAD51C):c.233del (p.Thr78fs) | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "RAD51C",
"source_db": "UniProt",
"payload": {
"accession": "O43502",
"sequence": "MRGKTFRFEMQRDLVSFPLSPAVRVKLVSAGFQTAEELLEVKPSELSKEVGISKAEALETLQIIRRECLTNKPRYAGTSESHKKCTALELLEQEHTQGFIITFCSALDDILGGGVPLMKTTEICGAPGVGKT... | [
{
"source_db": "ClinVar",
"source_id": "NC_000017.11:g.(?_58720736)_(58720822_?)dup",
"text": "NC_000017.11:g.(?_58720736)_(58720822_?)dup VARIANT_IN_GENE RAD51C",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0013248",
"text": "NC_000017.11:g.(?_58720736)_(5872082... | {
"gene": "RAD51C",
"disease": "Fanconi anemia complementation group O",
"pathogenic_variants": [
"NC_000017.10:g.(56780691_56787219)_(56801462_56809844)del",
"NM_058216.3(RAD51C):c.471dup (p.Ile158fs)",
"NM_058216.3(RAD51C):c.728del (p.Gly243fs)",
"NM_058216.3(RAD51C):c.559_563dup (p.Lys188fs)",
... | 0.83666 |
co_dise_00202 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in APC are classified as Pathogenic or Likely Pathogenic for colorectal cancer? | NM_000038.6(APC):c.645+2T>C VARIANT_IN_GENE APC -> NM_000038.6(APC):c.645+2T>C VARIANT_HAS_CLINICAL_SIGNIFICANCE colorectal cancer | {
"steps": [
{
"hop": 1,
"source_node_id": "APC",
"source_node_type": "GENE",
"source_node_label": "APC",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_000038.6(APC... | NM_000038.6(APC):c.645+2T>C | null | [
"expression",
"protein_sequence"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "APC",
"source_db": "UniProt",
"payload": {
"accession": "P25054",
"sequence": "MAAASYDQLLKQVEALKMENSNLRQELEDNSNHLTKLETEASNMKEVLKQLQGSIEDEAMASSGQIDLLERLKELNLDSSNFPGVKLRSKMSLRSYGSREGSVSSRSGECSPVPMGSFPRRGFVNGSRESTGYLE... | [
{
"source_db": "ClinVar",
"source_id": "NM_000038.6(APC):c.645+2T>C",
"text": "NM_000038.6(APC):c.645+2T>C VARIANT_IN_GENE APC",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0005575",
"text": "NM_000038.6(APC):c.645+2T>C VARIANT_HAS_CLINICAL_SIGNIFICANCE colorecta... | {
"gene": "APC",
"disease": "colorectal cancer",
"pathogenic_variants": [
"NM_000038.6(APC):c.645+2T>C"
]
} | 0.83666 |
co_dise_00203 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in AKAP11 are classified as Pathogenic or Likely Pathogenic for not provided? | GRCh37/hg19 13q12.3-14.3(chr13:32076445-54495559)x1 VARIANT_IN_GENE AKAP11 -> GRCh37/hg19 13q12.3-14.3(chr13:32076445-54495559)x1 VARIANT_HAS_CLINICAL_SIGNIFICANCE not provided | {
"steps": [
{
"hop": 1,
"source_node_id": "AKAP11",
"source_node_type": "GENE",
"source_node_label": "AKAP11",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "GRCh37/hg... | GRCh37/hg19 13q12.3-14.3(chr13:32076445-54495559)x1; GRCh37/hg19 13q11-22.1(chr13:19436286-74045459)x3 | null | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "AKAP11",
"source_db": "UniProt",
"payload": {
"accession": "Q9UKA4",
"sequence": "MATFRNNHMKTKASVRKSFSEDVFQSVKSLLQSQKELCSVTAEDCLQQDEHANLTEVTFLGFNEETDAAHIQDLAAVSLELPDILNSLHFCSLNENEIICMKNINKPLDISSDPLNQSHPSGMLCVMRVSPT... | [
{
"source_db": "ClinVar",
"source_id": "GRCh37/hg19 13q12.3-14.3(chr13:32076445-54495559)x1",
"text": "GRCh37/hg19 13q12.3-14.3(chr13:32076445-54495559)x1 VARIANT_IN_GENE AKAP11",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:not_provided",
"text": "GRCh37/hg19 1... | {
"gene": "AKAP11",
"disease": "not provided",
"pathogenic_variants": [
"GRCh37/hg19 13q12.3-14.3(chr13:32076445-54495559)x1",
"GRCh37/hg19 13q11-22.1(chr13:19436286-74045459)x3"
]
} | 0.83666 |
co_dise_00204 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in CDH1 are classified as Pathogenic or Likely Pathogenic for hereditary diffuse gastric adenocarcinoma? | NM_004360.5(CDH1):c.2440-396_*223del VARIANT_IN_GENE CDH1 -> NM_004360.5(CDH1):c.2440-396_*223del VARIANT_HAS_CLINICAL_SIGNIFICANCE hereditary diffuse gastric adenocarcinoma | {
"steps": [
{
"hop": 1,
"source_node_id": "CDH1",
"source_node_type": "GENE",
"source_node_label": "CDH1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_004360.5(C... | NM_004360.5(CDH1):c.897del (p.Ile300fs); NM_004360.5(CDH1):c.1900_1906del (p.Ala634fs); NM_004360.5(CDH1):c.2260del (p.Tyr754fs); NM_004360.5(CDH1):c.2470del (p.Ala824fs); NM_004360.5(CDH1):c.946_947del (p.Met316fs) | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CDH1",
"source_db": "UniProt",
"payload": {
"accession": "P12830",
"sequence": "MGPWSRSLSALLLLLQVSSWLCQEPEPCHPGFDAESYTFTVPRRHLERGRVLGRVNFEDCTGRQRTAYFSLDTRFKVGTDGVITVKRPLRFHNPQIHFLVYAWDSTYRKFSTKVTLNTVGHHHRPPPHQASVSG... | [
{
"source_db": "ClinVar",
"source_id": "NM_004360.5(CDH1):c.2440-396_*223del",
"text": "NM_004360.5(CDH1):c.2440-396_*223del VARIANT_IN_GENE CDH1",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0007648",
"text": "NM_004360.5(CDH1):c.2440-396_*223del VARIANT_HAS_CLI... | {
"gene": "CDH1",
"disease": "hereditary diffuse gastric adenocarcinoma",
"pathogenic_variants": [
"NM_004360.5(CDH1):c.897del (p.Ile300fs)",
"NM_004360.5(CDH1):c.1900_1906del (p.Ala634fs)",
"NM_004360.5(CDH1):c.2260del (p.Tyr754fs)",
"NM_004360.5(CDH1):c.2470del (p.Ala824fs)",
"NM_004360.5(CD... | 0.83666 |
co_dise_00205 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in PIK3CA are classified as Pathogenic or Likely Pathogenic for gastric cancer? | NM_006218.4(PIK3CA):c.113G>A (p.Arg38His) VARIANT_IN_GENE PIK3CA -> NM_006218.4(PIK3CA):c.113G>A (p.Arg38His) VARIANT_HAS_CLINICAL_SIGNIFICANCE gastric cancer | {
"steps": [
{
"hop": 1,
"source_node_id": "PIK3CA",
"source_node_type": "GENE",
"source_node_label": "PIK3CA",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_006218... | NM_006218.4(PIK3CA):c.113G>A (p.Arg38His) | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "PIK3CA",
"source_db": "UniProt",
"payload": {
"accession": "P42336",
"sequence": "MPPRPSSGELWGIHLMPPRILVECLLPNGMIVTLECLREATLITIKHELFKEARKYPLHQLLQDESSYIFVSVTQEAEREEFFDETRRLCDLRLFQPFLKVIEPVGNREEKILNREIGFAIGMPVCEFDMVK... | [
{
"source_db": "ClinVar",
"source_id": "NM_006218.4(PIK3CA):c.113G>A (p.Arg38His)",
"text": "NM_006218.4(PIK3CA):c.113G>A (p.Arg38His) VARIANT_IN_GENE PIK3CA",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0001056",
"text": "NM_006218.4(PIK3CA):c.113G>A (p.Arg38His... | {
"gene": "PIK3CA",
"disease": "gastric cancer",
"pathogenic_variants": [
"NM_006218.4(PIK3CA):c.113G>A (p.Arg38His)"
]
} | 0.921954 |
co_dise_00206 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in AFDN are classified as Pathogenic or Likely Pathogenic for polydactyly? | Single allele VARIANT_IN_GENE AFDN -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE polydactyly | {
"steps": [
{
"hop": 1,
"source_node_id": "AFDN",
"source_node_type": "GENE",
"source_node_label": "AFDN",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single allele... | Single allele | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "AFDN",
"source_db": "UniProt",
"payload": {
"accession": "P55196",
"sequence": "MSAGGRDEERRKLADIIHHWNANRLDLFEISQPTEDLEFHGVMRFYFQDKAAGNFATKCIRVSSTATTQDVIETLAEKFRPDMRMLSSPKYSLYEVHVSGERRLDIDEKPLVVQLNWNKDDREGRFVLKNENDA... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE AFDN",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0021003",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE polydactyly",
"confidence": 0.5
}
] | {
"gene": "AFDN",
"disease": "polydactyly",
"pathogenic_variants": [
"Single allele"
]
} | 0.707107 |
co_dise_00207 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in BARD1 are classified as Pathogenic or Likely Pathogenic for gastric cancer? | NM_000465.4(BARD1):c.829_833dup (p.Ser279fs) VARIANT_IN_GENE BARD1 -> NM_000465.4(BARD1):c.829_833dup (p.Ser279fs) VARIANT_HAS_CLINICAL_SIGNIFICANCE gastric cancer | {
"steps": [
{
"hop": 1,
"source_node_id": "BARD1",
"source_node_type": "GENE",
"source_node_label": "BARD1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_000465.4... | NM_000465.4(BARD1):c.417_427del (p.Lys139fs); NM_000465.4(BARD1):c.629del (p.Thr210fs); NM_000465.4(BARD1):c.735del (p.Gln245fs); NM_000465.4(BARD1):c.829_833dup (p.Ser279fs); NM_000465.4(BARD1):c.1810+1G>T | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "BARD1",
"source_db": "UniProt",
"payload": {
"accession": "Q99728",
"sequence": "MPDNRQPRNRQPRIRSGNEPRSAPAMEPDGRGAWAHSRAALDRLEKLLRCSRCTNILREPVCLGGCEHIFCSNCVSDCIGTGCPVCYTPAWIQDLKINRQLDSMIQLCSKLRNLLHDNELSDLKEDKPRKSLF... | [
{
"source_db": "ClinVar",
"source_id": "NM_000465.4(BARD1):c.829_833dup (p.Ser279fs)",
"text": "NM_000465.4(BARD1):c.829_833dup (p.Ser279fs) VARIANT_IN_GENE BARD1",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0001056",
"text": "NM_000465.4(BARD1):c.829_833dup (p.... | {
"gene": "BARD1",
"disease": "gastric cancer",
"pathogenic_variants": [
"NM_000465.4(BARD1):c.417_427del (p.Lys139fs)",
"NM_000465.4(BARD1):c.629del (p.Thr210fs)",
"NM_000465.4(BARD1):c.735del (p.Gln245fs)",
"NM_000465.4(BARD1):c.829_833dup (p.Ser279fs)",
"NM_000465.4(BARD1):c.1810+1G>T"
]
... | 0.707107 |
co_dise_00208 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in ACTB are classified as Pathogenic or Likely Pathogenic for Inborn genetic diseases? | NM_001101.5(ACTB):c.887_888delinsG (p.Asn296fs) VARIANT_IN_GENE ACTB -> NM_001101.5(ACTB):c.887_888delinsG (p.Asn296fs) VARIANT_HAS_CLINICAL_SIGNIFICANCE Inborn genetic diseases | {
"steps": [
{
"hop": 1,
"source_node_id": "ACTB",
"source_node_type": "GENE",
"source_node_label": "ACTB",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_001101.5(A... | NM_001101.5(ACTB):c.887_888delinsG (p.Asn296fs); NM_001101.5(ACTB):c.987_990dup (p.Ala331fs); NM_001101.5(ACTB):c.259C>G (p.His87Asp); NM_001101.5(ACTB):c.617G>A (p.Arg206Gln); NM_001101.5(ACTB):c.587G>A (p.Arg196His) | 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": "ClinVar",
"source_id": "NM_001101.5(ACTB):c.887_888delinsG (p.Asn296fs)",
"text": "NM_001101.5(ACTB):c.887_888delinsG (p.Asn296fs) VARIANT_IN_GENE ACTB",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:inborn_genetic_diseases",
"text": "NM_001101.5(... | {
"gene": "ACTB",
"disease": "Inborn genetic diseases",
"pathogenic_variants": [
"NM_001101.5(ACTB):c.887_888delinsG (p.Asn296fs)",
"NM_001101.5(ACTB):c.987_990dup (p.Ala331fs)",
"NM_001101.5(ACTB):c.259C>G (p.His87Asp)",
"NM_001101.5(ACTB):c.617G>A (p.Arg206Gln)",
"NM_001101.5(ACTB):c.587G>A ... | 0.83666 |
co_dise_00209 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in SPOP are classified as Pathogenic or Likely Pathogenic for neurodevelopmental disorder with microcephaly and dysmorphic facies? | NM_001007228.2(SPOP):c.362G>A (p.Arg121Gln) VARIANT_IN_GENE SPOP -> NM_001007228.2(SPOP):c.362G>A (p.Arg121Gln) VARIANT_HAS_CLINICAL_SIGNIFICANCE neurodevelopmental disorder with microcephaly and dysmorphic facies | {
"steps": [
{
"hop": 1,
"source_node_id": "SPOP",
"source_node_type": "GENE",
"source_node_label": "SPOP",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_001007228.... | NM_001007228.2(SPOP):c.430G>A (p.Asp144Asn); NM_001007228.2(SPOP):c.362G>A (p.Arg121Gln); NM_001007228.2(SPOP):c.312C>A (p.Phe104Leu) | null | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "SPOP",
"source_db": "UniProt",
"payload": {
"accession": "O43791",
"sequence": "MSRVPSPPPPAEMSSGPVAESWCYTQIKVVKFSYMWTINNFSFCREEMGEVIKSSTFSSGANDKLKWCLRVNPKGLDEESKDYLSLYLLLVSCPKSEVRAKFKFSILNAKGEETKAMESQRAYRFVQGKDWGFK... | [
{
"source_db": "ClinVar",
"source_id": "NM_001007228.2(SPOP):c.362G>A (p.Arg121Gln)",
"text": "NM_001007228.2(SPOP):c.362G>A (p.Arg121Gln) VARIANT_IN_GENE SPOP",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0032942",
"text": "NM_001007228.2(SPOP):c.362G>A (p.Arg12... | {
"gene": "SPOP",
"disease": "neurodevelopmental disorder with microcephaly and dysmorphic facies",
"pathogenic_variants": [
"NM_001007228.2(SPOP):c.430G>A (p.Asp144Asn)",
"NM_001007228.2(SPOP):c.362G>A (p.Arg121Gln)",
"NM_001007228.2(SPOP):c.312C>A (p.Phe104Leu)"
]
} | 0.921954 |
co_dise_00210 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in KMT2C are classified as Pathogenic or Likely Pathogenic for tricho-dento-osseous syndrome? | Single allele VARIANT_IN_GENE KMT2C -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE tricho-dento-osseous syndrome | {
"steps": [
{
"hop": 1,
"source_node_id": "KMT2C",
"source_node_type": "GENE",
"source_node_label": "KMT2C",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single alle... | Single allele | null | [
"expression",
"protein_sequence"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "KMT2C",
"source_db": "UniProt",
"payload": {
"accession": "Q8NEZ4",
"sequence": "MSSEEDKSVEQPQPPPPPPEEPGAPAPSPAAADKRPRGRPRKDGASPFQRARKKPRSRGKTAVEDEDSMDGLETTETETIVETEIKEQSAEEDAEAEVDNSKQLIPTLQRSVSEESANSLVSVGVEAKISEQL... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE KMT2C",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0008592",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE tricho-dento-osseous syndrome",
"confidence":... | {
"gene": "KMT2C",
"disease": "tricho-dento-osseous syndrome",
"pathogenic_variants": [
"Single allele"
]
} | 0.83666 |
co_dise_00211 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in RAD51C are classified as Pathogenic or Likely Pathogenic for Breast and/or ovarian cancer? | NM_058216.3(RAD51C):c.572-1G>T VARIANT_IN_GENE RAD51C -> NM_058216.3(RAD51C):c.572-1G>T VARIANT_HAS_CLINICAL_SIGNIFICANCE Breast and/or ovarian cancer | {
"steps": [
{
"hop": 1,
"source_node_id": "RAD51C",
"source_node_type": "GENE",
"source_node_label": "RAD51C",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_058216... | NM_058216.3(RAD51C):c.572-1G>T; NM_058216.3(RAD51C):c.905-2_905-1del | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "RAD51C",
"source_db": "UniProt",
"payload": {
"accession": "O43502",
"sequence": "MRGKTFRFEMQRDLVSFPLSPAVRVKLVSAGFQTAEELLEVKPSELSKEVGISKAEALETLQIIRRECLTNKPRYAGTSESHKKCTALELLEQEHTQGFIITFCSALDDILGGGVPLMKTTEICGAPGVGKT... | [
{
"source_db": "ClinVar",
"source_id": "NM_058216.3(RAD51C):c.572-1G>T",
"text": "NM_058216.3(RAD51C):c.572-1G>T VARIANT_IN_GENE RAD51C",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:breast_and_or_ovarian_cancer",
"text": "NM_058216.3(RAD51C):c.572-1G>T VARIANT_... | {
"gene": "RAD51C",
"disease": "Breast and/or ovarian cancer",
"pathogenic_variants": [
"NM_058216.3(RAD51C):c.572-1G>T",
"NM_058216.3(RAD51C):c.905-2_905-1del"
]
} | 0.921954 |
co_dise_00212 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in MYC are classified as Pathogenic or Likely Pathogenic for Li-Fraumeni syndrome? | Single allele VARIANT_IN_GENE MYC -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE Li-Fraumeni syndrome | {
"steps": [
{
"hop": 1,
"source_node_id": "MYC",
"source_node_type": "GENE",
"source_node_label": "MYC",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single allele",... | Single allele | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "MYC",
"source_db": "UniProt",
"payload": {
"accession": "P01106",
"sequence": "MDFFRVVENQQPPATMPLNVSFTNRNYDLDYDSVQPYFYCDEEENFYQQQQQSELQPPAPSEDIWKKFELLPTPPLSPSRRSGLCSPSYVAVTPFSLRGDNDGGGGSFSTADQLEMVTELLGGDMVNQSFICDPD... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE MYC",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0018875",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE Li-Fraumeni syndrome",
"confidence": 0.7
}
] | {
"gene": "MYC",
"disease": "Li-Fraumeni syndrome",
"pathogenic_variants": [
"Single allele"
]
} | 0.83666 |
co_dise_00213 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in BCOR are classified as Pathogenic or Likely Pathogenic for X-linked BCOR-related disorders? | NM_001123385.2(BCOR):c.3394del (p.Val1132fs) VARIANT_IN_GENE BCOR -> NM_001123385.2(BCOR):c.3394del (p.Val1132fs) VARIANT_HAS_CLINICAL_SIGNIFICANCE X-linked BCOR-related disorders | {
"steps": [
{
"hop": 1,
"source_node_id": "BCOR",
"source_node_type": "GENE",
"source_node_label": "BCOR",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_001123385.... | NM_001123385.2(BCOR):c.3394del (p.Val1132fs) | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "BCOR",
"source_db": "UniProt",
"payload": {
"accession": "Q6W2J9",
"sequence": "MLSATPLYGNVHSWMNSERVRMCGASEDRKILVNDGDASKARLELREENPLNHNVVDASTAHRIDGLAALSMDRTGLIREGLRVPGNIVYSSLCGLGSEKGREAATSTLGGLGFSSERNPEMQFKPNTPETVEA... | [
{
"source_db": "ClinVar",
"source_id": "NM_001123385.2(BCOR):c.3394del (p.Val1132fs)",
"text": "NM_001123385.2(BCOR):c.3394del (p.Val1132fs) VARIANT_IN_GENE BCOR",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:x_linked_bcor_related_disorders",
"text": "NM_0011233... | {
"gene": "BCOR",
"disease": "X-linked BCOR-related disorders",
"pathogenic_variants": [
"NM_001123385.2(BCOR):c.3394del (p.Val1132fs)"
]
} | 0.83666 |
co_dise_00214 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in ANXA11 are classified as Pathogenic or Likely Pathogenic for chromosome 4q21 deletion syndrome? | Single allele VARIANT_IN_GENE ANXA11 -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE chromosome 4q21 deletion syndrome | {
"steps": [
{
"hop": 1,
"source_node_id": "ANXA11",
"source_node_type": "GENE",
"source_node_label": "ANXA11",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single al... | Single allele | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ANXA11",
"source_db": "UniProt",
"payload": {
"accession": "P50995",
"sequence": "MSYPGYPPPPGGYPPAAPGGGPWGGAAYPPPPSMPPIGLDNVATYAGQFNQDYLSGMAANMSGTFGGANMPNLYPGAPGAGYPPVPPGGFGQPPSAQQPVPPYGMYPPPGGNPPSRMPSYPPYPGAPVPGQP... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE ANXA11",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0013292",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE chromosome 4q21 deletion syndrome",
"confide... | {
"gene": "ANXA11",
"disease": "chromosome 4q21 deletion syndrome",
"pathogenic_variants": [
"Single allele"
]
} | 0.83666 |
co_dise_00215 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in MYC are classified as Pathogenic or Likely Pathogenic for aniridia 1? | Single allele VARIANT_IN_GENE MYC -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE aniridia 1 | {
"steps": [
{
"hop": 1,
"source_node_id": "MYC",
"source_node_type": "GENE",
"source_node_label": "MYC",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single allele",... | Single allele | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "MYC",
"source_db": "UniProt",
"payload": {
"accession": "P01106",
"sequence": "MDFFRVVENQQPPATMPLNVSFTNRNYDLDYDSVQPYFYCDEEENFYQQQQQSELQPPAPSEDIWKKFELLPTPPLSPSRRSGLCSPSYVAVTPFSLRGDNDGGGGSFSTADQLEMVTELLGGDMVNQSFICDPD... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE MYC",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0024507",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE aniridia 1",
"confidence": 0.5
}
] | {
"gene": "MYC",
"disease": "aniridia 1",
"pathogenic_variants": [
"Single allele"
]
} | 0.707107 |
co_dise_00216 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in TP53 are classified as Pathogenic or Likely Pathogenic for schizophrenia? | Single allele VARIANT_IN_GENE TP53 -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE schizophrenia | {
"steps": [
{
"hop": 1,
"source_node_id": "TP53",
"source_node_type": "GENE",
"source_node_label": "TP53",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single allele... | Single allele | 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": "Single allele",
"text": "Single allele VARIANT_IN_GENE TP53",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0005090",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE schizophrenia",
"confidence": 0.7
}
] | {
"gene": "TP53",
"disease": "schizophrenia",
"pathogenic_variants": [
"Single allele"
]
} | 0.83666 |
co_dise_00217 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in KMT2D are classified as Pathogenic or Likely Pathogenic for Marfanoid habitus and intellectual disability? | Single allele VARIANT_IN_GENE KMT2D -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE Marfanoid habitus and intellectual disability | {
"steps": [
{
"hop": 1,
"source_node_id": "KMT2D",
"source_node_type": "GENE",
"source_node_label": "KMT2D",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single alle... | Single allele | null | [
"expression",
"protein_sequence"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "KMT2D",
"source_db": "UniProt",
"payload": {
"accession": "O14686",
"sequence": "MDSQKLAGEDKDSEPAADGPAASEDPSATESDLPNPHVGEVSVLSSGSPRLQETPQDCSGGPVRRCALCNCGEPSLHGQRELRRFELPFDWPRCPVVSPGGSPGPNEAVLPSEDLSQIGFPEGLTPAHLGEPG... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE KMT2D",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:marfanoid_habitus_and_intellectual_disability",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE Marfanoid... | {
"gene": "KMT2D",
"disease": "Marfanoid habitus and intellectual disability",
"pathogenic_variants": [
"Single allele"
]
} | 0.83666 |
co_dise_00218 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in TP53 are classified as Pathogenic or Likely Pathogenic for Noonan syndrome 1? | Single allele VARIANT_IN_GENE TP53 -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE Noonan syndrome 1 | {
"steps": [
{
"hop": 1,
"source_node_id": "TP53",
"source_node_type": "GENE",
"source_node_label": "TP53",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single allele... | Single allele | 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": "Single allele",
"text": "Single allele VARIANT_IN_GENE TP53",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0008104",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE Noonan syndrome 1",
"confidence": 0.7
}
] | {
"gene": "TP53",
"disease": "Noonan syndrome 1",
"pathogenic_variants": [
"Single allele"
]
} | 0.83666 |
co_dise_00219 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in CEBPA are classified as Pathogenic or Likely Pathogenic for acute myeloid leukemia? | NM_004364.5(CEBPA):c.146del (p.Pro49fs) VARIANT_IN_GENE CEBPA -> NM_004364.5(CEBPA):c.146del (p.Pro49fs) VARIANT_HAS_CLINICAL_SIGNIFICANCE acute myeloid leukemia | {
"steps": [
{
"hop": 1,
"source_node_id": "CEBPA",
"source_node_type": "GENE",
"source_node_label": "CEBPA",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_004364.5... | NM_004364.5(CEBPA):c.134dup (p.Pro46fs); NM_004364.5(CEBPA):c.253dup (p.Ser85fs); NM_004364.5(CEBPA):c.62del (p.Ser21fs); NM_004364.5(CEBPA):c.96del (p.Arg35fs); NM_004364.5(CEBPA):c.63_64delinsA (p.Ser21fs) | null | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CEBPA",
"source_db": "UniProt",
"payload": {
"accession": "P49715",
"sequence": "MESADFYEAEPRPPMSSHLQSPPHAPSSAAFGFPRGAGPAQPPAPPAAPEPLGGICEHETSIDISAYIDPAAFNDEFLADLFQHSRQQEKAKAAVGPTGGGGGGDFDYPGAPAGPGGAVMPGGAHGPPPGYGC... | [
{
"source_db": "ClinVar",
"source_id": "NM_004364.5(CEBPA):c.146del (p.Pro49fs)",
"text": "NM_004364.5(CEBPA):c.146del (p.Pro49fs) VARIANT_IN_GENE CEBPA",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0018874",
"text": "NM_004364.5(CEBPA):c.146del (p.Pro49fs) VARIA... | {
"gene": "CEBPA",
"disease": "acute myeloid leukemia",
"pathogenic_variants": [
"NM_004364.5(CEBPA):c.134dup (p.Pro46fs)",
"NM_004364.5(CEBPA):c.253dup (p.Ser85fs)",
"NM_004364.5(CEBPA):c.62del (p.Ser21fs)",
"NM_004364.5(CEBPA):c.96del (p.Arg35fs)",
"NM_004364.5(CEBPA):c.63_64delinsA (p.Ser21... | 0.83666 |
co_dise_00220 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in HTT are classified as Pathogenic or Likely Pathogenic for Lopes-Maciel-Rodan syndrome? | NM_001388492.1(HTT):c.6921C>G (p.Leu2307=) VARIANT_IN_GENE HTT -> NM_001388492.1(HTT):c.6921C>G (p.Leu2307=) VARIANT_HAS_CLINICAL_SIGNIFICANCE Lopes-Maciel-Rodan syndrome | {
"steps": [
{
"hop": 1,
"source_node_id": "HTT",
"source_node_type": "GENE",
"source_node_label": "HTT",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_001388492.1(... | NM_001388492.1(HTT):c.8150T>A (p.Phe2717Tyr); NM_001388492.1(HTT):c.6921C>G (p.Leu2307=) | null | [
"conservation",
"expression",
"protein_sequence"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "HTT",
"source_db": "UniProt",
"payload": {
"accession": "P42858",
"sequence": "MATLEKLMKAFESLKSFQQQQQQQQQQQQQQQQQQQQQPPPPPPPPPPPQLPQPPPQAQPLLPQPQPPPPPPPPPPGPAVAEEPLHRPKKELSATKKDRVNHCLTICENIVAQSVRNSPEFQKLLGIAMELFLLC... | [
{
"source_db": "ClinVar",
"source_id": "NM_001388492.1(HTT):c.6921C>G (p.Leu2307=)",
"text": "NM_001388492.1(HTT):c.6921C>G (p.Leu2307=) VARIANT_IN_GENE HTT",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0054573",
"text": "NM_001388492.1(HTT):c.6921C>G (p.Leu2307=... | {
"gene": "HTT",
"disease": "Lopes-Maciel-Rodan syndrome",
"pathogenic_variants": [
"NM_001388492.1(HTT):c.8150T>A (p.Phe2717Tyr)",
"NM_001388492.1(HTT):c.6921C>G (p.Leu2307=)"
]
} | 0.83666 |
co_dise_00221 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in NOTCH1 are classified as Pathogenic or Likely Pathogenic for intellectual disability? | Single allele VARIANT_IN_GENE NOTCH1 -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE intellectual disability | {
"steps": [
{
"hop": 1,
"source_node_id": "NOTCH1",
"source_node_type": "GENE",
"source_node_label": "NOTCH1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single al... | Single allele | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "NOTCH1",
"source_db": "UniProt",
"payload": {
"accession": "P46531",
"sequence": "MPPLLAPLLCLALLPALAARGPRCSQPGETCLNGGKCEAANGTEACVCGGAFVGPRCQDPNPCLSTPCKNAGTCHVVDRRGVADYACSCALGFSGPLCLTPLDNACLTNPCRNGGTCDLLTLTEYKCRCPPG... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE NOTCH1",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0001071",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE intellectual disability",
"confidence": 0.7
... | {
"gene": "NOTCH1",
"disease": "intellectual disability",
"pathogenic_variants": [
"Single allele"
]
} | 0.83666 |
co_dise_00222 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in ABL1 are classified as Pathogenic or Likely Pathogenic for Alzheimer disease? | Single allele VARIANT_IN_GENE ABL1 -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE Alzheimer disease | {
"steps": [
{
"hop": 1,
"source_node_id": "ABL1",
"source_node_type": "GENE",
"source_node_label": "ABL1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single allele... | Single allele | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ABL1",
"source_db": "UniProt",
"payload": {
"accession": "P00519",
"sequence": "MLEICLKLVGCKSKKGLSSSSSCYLEEALQRPVASDFEPQGLSEAARWNSKENLLAGPSENDPNLFVALYDFVASGDNTLSITKGEKLRVLGYNHNGEWCEAQTKNGQGWVPSNYITPVNSLEKHSWYHGPVSR... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE ABL1",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0004975",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE Alzheimer disease",
"confidence": 0.7
}
] | {
"gene": "ABL1",
"disease": "Alzheimer disease",
"pathogenic_variants": [
"Single allele"
]
} | 0.83666 |
co_dise_00223 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in TP53 are classified as Pathogenic or Likely Pathogenic for Lynch syndrome 1? | Single allele VARIANT_IN_GENE TP53 -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE Lynch syndrome 1 | {
"steps": [
{
"hop": 1,
"source_node_id": "TP53",
"source_node_type": "GENE",
"source_node_label": "TP53",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single allele... | Single allele | 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": "Single allele",
"text": "Single allele VARIANT_IN_GENE TP53",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0007356",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE Lynch syndrome 1",
"confidence": 0.7
}
] | {
"gene": "TP53",
"disease": "Lynch syndrome 1",
"pathogenic_variants": [
"Single allele"
]
} | 0.83666 |
co_dise_00224 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in ACVR1 are classified as Pathogenic or Likely Pathogenic for autosomal recessive juvenile Parkinson disease 2? | Single allele VARIANT_IN_GENE ACVR1 -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE autosomal recessive juvenile Parkinson disease 2 | {
"steps": [
{
"hop": 1,
"source_node_id": "ACVR1",
"source_node_type": "GENE",
"source_node_label": "ACVR1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single alle... | Single allele | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ACVR1",
"source_db": "UniProt",
"payload": {
"accession": "Q04771",
"sequence": "MVDGVMILPVLIMIALPSPSMEDEKPKVNPKLYMCVCEGLSCGNEDHCEGQQCFSSLSINDGFHVYQKGCFQVYEQGKMTCKTPPSPGQAVECCQGDWCNRNITAQLPTKGKSFPGTQNFHLEVGLIILSVVF... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE ACVR1",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0010820",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE autosomal recessive juvenile Parkinson disease 2"... | {
"gene": "ACVR1",
"disease": "autosomal recessive juvenile Parkinson disease 2",
"pathogenic_variants": [
"Single allele"
]
} | 0.83666 |
co_dise_00225 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in FIG4 are classified as Pathogenic or Likely Pathogenic for See cases? | NM_014845.6(FIG4):c.863G>A (p.Gly288Asp) VARIANT_IN_GENE FIG4 -> NM_014845.6(FIG4):c.863G>A (p.Gly288Asp) VARIANT_HAS_CLINICAL_SIGNIFICANCE See cases | {
"steps": [
{
"hop": 1,
"source_node_id": "FIG4",
"source_node_type": "GENE",
"source_node_label": "FIG4",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_014845.6(F... | NM_014845.6(FIG4):c.863G>A (p.Gly288Asp) | null | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "FIG4",
"source_db": "UniProt",
"payload": {
"accession": "Q92562",
"sequence": "MPTAAAPIISSVQKLVLYETRARYFLVGSNNAETKYRVLKIDRTEPKDLVIIDDRHVYTQQEVRELLGRLDLGNRTKMGQKGSSGLFRAVSAFGVVGFVRFLEGYYIVLITKRRKMADIGGHAIYKVEDTNMIY... | [
{
"source_db": "ClinVar",
"source_id": "NM_014845.6(FIG4):c.863G>A (p.Gly288Asp)",
"text": "NM_014845.6(FIG4):c.863G>A (p.Gly288Asp) VARIANT_IN_GENE FIG4",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:see_cases",
"text": "NM_014845.6(FIG4):c.863G>A (p.Gly288Asp)... | {
"gene": "FIG4",
"disease": "See cases",
"pathogenic_variants": [
"NM_014845.6(FIG4):c.863G>A (p.Gly288Asp)"
]
} | 0.83666 |
co_dise_00226 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in DNMT3A are classified as Pathogenic or Likely Pathogenic for Rare genetic intellectual disability? | NM_022552.5(DNMT3A):c.1668G>C (p.Arg556Ser) VARIANT_IN_GENE DNMT3A -> NM_022552.5(DNMT3A):c.1668G>C (p.Arg556Ser) VARIANT_HAS_CLINICAL_SIGNIFICANCE Rare genetic intellectual disability | {
"steps": [
{
"hop": 1,
"source_node_id": "DNMT3A",
"source_node_type": "GENE",
"source_node_label": "DNMT3A",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_022552... | NM_022552.5(DNMT3A):c.1668G>C (p.Arg556Ser) | 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": "ClinVar",
"source_id": "NM_022552.5(DNMT3A):c.1668G>C (p.Arg556Ser)",
"text": "NM_022552.5(DNMT3A):c.1668G>C (p.Arg556Ser) VARIANT_IN_GENE DNMT3A",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:rare_genetic_intellectual_disability",
"text": "NM_02... | {
"gene": "DNMT3A",
"disease": "Rare genetic intellectual disability",
"pathogenic_variants": [
"NM_022552.5(DNMT3A):c.1668G>C (p.Arg556Ser)"
]
} | 0.707107 |
co_dise_00227 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in APC are classified as Pathogenic or Likely Pathogenic for partial duplication of the long arm of chromosome 7? | Single allele VARIANT_IN_GENE APC -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE partial duplication of the long arm of chromosome 7 | {
"steps": [
{
"hop": 1,
"source_node_id": "APC",
"source_node_type": "GENE",
"source_node_label": "APC",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single allele",... | Single allele | null | [
"expression",
"protein_sequence"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "APC",
"source_db": "UniProt",
"payload": {
"accession": "P25054",
"sequence": "MAAASYDQLLKQVEALKMENSNLRQELEDNSNHLTKLETEASNMKEVLKQLQGSIEDEAMASSGQIDLLERLKELNLDSSNFPGVKLRSKMSLRSYGSREGSVSSRSGECSPVPMGSFPRRGFVNGSRESTGYLE... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE APC",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0016958",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE partial duplication of the long arm of chromosome 7... | {
"gene": "APC",
"disease": "partial duplication of the long arm of chromosome 7",
"pathogenic_variants": [
"Single allele"
]
} | 0.83666 |
co_dise_00228 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in AOPEP are classified as Pathogenic or Likely Pathogenic for FANCC-related disorder? | NM_000136.3(FANCC):c.1661T>C (p.Leu554Pro) VARIANT_IN_GENE AOPEP -> NM_000136.3(FANCC):c.1661T>C (p.Leu554Pro) VARIANT_HAS_CLINICAL_SIGNIFICANCE FANCC-related disorder | {
"steps": [
{
"hop": 1,
"source_node_id": "AOPEP",
"source_node_type": "GENE",
"source_node_label": "AOPEP",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_000136.3... | NM_000136.3(FANCC):c.1661T>C (p.Leu554Pro); NM_000136.3(FANCC):c.1155-1G>T | null | [
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "AOPEP",
"source_db": "UniProt",
"payload": {
"accession": "Q8N6M6",
"sequence": "MDIQLDPARDDLPLMANTSHILVKHYVLDLDVDFESQVIEGTIVLFLEDGNRFKKQNSSIEEACQSESNKACKFGMPEPCHIPVTNARTFSSEMEYNDFAICSKGEKDTSDKDGNHDNQEHASGISSSKYCCD... | [
{
"source_db": "ClinVar",
"source_id": "NM_000136.3(FANCC):c.1661T>C (p.Leu554Pro)",
"text": "NM_000136.3(FANCC):c.1661T>C (p.Leu554Pro) VARIANT_IN_GENE AOPEP",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:fancc_related_disorder",
"text": "NM_000136.3(FANCC):c.1... | {
"gene": "AOPEP",
"disease": "FANCC-related disorder",
"pathogenic_variants": [
"NM_000136.3(FANCC):c.1661T>C (p.Leu554Pro)",
"NM_000136.3(FANCC):c.1155-1G>T"
]
} | 0.921954 |
co_dise_00229 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in APC are classified as Pathogenic or Likely Pathogenic for colon carcinoma? | NM_000038.6(APC):c.933+1G>A VARIANT_IN_GENE APC -> NM_000038.6(APC):c.933+1G>A VARIANT_HAS_CLINICAL_SIGNIFICANCE colon carcinoma | {
"steps": [
{
"hop": 1,
"source_node_id": "APC",
"source_node_type": "GENE",
"source_node_label": "APC",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_000038.6(APC... | NM_000038.6(APC):c.933+1G>A | null | [
"expression",
"protein_sequence"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "APC",
"source_db": "UniProt",
"payload": {
"accession": "P25054",
"sequence": "MAAASYDQLLKQVEALKMENSNLRQELEDNSNHLTKLETEASNMKEVLKQLQGSIEDEAMASSGQIDLLERLKELNLDSSNFPGVKLRSKMSLRSYGSREGSVSSRSGECSPVPMGSFPRRGFVNGSRESTGYLE... | [
{
"source_db": "ClinVar",
"source_id": "NM_000038.6(APC):c.933+1G>A",
"text": "NM_000038.6(APC):c.933+1G>A VARIANT_IN_GENE APC",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0002032",
"text": "NM_000038.6(APC):c.933+1G>A VARIANT_HAS_CLINICAL_SIGNIFICANCE colon car... | {
"gene": "APC",
"disease": "colon carcinoma",
"pathogenic_variants": [
"NM_000038.6(APC):c.933+1G>A"
]
} | 0.921954 |
co_dise_00230 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in ATM are classified as Pathogenic or Likely Pathogenic for Seizure? | Single allele VARIANT_IN_GENE ATM -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE Seizure | {
"steps": [
{
"hop": 1,
"source_node_id": "ATM",
"source_node_type": "GENE",
"source_node_label": "ATM",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single allele",... | Single allele | null | [
"expression",
"protein_sequence"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ATM",
"source_db": "UniProt",
"payload": {
"accession": "Q13315",
"sequence": "MSLVLNDLLICCRQLEHDRATERKKEVEKFKRLIRDPETIKHLDRHSDSKQGKYLNWDAVFRFLQKYIQKETECLRIAKPNVSASTQASRQKKMQEISSLVKYFIKCANRRAPRLKCQELLNYIMDTVKDSSNGA... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE ATM",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:seizure",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE Seizure",
"confidence": 0.5
}
] | {
"gene": "ATM",
"disease": "Seizure",
"pathogenic_variants": [
"Single allele"
]
} | 0.707107 |
co_dise_00231 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in APP are classified as Pathogenic or Likely Pathogenic for See cases? | Single allele VARIANT_IN_GENE APP -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE See cases | {
"steps": [
{
"hop": 1,
"source_node_id": "APP",
"source_node_type": "GENE",
"source_node_label": "APP",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single allele",... | Single allele | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "APP",
"source_db": "UniProt",
"payload": {
"accession": "P05067",
"sequence": "MLPGLALLLLAAWTARALEVPTDGNAGLLAEPQIAMFCGRLNMHMNVQNGKWDSDPSGTKTCIDTKEGILQYCQEVYPELQITNVVEANQPVTIQNWCKRGRKQCKTHPHFVIPYRCLVGEFVSDALLVPDKCKF... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE APP",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:see_cases",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE See cases",
"confidence": 0.5
}
] | {
"gene": "APP",
"disease": "See cases",
"pathogenic_variants": [
"Single allele"
]
} | 0.707107 |
co_dise_00232 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in ADRA2B are classified as Pathogenic or Likely Pathogenic for bilateral polymicrogyria? | Single allele VARIANT_IN_GENE ADRA2B -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE bilateral polymicrogyria | {
"steps": [
{
"hop": 1,
"source_node_id": "ADRA2B",
"source_node_type": "GENE",
"source_node_label": "ADRA2B",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single al... | Single allele | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ADRA2B",
"source_db": "UniProt",
"payload": {
"accession": "P18089",
"sequence": "MDHQDPYSVQATAAIAAAITFLILFTIFGNALVILAVLTSRSLRAPQNLFLVSLAAADILVATLIIPFSLANELLGYWYFRRTWCEVYLALDVLFCTSSIVHLCAISLDRYWAVSRALEYNSKRTPRRIKCI... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE ADRA2B",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0017091",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE bilateral polymicrogyria",
"confidence": 0.7... | {
"gene": "ADRA2B",
"disease": "bilateral polymicrogyria",
"pathogenic_variants": [
"Single allele"
]
} | 0.83666 |
co_dise_00233 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in NEK1 are classified as Pathogenic or Likely Pathogenic for orofaciodigital syndrome type II? | NM_001199397.3(NEK1):c.598A>T (p.Lys200Ter) VARIANT_IN_GENE NEK1 -> NM_001199397.3(NEK1):c.598A>T (p.Lys200Ter) VARIANT_HAS_CLINICAL_SIGNIFICANCE orofaciodigital syndrome type II | {
"steps": [
{
"hop": 1,
"source_node_id": "NEK1",
"source_node_type": "GENE",
"source_node_label": "NEK1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_001199397.... | NM_001199397.3(NEK1):c.464G>C (p.Ser155Thr); NM_001199397.3(NEK1):c.598A>T (p.Lys200Ter) | null | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "NEK1",
"source_db": "UniProt",
"payload": {
"accession": "Q96PY6",
"sequence": "MEKYVRLQKIGEGSFGKAILVKSTEDGRQYVIKEINISRMSSKEREESRREVAVLANMKHPNIVQYRESFEENGSLYIVMDYCEGGDLFKRINAQKGVLFQEDQILDWFVQICLALKHVHDRKILHRDIKSQNI... | [
{
"source_db": "ClinVar",
"source_id": "NM_001199397.3(NEK1):c.598A>T (p.Lys200Ter)",
"text": "NM_001199397.3(NEK1):c.598A>T (p.Lys200Ter) VARIANT_IN_GENE NEK1",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0009642",
"text": "NM_001199397.3(NEK1):c.598A>T (p.Lys20... | {
"gene": "NEK1",
"disease": "orofaciodigital syndrome type II",
"pathogenic_variants": [
"NM_001199397.3(NEK1):c.464G>C (p.Ser155Thr)",
"NM_001199397.3(NEK1):c.598A>T (p.Lys200Ter)"
]
} | 0.83666 |
co_dise_00234 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in KMT2C are classified as Pathogenic or Likely Pathogenic for ZTTK syndrome? | Single allele VARIANT_IN_GENE KMT2C -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE ZTTK syndrome | {
"steps": [
{
"hop": 1,
"source_node_id": "KMT2C",
"source_node_type": "GENE",
"source_node_label": "KMT2C",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single alle... | Single allele | null | [
"expression",
"protein_sequence"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "KMT2C",
"source_db": "UniProt",
"payload": {
"accession": "Q8NEZ4",
"sequence": "MSSEEDKSVEQPQPPPPPPEEPGAPAPSPAAADKRPRGRPRKDGASPFQRARKKPRSRGKTAVEDEDSMDGLETTETETIVETEIKEQSAEEDAEAEVDNSKQLIPTLQRSVSEESANSLVSVGVEAKISEQL... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE KMT2C",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0014936",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE ZTTK syndrome",
"confidence": 0.7
}
] | {
"gene": "KMT2C",
"disease": "ZTTK syndrome",
"pathogenic_variants": [
"Single allele"
]
} | 0.83666 |
co_dise_00235 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in TP53 are classified as Pathogenic or Likely Pathogenic for Alzheimer disease? | Single allele VARIANT_IN_GENE TP53 -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE Alzheimer disease | {
"steps": [
{
"hop": 1,
"source_node_id": "TP53",
"source_node_type": "GENE",
"source_node_label": "TP53",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single allele... | Single allele | 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": "Single allele",
"text": "Single allele VARIANT_IN_GENE TP53",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0004975",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE Alzheimer disease",
"confidence": 0.7
}
] | {
"gene": "TP53",
"disease": "Alzheimer disease",
"pathogenic_variants": [
"Single allele"
]
} | 0.83666 |
co_dise_00236 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in ADORA2A are classified as Pathogenic or Likely Pathogenic for Hereditary nonpolyposis colorectal neoplasms? | Single allele VARIANT_IN_GENE ADORA2A -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE Hereditary nonpolyposis colorectal neoplasms | {
"steps": [
{
"hop": 1,
"source_node_id": "ADORA2A",
"source_node_type": "GENE",
"source_node_label": "ADORA2A",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single ... | Single allele | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ADORA2A",
"source_db": "UniProt",
"payload": {
"accession": "P29274",
"sequence": "MPIMGSSVYITVELAIAVLAILGNVLVCWAVWLNSNLQNVTNYFVVSLAAADIAVGVLAIPFAITISTGFCAACHGCLFIACFVLVLTQSSIFSLLAIAIDRYIAIRIPLRYNGLVTGTRAKGIIAICWVL... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE ADORA2A",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:hereditary_nonpolyposis_colorectal_neoplasms",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE Heredita... | {
"gene": "ADORA2A",
"disease": "Hereditary nonpolyposis colorectal neoplasms",
"pathogenic_variants": [
"Single allele"
]
} | 0.83666 |
co_dise_00237 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in CBL are classified as Pathogenic or Likely Pathogenic for Noonan syndrome and Noonan-related syndrome? | NM_005188.4(CBL):c.1930G>T (p.Asp644Tyr) VARIANT_IN_GENE CBL -> NM_005188.4(CBL):c.1930G>T (p.Asp644Tyr) VARIANT_HAS_CLINICAL_SIGNIFICANCE Noonan syndrome and Noonan-related syndrome | {
"steps": [
{
"hop": 1,
"source_node_id": "CBL",
"source_node_type": "GENE",
"source_node_label": "CBL",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_005188.4(CBL... | NM_005188.4(CBL):c.1930G>T (p.Asp644Tyr); NM_005188.4(CBL):c.1516C>T (p.Arg506Ter) | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CBL",
"source_db": "UniProt",
"payload": {
"accession": "P22681",
"sequence": "MAGNVKKSSGAGGGSGSGGSGSGGLIGLMKDAFQPHHHHHHHLSPHPPGTVDKKMVEKCWKLMDKVVRLCQNPKLALKNSPPYILDLLPDTYQHLRTILSRYEGKMETLGENEYFRVFMENLMKKTKQTISLFKE... | [
{
"source_db": "ClinVar",
"source_id": "NM_005188.4(CBL):c.1930G>T (p.Asp644Tyr)",
"text": "NM_005188.4(CBL):c.1930G>T (p.Asp644Tyr) VARIANT_IN_GENE CBL",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0020297",
"text": "NM_005188.4(CBL):c.1930G>T (p.Asp644Tyr) VARI... | {
"gene": "CBL",
"disease": "Noonan syndrome and Noonan-related syndrome",
"pathogenic_variants": [
"NM_005188.4(CBL):c.1930G>T (p.Asp644Tyr)",
"NM_005188.4(CBL):c.1516C>T (p.Arg506Ter)"
]
} | 0.83666 |
co_dise_00238 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in MSH6 are classified as Pathogenic or Likely Pathogenic for schizophrenia? | Single allele VARIANT_IN_GENE MSH6 -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE schizophrenia | {
"steps": [
{
"hop": 1,
"source_node_id": "MSH6",
"source_node_type": "GENE",
"source_node_label": "MSH6",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single allele... | Single allele | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "MSH6",
"source_db": "UniProt",
"payload": {
"accession": "P52701",
"sequence": "MSRQSTLYSFFPKSPALSDANKASARASREGGRAAAAPGASPSPGGDAAWSEAGPGPRPLARSASPPKAKNLNGGLRRSVAPAAPTSCDFSPGDLVWAKMEGYPWWPCLVYNHPFDGTFIREKGKSVRVHVQFF... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE MSH6",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0005090",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE schizophrenia",
"confidence": 0.7
}
] | {
"gene": "MSH6",
"disease": "schizophrenia",
"pathogenic_variants": [
"Single allele"
]
} | 0.83666 |
co_dise_00239 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in TIA1 are classified as Pathogenic or Likely Pathogenic for not provided? | NM_022173.4(TIA1):c.1150G>A (p.Glu384Lys) VARIANT_IN_GENE TIA1 -> NM_022173.4(TIA1):c.1150G>A (p.Glu384Lys) VARIANT_HAS_CLINICAL_SIGNIFICANCE not provided | {
"steps": [
{
"hop": 1,
"source_node_id": "TIA1",
"source_node_type": "GENE",
"source_node_label": "TIA1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_022173.4(T... | NM_022173.4(TIA1):c.1150G>A (p.Glu384Lys) | null | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "TIA1",
"source_db": "UniProt",
"payload": {
"accession": "P31483",
"sequence": "MEDEMPKTLYVGNLSRDVTEALILQLFSQIGPCKNCKMIMDTAGNDPYCFVEFHEHRHAAAALAAMNGRKIMGKEVKVNWATTPSSQKKDTSSSTVVSTQRSQDHFHVFVGDLSPEITTEDIKAAFAPFGRISD... | [
{
"source_db": "ClinVar",
"source_id": "NM_022173.4(TIA1):c.1150G>A (p.Glu384Lys)",
"text": "NM_022173.4(TIA1):c.1150G>A (p.Glu384Lys) VARIANT_IN_GENE TIA1",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:not_provided",
"text": "NM_022173.4(TIA1):c.1150G>A (p.Glu3... | {
"gene": "TIA1",
"disease": "not provided",
"pathogenic_variants": [
"NM_022173.4(TIA1):c.1150G>A (p.Glu384Lys)"
]
} | 0.921954 |
co_dise_00240 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in NOTCH1 are classified as Pathogenic or Likely Pathogenic for Hereditary nonpolyposis colorectal neoplasms? | Single allele VARIANT_IN_GENE NOTCH1 -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE Hereditary nonpolyposis colorectal neoplasms | {
"steps": [
{
"hop": 1,
"source_node_id": "NOTCH1",
"source_node_type": "GENE",
"source_node_label": "NOTCH1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single al... | Single allele | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "NOTCH1",
"source_db": "UniProt",
"payload": {
"accession": "P46531",
"sequence": "MPPLLAPLLCLALLPALAARGPRCSQPGETCLNGGKCEAANGTEACVCGGAFVGPRCQDPNPCLSTPCKNAGTCHVVDRRGVADYACSCALGFSGPLCLTPLDNACLTNPCRNGGTCDLLTLTEYKCRCPPG... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE NOTCH1",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:hereditary_nonpolyposis_colorectal_neoplasms",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE Hereditar... | {
"gene": "NOTCH1",
"disease": "Hereditary nonpolyposis colorectal neoplasms",
"pathogenic_variants": [
"Single allele"
]
} | 0.83666 |
co_dise_00241 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in MTA3 are classified as Pathogenic or Likely Pathogenic for Short stature? | NM_001330442.2(MTA3):c.635G>A (p.Cys212Tyr) VARIANT_IN_GENE MTA3 -> NM_001330442.2(MTA3):c.635G>A (p.Cys212Tyr) VARIANT_HAS_CLINICAL_SIGNIFICANCE Short stature | {
"steps": [
{
"hop": 1,
"source_node_id": "MTA3",
"source_node_type": "GENE",
"source_node_label": "MTA3",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_001330442.... | NM_001330442.2(MTA3):c.635G>A (p.Cys212Tyr) | null | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "MTA3",
"source_db": "UniProt",
"payload": {
"accession": "Q9BTC8",
"sequence": "MAANMYRVGDYVYFENSSSNPYLIRRIEELNKTASGNVEAKVVCFYRRRDISNTLIMLADKHAKEIEEESETTVEADLTDKQKHQLKHRELFLSRQYESLPATHIRGKCSVALLNETESVLSYLDKEDTFFYSL... | [
{
"source_db": "ClinVar",
"source_id": "NM_001330442.2(MTA3):c.635G>A (p.Cys212Tyr)",
"text": "NM_001330442.2(MTA3):c.635G>A (p.Cys212Tyr) VARIANT_IN_GENE MTA3",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:short_stature",
"text": "NM_001330442.2(MTA3):c.635G>A ... | {
"gene": "MTA3",
"disease": "Short stature",
"pathogenic_variants": [
"NM_001330442.2(MTA3):c.635G>A (p.Cys212Tyr)"
]
} | 0.707107 |
co_dise_00242 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in LEPR are classified as Pathogenic or Likely Pathogenic for schizophrenia? | Single allele VARIANT_IN_GENE LEPR -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE schizophrenia | {
"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... | Single allele | 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": "MONDO:0005090",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE schizophrenia",
"confidence": 0.7
}
] | {
"gene": "LEPR",
"disease": "schizophrenia",
"pathogenic_variants": [
"Single allele"
]
} | 0.83666 |
co_dise_00243 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in APC are classified as Pathogenic or Likely Pathogenic for autosomal dominant polycystic kidney disease? | Single allele VARIANT_IN_GENE APC -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE autosomal dominant polycystic kidney disease | {
"steps": [
{
"hop": 1,
"source_node_id": "APC",
"source_node_type": "GENE",
"source_node_label": "APC",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single allele",... | Single allele | null | [
"expression",
"protein_sequence"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "APC",
"source_db": "UniProt",
"payload": {
"accession": "P25054",
"sequence": "MAAASYDQLLKQVEALKMENSNLRQELEDNSNHLTKLETEASNMKEVLKQLQGSIEDEAMASSGQIDLLERLKELNLDSSNFPGVKLRSKMSLRSYGSREGSVSSRSGECSPVPMGSFPRRGFVNGSRESTGYLE... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE APC",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0004691",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE autosomal dominant polycystic kidney disease",
... | {
"gene": "APC",
"disease": "autosomal dominant polycystic kidney disease",
"pathogenic_variants": [
"Single allele"
]
} | 0.83666 |
co_dise_00244 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in AXIN2 are classified as Pathogenic or Likely Pathogenic for tooth agenesis? | NM_004655.4(AXIN2):c.1460_1472dup (p.Pro494fs) VARIANT_IN_GENE AXIN2 -> NM_004655.4(AXIN2):c.1460_1472dup (p.Pro494fs) VARIANT_HAS_CLINICAL_SIGNIFICANCE tooth agenesis | {
"steps": [
{
"hop": 1,
"source_node_id": "AXIN2",
"source_node_type": "GENE",
"source_node_label": "AXIN2",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_004655.4... | NM_004655.4(AXIN2):c.1460_1472dup (p.Pro494fs) | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "AXIN2",
"source_db": "UniProt",
"payload": {
"accession": "Q9Y2T1",
"sequence": "MSSAMLVTCLPDPSSSFREDAPRPPVPGEEGETPPCQPGVGKGQVTKPMPVSSNTRRNEDGLGEPEGRASPDSPLTRWTKSLHSLLGDQDGAYLFRTFLEREKCVDTLDFWFACNGFRQMNLKDTKTLRVAKA... | [
{
"source_db": "ClinVar",
"source_id": "NM_004655.4(AXIN2):c.1460_1472dup (p.Pro494fs)",
"text": "NM_004655.4(AXIN2):c.1460_1472dup (p.Pro494fs) VARIANT_IN_GENE AXIN2",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0005486",
"text": "NM_004655.4(AXIN2):c.1460_1472d... | {
"gene": "AXIN2",
"disease": "tooth agenesis",
"pathogenic_variants": [
"NM_004655.4(AXIN2):c.1460_1472dup (p.Pro494fs)"
]
} | 0.921954 |
co_dise_00245 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in MSH6 are classified as Pathogenic or Likely Pathogenic for KBG syndrome? | Single allele VARIANT_IN_GENE MSH6 -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE KBG syndrome | {
"steps": [
{
"hop": 1,
"source_node_id": "MSH6",
"source_node_type": "GENE",
"source_node_label": "MSH6",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single allele... | Single allele | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "MSH6",
"source_db": "UniProt",
"payload": {
"accession": "P52701",
"sequence": "MSRQSTLYSFFPKSPALSDANKASARASREGGRAAAAPGASPSPGGDAAWSEAGPGPRPLARSASPPKAKNLNGGLRRSVAPAAPTSCDFSPGDLVWAKMEGYPWWPCLVYNHPFDGTFIREKGKSVRVHVQFF... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE MSH6",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0007846",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE KBG syndrome",
"confidence": 0.7
}
] | {
"gene": "MSH6",
"disease": "KBG syndrome",
"pathogenic_variants": [
"Single allele"
]
} | 0.83666 |
no_tiss_00000 | tissue_specific | noncoding_regulatory | easy | 1 | According to GTEx v8, in which tissue is FUS most highly expressed? | FUS GENE_EXPRESSED_IN_TISSUE Ovary | {
"steps": [
{
"hop": 1,
"source_node_id": "FUS",
"source_node_type": "GENE",
"source_node_label": "FUS",
"edge_relation": "GENE_EXPRESSED_IN_TISSUE",
"edge_evidence_type": "expression",
"edge_confidence": 0.7626349216,
"edge_source_db": "GTEx",
"target_node_i... | B | [
"A. Heart_Left_Ventricle",
"B. Ovary",
"C. Pancreas",
"D. Liver"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "FUS",
"source_db": "UniProt",
"payload": {
"accession": "P35637",
"sequence": "MASNDYTQQATQSYGAYPTQPGQGYSQQSSQPYGQQSYSGYSQSTDTSGYGQSSYSSYGQSQNTGYGTQSTPQGYGSTGGYGSSQSSQSSYGQQSSYPGYGQQPAPSSTSGSYGSSSQSSSYGQPQSGSYSQQPS... | [
{
"source_db": "GTEx",
"source_id": "Ovary",
"text": "FUS GENE_EXPRESSED_IN_TISSUE Ovary",
"confidence": 0.7626349216
}
] | {
"gene": "FUS",
"top_tissue": "Ovary",
"top_tpm": 193.194
} | 0.762635 |
no_tiss_00001 | tissue_specific | noncoding_regulatory | easy | 1 | According to GTEx v8, in which tissue is ADAM10 most highly expressed? | ADAM10 GENE_EXPRESSED_IN_TISSUE Cells_Cultured_fibroblasts | {
"steps": [
{
"hop": 1,
"source_node_id": "ADAM10",
"source_node_type": "GENE",
"source_node_label": "ADAM10",
"edge_relation": "GENE_EXPRESSED_IN_TISSUE",
"edge_evidence_type": "expression",
"edge_confidence": 0.5245177869,
"edge_source_db": "GTEx",
"target_... | B | [
"A. Pancreas",
"B. Cells_Cultured_fibroblasts",
"C. Muscle_Skeletal",
"D. Heart_Left_Ventricle"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ADAM10",
"source_db": "UniProt",
"payload": {
"accession": "O14672",
"sequence": "MVLLRVLILLLSWAAGMGGQYGNPLNKYIRHYEGLSYNVDSLHQKHQRAKRAVSHEDQFLRLDFHAHGRHFNLRMKRDTSLFSDEFKVETSNKVLDYDTSHIYTGHIYGEEGSFSHGSVIDGRFEGFIQTRG... | [
{
"source_db": "GTEx",
"source_id": "Cells_Cultured_fibroblasts",
"text": "ADAM10 GENE_EXPRESSED_IN_TISSUE Cells_Cultured_fibroblasts",
"confidence": 0.5245177869
}
] | {
"gene": "ADAM10",
"top_tissue": "Cells_Cultured_fibroblasts",
"top_tpm": 36.4784
} | 0.524518 |
no_tiss_00002 | tissue_specific | noncoding_regulatory | easy | 1 | According to GTEx v8, in which tissue is ACVR1B most highly expressed? | ACVR1B GENE_EXPRESSED_IN_TISSUE Skin_Sun_Exposed_Lower_leg | {
"steps": [
{
"hop": 1,
"source_node_id": "ACVR1B",
"source_node_type": "GENE",
"source_node_label": "ACVR1B",
"edge_relation": "GENE_EXPRESSED_IN_TISSUE",
"edge_evidence_type": "expression",
"edge_confidence": 0.6068893407,
"edge_source_db": "GTEx",
"target_... | A | [
"A. Skin_Sun_Exposed_Lower_leg",
"B. Heart_Left_Ventricle",
"C. Heart_Atrial_Appendage",
"D. Cells_EBV-transformed_lymphocytes"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ACVR1B",
"source_db": "UniProt",
"payload": {
"accession": "P36896",
"sequence": "MAESAGASSFFPLVVLLLAGSGGSGPRGVQALLCACTSCLQANYTCETDGACMVSIFNLDGMEHHVRTCIPKVELVPAGKPFYCLSSEDLRNTHCCYTDYCNRIDLRVPSGHLKEPEHPSMWGPVELVGIIA... | [
{
"source_db": "GTEx",
"source_id": "Skin_Sun_Exposed_Lower_leg",
"text": "ACVR1B GENE_EXPRESSED_IN_TISSUE Skin_Sun_Exposed_Lower_leg",
"confidence": 0.6068893407
}
] | {
"gene": "ACVR1B",
"top_tissue": "Skin_Sun_Exposed_Lower_leg",
"top_tpm": 65.2112
} | 0.606889 |
no_tiss_00003 | tissue_specific | noncoding_regulatory | easy | 1 | According to GTEx v8, in which tissue is ESR1 most highly expressed? | ESR1 GENE_EXPRESSED_IN_TISSUE Cervix_Endocervix | {
"steps": [
{
"hop": 1,
"source_node_id": "ESR1",
"source_node_type": "GENE",
"source_node_label": "ESR1",
"edge_relation": "GENE_EXPRESSED_IN_TISSUE",
"edge_evidence_type": "expression",
"edge_confidence": 0.651105227,
"edge_source_db": "GTEx",
"target_node_... | D | [
"A. Whole_Blood",
"B. Cells_EBV-transformed_lymphocytes",
"C. Brain_Putamen_basal_ganglia",
"D. Cervix_Endocervix"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ESR1",
"source_db": "UniProt",
"payload": {
"accession": "P03372",
"sequence": "MTMTLHTKASGMALLHQIQGNELEPLNRPQLKIPLERPLGEVYLDSSKPAVYNYPEGAAYEFNAAAAANAQVYGQTGLPYGPGSEAAAFGSNGLGGFPPLNSVSPSPLMLLHPPPQLSPFLQPHGQQVPYYLEN... | [
{
"source_db": "GTEx",
"source_id": "Cervix_Endocervix",
"text": "ESR1 GENE_EXPRESSED_IN_TISSUE Cervix_Endocervix",
"confidence": 0.651105227
}
] | {
"gene": "ESR1",
"top_tissue": "Cervix_Endocervix",
"top_tpm": 88.8666
} | 0.651105 |
no_tiss_00004 | tissue_specific | noncoding_regulatory | easy | 1 | According to GTEx v8, in which tissue is BRCA2 most highly expressed? | BRCA2 GENE_EXPRESSED_IN_TISSUE Cells_EBV-transformed_lymphocytes | {
"steps": [
{
"hop": 1,
"source_node_id": "BRCA2",
"source_node_type": "GENE",
"source_node_label": "BRCA2",
"edge_relation": "GENE_EXPRESSED_IN_TISSUE",
"edge_evidence_type": "expression",
"edge_confidence": 0.3620651822,
"edge_source_db": "GTEx",
"target_no... | A | [
"A. Cells_EBV-transformed_lymphocytes",
"B. Brain_Hippocampus",
"C. Muscle_Skeletal",
"D. Heart_Left_Ventricle"
] | [
"expression",
"protein_sequence"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "BRCA2",
"source_db": "UniProt",
"payload": {
"accession": "P51587",
"sequence": "MPIGSKERPTFFEIFKTRCNKADLGPISLNWFEELSSEAPPYNSEPAEESEHKNNNYEPNLFKTPQRKPSYNQLASTPIIFKEQGLTLPLYQSPVKELDKFKLDLGRNVPNSRHKSLRTVKTKMDQADDVSCP... | [
{
"source_db": "GTEx",
"source_id": "Cells_EBV-transformed_lymphocytes",
"text": "BRCA2 GENE_EXPRESSED_IN_TISSUE Cells_EBV-transformed_lymphocytes",
"confidence": 0.3620651822
}
] | {
"gene": "BRCA2",
"top_tissue": "Cells_EBV-transformed_lymphocytes",
"top_tpm": 11.1998
} | 0.362065 |
no_tiss_00005 | tissue_specific | noncoding_regulatory | easy | 1 | According to GTEx v8, in which tissue is CD44 most highly expressed? | CD44 GENE_EXPRESSED_IN_TISSUE Skin_Not_Sun_Exposed_Suprapubic | {
"steps": [
{
"hop": 1,
"source_node_id": "CD44",
"source_node_type": "GENE",
"source_node_label": "CD44",
"edge_relation": "GENE_EXPRESSED_IN_TISSUE",
"edge_evidence_type": "expression",
"edge_confidence": 0.7901935614,
"edge_source_db": "GTEx",
"target_node... | C | [
"A. Brain_Frontal_Cortex_BA9",
"B. Brain_Nucleus_accumbens_basal_ganglia",
"C. Skin_Not_Sun_Exposed_Suprapubic",
"D. Brain_Putamen_basal_ganglia"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CD44",
"source_db": "UniProt",
"payload": {
"accession": "P16070",
"sequence": "MDKFWWHAAWGLCLVPLSLAQIDLNITCRFAGVFHVEKNGRYSISRTEAADLCKAFNSTLPTMAQMEKALSIGFETCRYGFIEGHVVIPRIHPNSICAANNTGVYILTSNTSQYDTYCFNASAPPEEDCTSVTD... | [
{
"source_db": "GTEx",
"source_id": "Skin_Not_Sun_Exposed_Suprapubic",
"text": "CD44 GENE_EXPRESSED_IN_TISSUE Skin_Not_Sun_Exposed_Suprapubic",
"confidence": 0.7901935614
}
] | {
"gene": "CD44",
"top_tissue": "Skin_Not_Sun_Exposed_Suprapubic",
"top_tpm": 233.922
} | 0.790194 |
no_tiss_00006 | tissue_specific | noncoding_regulatory | easy | 1 | According to GTEx v8, in which tissue is FLT3 most highly expressed? | FLT3 GENE_EXPRESSED_IN_TISSUE Brain_Cerebellar_Hemisphere | {
"steps": [
{
"hop": 1,
"source_node_id": "FLT3",
"source_node_type": "GENE",
"source_node_label": "FLT3",
"edge_relation": "GENE_EXPRESSED_IN_TISSUE",
"edge_evidence_type": "expression",
"edge_confidence": 0.4572315624,
"edge_source_db": "GTEx",
"target_node... | B | [
"A. Cells_Cultured_fibroblasts",
"B. Brain_Cerebellar_Hemisphere",
"C. Kidney_Medulla",
"D. Muscle_Skeletal"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "FLT3",
"source_db": "UniProt",
"payload": {
"accession": "P36888",
"sequence": "MPALARDGGQLPLLVVFSAMIFGTITNQDLPVIKCVLINHKNNDSSVGKSSSYPMVSESPEDLGCALRPQSSGTVYEAAAVEVDVSASITLQVLVDAPGNISCLWVFKHSSLNCQPHFDLQNRGVVSMVILKMT... | [
{
"source_db": "GTEx",
"source_id": "Brain_Cerebellar_Hemisphere",
"text": "FLT3 GENE_EXPRESSED_IN_TISSUE Brain_Cerebellar_Hemisphere",
"confidence": 0.4572315624
}
] | {
"gene": "FLT3",
"top_tissue": "Brain_Cerebellar_Hemisphere",
"top_tpm": 22.5447
} | 0.457232 |
no_tiss_00007 | tissue_specific | noncoding_regulatory | easy | 1 | According to GTEx v8, in which tissue is DNMT3A most highly expressed? | DNMT3A GENE_EXPRESSED_IN_TISSUE Brain_Cerebellum | {
"steps": [
{
"hop": 1,
"source_node_id": "DNMT3A",
"source_node_type": "GENE",
"source_node_label": "DNMT3A",
"edge_relation": "GENE_EXPRESSED_IN_TISSUE",
"edge_evidence_type": "expression",
"edge_confidence": 0.4467203186,
"edge_source_db": "GTEx",
"target_... | D | [
"A. Kidney_Cortex",
"B. Heart_Left_Ventricle",
"C. Liver",
"D. Brain_Cerebellum"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "DNMT3A",
"source_db": "UniProt",
"payload": {
"accession": "Q9Y6K1",
"sequence": "MPAMPSSGPGDTSSSAAEREEDRKDGEEQEEPRGKEERQEPSTTARKVGRPGRKRKHPPVESGDTPKDPAVISKSPSMAQDSGASELLPNGDLEKRSEPQPEEGSPAGGQKGGAPAEGEGAAETLPEASRAV... | [
{
"source_db": "GTEx",
"source_id": "Brain_Cerebellum",
"text": "DNMT3A GENE_EXPRESSED_IN_TISSUE Brain_Cerebellum",
"confidence": 0.4467203186
}
] | {
"gene": "DNMT3A",
"top_tissue": "Brain_Cerebellum",
"top_tpm": 20.8955
} | 0.44672 |
no_tiss_00008 | tissue_specific | noncoding_regulatory | easy | 1 | According to GTEx v8, in which tissue is MET most highly expressed? | MET GENE_EXPRESSED_IN_TISSUE Nerve_Tibial | {
"steps": [
{
"hop": 1,
"source_node_id": "MET",
"source_node_type": "GENE",
"source_node_label": "MET",
"edge_relation": "GENE_EXPRESSED_IN_TISSUE",
"edge_evidence_type": "expression",
"edge_confidence": 0.4490840585,
"edge_source_db": "GTEx",
"target_node_i... | D | [
"A. Brain_Cerebellar_Hemisphere",
"B. Whole_Blood",
"C. Cells_EBV-transformed_lymphocytes",
"D. Nerve_Tibial"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "MET",
"source_db": "UniProt",
"payload": {
"accession": "P08581",
"sequence": "MKAPAVLAPGILVLLFTLVQRSNGECKEALAKSEMNVNMKYQLPNFTAETPIQNVILHEHHIFLGATNYIYVLNEEDLQKVAEYKTGPVLEHPDCFPCQDCSSKANLSGGVWKDNINMALVVDTYYDDQLISCGS... | [
{
"source_db": "GTEx",
"source_id": "Nerve_Tibial",
"text": "MET GENE_EXPRESSED_IN_TISSUE Nerve_Tibial",
"confidence": 0.4490840585
}
] | {
"gene": "MET",
"top_tissue": "Nerve_Tibial",
"top_tpm": 21.256
} | 0.449084 |
no_tiss_00009 | tissue_specific | noncoding_regulatory | easy | 1 | According to GTEx v8, in which tissue is MLH3 most highly expressed? | MLH3 GENE_EXPRESSED_IN_TISSUE Thyroid | {
"steps": [
{
"hop": 1,
"source_node_id": "MLH3",
"source_node_type": "GENE",
"source_node_label": "MLH3",
"edge_relation": "GENE_EXPRESSED_IN_TISSUE",
"edge_evidence_type": "expression",
"edge_confidence": 0.4127979251,
"edge_source_db": "GTEx",
"target_node... | C | [
"A. Heart_Left_Ventricle",
"B. Pancreas",
"C. Thyroid",
"D. Whole_Blood"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "MLH3",
"source_db": "UniProt",
"payload": {
"accession": "Q9UHC1",
"sequence": "MIKCLSVEVQAKLRSGLAISSLGQCVEELALNSIDAEAKCVAVRVNMETFQVQVIDNGFGMGSDDVEKVGNRYFTSKCHSVQDLENPRFYGFRGEALANIADMASAVEISSKKNRTMKTFVKLFQSGKALKACE... | [
{
"source_db": "GTEx",
"source_id": "Thyroid",
"text": "MLH3 GENE_EXPRESSED_IN_TISSUE Thyroid",
"confidence": 0.4127979251
}
] | {
"gene": "MLH3",
"top_tissue": "Thyroid",
"top_tpm": 16.321
} | 0.412798 |
no_tiss_00010 | tissue_specific | noncoding_regulatory | easy | 1 | According to GTEx v8, in which tissue is HGF most highly expressed? | HGF GENE_EXPRESSED_IN_TISSUE Lung | {
"steps": [
{
"hop": 1,
"source_node_id": "HGF",
"source_node_type": "GENE",
"source_node_label": "HGF",
"edge_relation": "GENE_EXPRESSED_IN_TISSUE",
"edge_evidence_type": "expression",
"edge_confidence": 0.4109367043,
"edge_source_db": "GTEx",
"target_node_i... | C | [
"A. Brain_Putamen_basal_ganglia",
"B. Brain_Cerebellar_Hemisphere",
"C. Lung",
"D. Cells_EBV-transformed_lymphocytes"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "HGF",
"source_db": "UniProt",
"payload": {
"accession": "P14210",
"sequence": "MWVTKLLPALLLQHVLLHLLLLPIAIPYAEGQRKRRNTIHEFKKSAKTTLIKIDPALKIKTKKVNTADQCANRCTRNKGLPFTCKAFVFDKARKQCLWFPFNSMSSGVKKEFGHEFDLYENKDYIRNCIIGKGRS... | [
{
"source_db": "GTEx",
"source_id": "Lung",
"text": "HGF GENE_EXPRESSED_IN_TISSUE Lung",
"confidence": 0.4109367043
}
] | {
"gene": "HGF",
"top_tissue": "Lung",
"top_tpm": 16.0997
} | 0.410937 |
no_tiss_00011 | tissue_specific | noncoding_regulatory | easy | 1 | According to GTEx v8, in which tissue is AFDN most highly expressed? | AFDN GENE_EXPRESSED_IN_TISSUE Esophagus_Mucosa | {
"steps": [
{
"hop": 1,
"source_node_id": "AFDN",
"source_node_type": "GENE",
"source_node_label": "AFDN",
"edge_relation": "GENE_EXPRESSED_IN_TISSUE",
"edge_evidence_type": "expression",
"edge_confidence": 0.606391148,
"edge_source_db": "GTEx",
"target_node_... | A | [
"A. Esophagus_Mucosa",
"B. Brain_Putamen_basal_ganglia",
"C. Whole_Blood",
"D. Brain_Amygdala"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "AFDN",
"source_db": "UniProt",
"payload": {
"accession": "P55196",
"sequence": "MSAGGRDEERRKLADIIHHWNANRLDLFEISQPTEDLEFHGVMRFYFQDKAAGNFATKCIRVSSTATTQDVIETLAEKFRPDMRMLSSPKYSLYEVHVSGERRLDIDEKPLVVQLNWNKDDREGRFVLKNENDA... | [
{
"source_db": "GTEx",
"source_id": "Esophagus_Mucosa",
"text": "AFDN GENE_EXPRESSED_IN_TISSUE Esophagus_Mucosa",
"confidence": 0.606391148
}
] | {
"gene": "AFDN",
"top_tissue": "Esophagus_Mucosa",
"top_tpm": 64.9837
} | 0.606391 |
no_tiss_00012 | tissue_specific | noncoding_regulatory | easy | 1 | According to GTEx v8, in which tissue is CASP1P1 most highly expressed? | CASP1P1 GENE_EXPRESSED_IN_TISSUE Adipose_Subcutaneous | {
"steps": [
{
"hop": 1,
"source_node_id": "CASP1P1",
"source_node_type": "GENE",
"source_node_label": "CASP1P1",
"edge_relation": "GENE_EXPRESSED_IN_TISSUE",
"edge_evidence_type": "expression",
"edge_confidence": 0.01,
"edge_source_db": "GTEx",
"target_node_i... | B | [
"A. Whole_Blood",
"B. Adipose_Subcutaneous",
"C. Uterus",
"D. Vagina"
] | [
"expression"
] | [
{
"family": "transcriptomic",
"tag": "expression",
"anchor_node_id": "CASP1P1",
"source_db": "GTEx",
"payload": {
"gene": "CASP1P1",
"tissues": [
"Adipose_Subcutaneous",
"Adipose_Visceral_Omentum",
"Adrenal_Gland",
"Artery_Aorta",
"Artery_Coron... | [
{
"source_db": "GTEx",
"source_id": "Adipose_Subcutaneous",
"text": "CASP1P1 GENE_EXPRESSED_IN_TISSUE Adipose_Subcutaneous",
"confidence": 0.01
}
] | {
"gene": "CASP1P1",
"top_tissue": "Adipose_Subcutaneous",
"top_tpm": 0
} | 0.01 |
no_tiss_00013 | tissue_specific | noncoding_regulatory | easy | 1 | According to GTEx v8, in which tissue is CTNNA1 most highly expressed? | CTNNA1 GENE_EXPRESSED_IN_TISSUE Nerve_Tibial | {
"steps": [
{
"hop": 1,
"source_node_id": "CTNNA1",
"source_node_type": "GENE",
"source_node_label": "CTNNA1",
"edge_relation": "GENE_EXPRESSED_IN_TISSUE",
"edge_evidence_type": "expression",
"edge_confidence": 0.8074896838,
"edge_source_db": "GTEx",
"target_... | B | [
"A. Liver",
"B. Nerve_Tibial",
"C. Brain_Cerebellar_Hemisphere",
"D. Whole_Blood"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CTNNA1",
"source_db": "UniProt",
"payload": {
"accession": "P35221",
"sequence": "MTAVHAGNINFKWDPKSLEIRTLAVERLLEPLVTQVTTLVNTNSKGPSNKKRGRSKKAHVLAASVEQATENFLEKGDKIAKESQFLKEELVAAVEDVRKQGDLMKAAAGEFADDPCSSVKRGNMVRAARALL... | [
{
"source_db": "GTEx",
"source_id": "Nerve_Tibial",
"text": "CTNNA1 GENE_EXPRESSED_IN_TISSUE Nerve_Tibial",
"confidence": 0.8074896838
}
] | {
"gene": "CTNNA1",
"top_tissue": "Nerve_Tibial",
"top_tpm": 263.74
} | 0.80749 |
no_tiss_00014 | tissue_specific | noncoding_regulatory | easy | 1 | According to GTEx v8, in which tissue is ALB most highly expressed? | ALB GENE_EXPRESSED_IN_TISSUE Liver | {
"steps": [
{
"hop": 1,
"source_node_id": "ALB",
"source_node_type": "GENE",
"source_node_label": "ALB",
"edge_relation": "GENE_EXPRESSED_IN_TISSUE",
"edge_evidence_type": "expression",
"edge_confidence": 1,
"edge_source_db": "GTEx",
"target_node_id": "Liver"... | A | [
"A. Liver",
"B. Cells_EBV-transformed_lymphocytes",
"C. Cells_Cultured_fibroblasts",
"D. Muscle_Skeletal"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ALB",
"source_db": "UniProt",
"payload": {
"accession": "P02768",
"sequence": "MKWVTFISLLFLFSSAYSRGVFRRDAHKSEVAHRFKDLGEENFKALVLIAFAQYLQQCPFEDHVKLVNEVTEFAKTCVADESAENCDKSLHTLFGDKLCTVATLRETYGEMADCCAKQEPERNECFLQHKDDNPN... | [
{
"source_db": "GTEx",
"source_id": "Liver",
"text": "ALB GENE_EXPRESSED_IN_TISSUE Liver",
"confidence": 1
}
] | {
"gene": "ALB",
"top_tissue": "Liver",
"top_tpm": 25201.3
} | 1 |
no_tiss_00015 | tissue_specific | noncoding_regulatory | easy | 1 | According to GTEx v8, in which tissue is CD8A most highly expressed? | CD8A GENE_EXPRESSED_IN_TISSUE Spleen | {
"steps": [
{
"hop": 1,
"source_node_id": "CD8A",
"source_node_type": "GENE",
"source_node_label": "CD8A",
"edge_relation": "GENE_EXPRESSED_IN_TISSUE",
"edge_evidence_type": "expression",
"edge_confidence": 0.6728277704,
"edge_source_db": "GTEx",
"target_node... | C | [
"A. Muscle_Skeletal",
"B. Cells_EBV-transformed_lymphocytes",
"C. Spleen",
"D. Cells_Cultured_fibroblasts"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CD8A",
"source_db": "UniProt",
"payload": {
"accession": "P01732",
"sequence": "MALPVTALLLPLALLLHAARPSQFRVSPLDRTWNLGETVELKCQVLLSNPTSGCSWLFQPRGAAASPTFLLYLSQNKPKAAEGLDTQRFSGKRLGDTFVLTLSDFRRENEGYYFCSALSNSIMYFSHFVPVFLP... | [
{
"source_db": "GTEx",
"source_id": "Spleen",
"text": "CD8A GENE_EXPRESSED_IN_TISSUE Spleen",
"confidence": 0.6728277704
}
] | {
"gene": "CD8A",
"top_tissue": "Spleen",
"top_tpm": 103.418
} | 0.672828 |
no_tiss_00016 | tissue_specific | noncoding_regulatory | easy | 1 | According to GTEx v8, in which tissue is NRAS most highly expressed? | NRAS GENE_EXPRESSED_IN_TISSUE Cells_EBV-transformed_lymphocytes | {
"steps": [
{
"hop": 1,
"source_node_id": "NRAS",
"source_node_type": "GENE",
"source_node_label": "NRAS",
"edge_relation": "GENE_EXPRESSED_IN_TISSUE",
"edge_evidence_type": "expression",
"edge_confidence": 0.6311424453,
"edge_source_db": "GTEx",
"target_node... | A | [
"A. Cells_EBV-transformed_lymphocytes",
"B. Heart_Atrial_Appendage",
"C. Heart_Left_Ventricle",
"D. Muscle_Skeletal"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "NRAS",
"source_db": "UniProt",
"payload": {
"accession": "P01111",
"sequence": "MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNSKSFADINLYREQIKRVKDSDDVPMVLVGNKCDLPTRTVDTKQAHELA... | [
{
"source_db": "GTEx",
"source_id": "Cells_EBV-transformed_lymphocytes",
"text": "NRAS GENE_EXPRESSED_IN_TISSUE Cells_EBV-transformed_lymphocytes",
"confidence": 0.6311424453
}
] | {
"gene": "NRAS",
"top_tissue": "Cells_EBV-transformed_lymphocytes",
"top_tpm": 77.2891
} | 0.631142 |
no_tiss_00017 | tissue_specific | noncoding_regulatory | easy | 1 | According to GTEx v8, in which tissue is RXRA most highly expressed? | RXRA GENE_EXPRESSED_IN_TISSUE Skin_Sun_Exposed_Lower_leg | {
"steps": [
{
"hop": 1,
"source_node_id": "RXRA",
"source_node_type": "GENE",
"source_node_label": "RXRA",
"edge_relation": "GENE_EXPRESSED_IN_TISSUE",
"edge_evidence_type": "expression",
"edge_confidence": 0.6120405821,
"edge_source_db": "GTEx",
"target_node... | D | [
"A. Brain_Cerebellar_Hemisphere",
"B. Brain_Spinal_cord_cervical_c-1",
"C. Brain_Cerebellum",
"D. Skin_Sun_Exposed_Lower_leg"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "RXRA",
"source_db": "UniProt",
"payload": {
"accession": "P19793",
"sequence": "MDTKHFLPLDFSTQVNSSLTSPTGRGSMAAPSLHPSLGPGIGSPGQLHSPISTLSSPINGMGPPFSVISSPMGPHSMSVPTTPTLGFSTGSPQLSSPMNPVSSSEDIKPPLGLNGVLKVPAHPSGNMASFTKHI... | [
{
"source_db": "GTEx",
"source_id": "Skin_Sun_Exposed_Lower_leg",
"text": "RXRA GENE_EXPRESSED_IN_TISSUE Skin_Sun_Exposed_Lower_leg",
"confidence": 0.6120405821
}
] | {
"gene": "RXRA",
"top_tissue": "Skin_Sun_Exposed_Lower_leg",
"top_tpm": 67.61
} | 0.612041 |
no_tiss_00018 | tissue_specific | noncoding_regulatory | easy | 1 | According to GTEx v8, in which tissue is AXIN2 most highly expressed? | AXIN2 GENE_EXPRESSED_IN_TISSUE Uterus | {
"steps": [
{
"hop": 1,
"source_node_id": "AXIN2",
"source_node_type": "GENE",
"source_node_label": "AXIN2",
"edge_relation": "GENE_EXPRESSED_IN_TISSUE",
"edge_evidence_type": "expression",
"edge_confidence": 0.5620735596,
"edge_source_db": "GTEx",
"target_no... | D | [
"A. Whole_Blood",
"B. Cells_EBV-transformed_lymphocytes",
"C. Liver",
"D. Uterus"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "AXIN2",
"source_db": "UniProt",
"payload": {
"accession": "Q9Y2T1",
"sequence": "MSSAMLVTCLPDPSSSFREDAPRPPVPGEEGETPPCQPGVGKGQVTKPMPVSSNTRRNEDGLGEPEGRASPDSPLTRWTKSLHSLLGDQDGAYLFRTFLEREKCVDTLDFWFACNGFRQMNLKDTKTLRVAKA... | [
{
"source_db": "GTEx",
"source_id": "Uterus",
"text": "AXIN2 GENE_EXPRESSED_IN_TISSUE Uterus",
"confidence": 0.5620735596
}
] | {
"gene": "AXIN2",
"top_tissue": "Uterus",
"top_tpm": 47.580799999999996
} | 0.562074 |
no_tiss_00019 | tissue_specific | noncoding_regulatory | easy | 1 | According to GTEx v8, in which tissue is CD2AP most highly expressed? | CD2AP GENE_EXPRESSED_IN_TISSUE Cells_EBV-transformed_lymphocytes | {
"steps": [
{
"hop": 1,
"source_node_id": "CD2AP",
"source_node_type": "GENE",
"source_node_label": "CD2AP",
"edge_relation": "GENE_EXPRESSED_IN_TISSUE",
"edge_evidence_type": "expression",
"edge_confidence": 0.5497299012,
"edge_source_db": "GTEx",
"target_no... | D | [
"A. Brain_Anterior_cingulate_cortex_BA24",
"B. Brain_Amygdala",
"C. Whole_Blood",
"D. Cells_EBV-transformed_lymphocytes"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CD2AP",
"source_db": "UniProt",
"payload": {
"accession": "Q9Y5K6",
"sequence": "MVDYIVEYDYDAVHDDELTIRVGEIIRNVKKLQEEGWLEGELNGRRGMFPDNFVKEIKRETEFKDDSLPIKRERHGNVASLVQRISTYGLPAGGIQPHPQTKNIKKKTKKRQCKVLFEYIPQNEDELELKVGD... | [
{
"source_db": "GTEx",
"source_id": "Cells_EBV-transformed_lymphocytes",
"text": "CD2AP GENE_EXPRESSED_IN_TISSUE Cells_EBV-transformed_lymphocytes",
"confidence": 0.5497299012
}
] | {
"gene": "CD2AP",
"top_tissue": "Cells_EBV-transformed_lymphocytes",
"top_tpm": 43.6096
} | 0.54973 |
no_tiss_00020 | tissue_specific | noncoding_regulatory | easy | 1 | According to GTEx v8, in which tissue is IGFL1P1 most highly expressed? | IGFL1P1 GENE_EXPRESSED_IN_TISSUE Skin_Sun_Exposed_Lower_leg | {
"steps": [
{
"hop": 1,
"source_node_id": "IGFL1P1",
"source_node_type": "GENE",
"source_node_label": "IGFL1P1",
"edge_relation": "GENE_EXPRESSED_IN_TISSUE",
"edge_evidence_type": "expression",
"edge_confidence": 0.2905163232,
"edge_source_db": "GTEx",
"targe... | D | [
"A. Stomach",
"B. Thyroid",
"C. Whole_Blood",
"D. Skin_Sun_Exposed_Lower_leg"
] | [
"expression"
] | [
{
"family": "transcriptomic",
"tag": "expression",
"anchor_node_id": "IGFL1P1",
"source_db": "GTEx",
"payload": {
"gene": "IGFL1P1",
"tissues": [
"Adipose_Subcutaneous",
"Adipose_Visceral_Omentum",
"Adrenal_Gland",
"Artery_Aorta",
"Artery_Coron... | [
{
"source_db": "GTEx",
"source_id": "Skin_Sun_Exposed_Lower_leg",
"text": "IGFL1P1 GENE_EXPRESSED_IN_TISSUE Skin_Sun_Exposed_Lower_leg",
"confidence": 0.2905163232
}
] | {
"gene": "IGFL1P1",
"top_tissue": "Skin_Sun_Exposed_Lower_leg",
"top_tpm": 6.44175
} | 0.290516 |
no_tiss_00021 | tissue_specific | noncoding_regulatory | easy | 1 | According to GTEx v8, in which tissue is ABL2 most highly expressed? | ABL2 GENE_EXPRESSED_IN_TISSUE Cells_Cultured_fibroblasts | {
"steps": [
{
"hop": 1,
"source_node_id": "ABL2",
"source_node_type": "GENE",
"source_node_label": "ABL2",
"edge_relation": "GENE_EXPRESSED_IN_TISSUE",
"edge_evidence_type": "expression",
"edge_confidence": 0.5045728982,
"edge_source_db": "GTEx",
"target_node... | C | [
"A. Heart_Left_Ventricle",
"B. Whole_Blood",
"C. Cells_Cultured_fibroblasts",
"D. Liver"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ABL2",
"source_db": "UniProt",
"payload": {
"accession": "P42684",
"sequence": "MGQQVGRVGEAPGLQQPQPRGIRGSSAARPSGRRRDPAGRTTETGFNIFTQHDHFASCVEDGFEGDKTGGSSPEALHRPYGCDVEPQALNEAIRWSSKENLLGATESDPNLFVALYDFVASGDNTLSITKGEKL... | [
{
"source_db": "GTEx",
"source_id": "Cells_Cultured_fibroblasts",
"text": "ABL2 GENE_EXPRESSED_IN_TISSUE Cells_Cultured_fibroblasts",
"confidence": 0.5045728982
}
] | {
"gene": "ABL2",
"top_tissue": "Cells_Cultured_fibroblasts",
"top_tpm": 31.6541
} | 0.504573 |
no_tiss_00022 | tissue_specific | noncoding_regulatory | easy | 1 | According to GTEx v8, in which tissue is KDM6A most highly expressed? | KDM6A GENE_EXPRESSED_IN_TISSUE Ovary | {
"steps": [
{
"hop": 1,
"source_node_id": "KDM6A",
"source_node_type": "GENE",
"source_node_label": "KDM6A",
"edge_relation": "GENE_EXPRESSED_IN_TISSUE",
"edge_evidence_type": "expression",
"edge_confidence": 0.4740475749,
"edge_source_db": "GTEx",
"target_no... | B | [
"A. Brain_Putamen_basal_ganglia",
"B. Ovary",
"C. Brain_Anterior_cingulate_cortex_BA24",
"D. Brain_Amygdala"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "KDM6A",
"source_db": "UniProt",
"payload": {
"accession": "O15550",
"sequence": "MKSCGVSLATAAAAAAAFGDEEKKMAAGKASGESEEASPSLTAEEREALGGLDSRLFGFVRFHEDGARTKALLGKAVRCYESLILKAEGKVESDFFCQLGHFNLLLEDYPKALSAYQRYYSLQSDYWKNAAFL... | [
{
"source_db": "GTEx",
"source_id": "Ovary",
"text": "KDM6A GENE_EXPRESSED_IN_TISSUE Ovary",
"confidence": 0.4740475749
}
] | {
"gene": "KDM6A",
"top_tissue": "Ovary",
"top_tpm": 25.4453
} | 0.474048 |
no_tiss_00023 | tissue_specific | noncoding_regulatory | easy | 1 | According to GTEx v8, in which tissue is CREBBP most highly expressed? | CREBBP GENE_EXPRESSED_IN_TISSUE Uterus | {
"steps": [
{
"hop": 1,
"source_node_id": "CREBBP",
"source_node_type": "GENE",
"source_node_label": "CREBBP",
"edge_relation": "GENE_EXPRESSED_IN_TISSUE",
"edge_evidence_type": "expression",
"edge_confidence": 0.578466563,
"edge_source_db": "GTEx",
"target_n... | C | [
"A. Brain_Substantia_nigra",
"B. Brain_Amygdala",
"C. Uterus",
"D. Brain_Putamen_basal_ganglia"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CREBBP",
"source_db": "UniProt",
"payload": {
"accession": "Q92793",
"sequence": "MAENLLDGPPNPKRAKLSSPGFSANDSTDFGSLFDLENDLPDELIPNGGELGLLNSGNLVPDAASKHKQLSELLRGGSGSSINPGIGNVSASSPVQQGLGGQAQGQPNSANMASLSAMGKSPLSQGDSSAPS... | [
{
"source_db": "GTEx",
"source_id": "Uterus",
"text": "CREBBP GENE_EXPRESSED_IN_TISSUE Uterus",
"confidence": 0.578466563
}
] | {
"gene": "CREBBP",
"top_tissue": "Uterus",
"top_tpm": 53.4065
} | 0.578467 |
no_tiss_00024 | tissue_specific | noncoding_regulatory | easy | 1 | According to GTEx v8, in which tissue is ADRB1 most highly expressed? | ADRB1 GENE_EXPRESSED_IN_TISSUE Lung | {
"steps": [
{
"hop": 1,
"source_node_id": "ADRB1",
"source_node_type": "GENE",
"source_node_label": "ADRB1",
"edge_relation": "GENE_EXPRESSED_IN_TISSUE",
"edge_evidence_type": "expression",
"edge_confidence": 0.4675979787,
"edge_source_db": "GTEx",
"target_no... | B | [
"A. Artery_Tibial",
"B. Lung",
"C. Whole_Blood",
"D. Cells_Cultured_fibroblasts"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ADRB1",
"source_db": "UniProt",
"payload": {
"accession": "P08588",
"sequence": "MGAGVLVLGASEPGNLSSAAPLPDGAATAARLLVPASPPASLLPPASESPEPLSQQWTAGMGLLMALIVLLIVAGNVLVIVAIAKTPRLQTLTNLFIMSLASADLVMGLLVVPFGATIVVWGRWEYGSFFCEL... | [
{
"source_db": "GTEx",
"source_id": "Lung",
"text": "ADRB1 GENE_EXPRESSED_IN_TISSUE Lung",
"confidence": 0.4675979787
}
] | {
"gene": "ADRB1",
"top_tissue": "Lung",
"top_tpm": 24.2928
} | 0.467598 |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.