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_stru_00133 | structural_effect | coding_variant | easy | 1 | NM_000249.4(MLH1):c.386_392dup (p.Asp132fs) introduces a premature truncation at residue 132 of MLH1's 756-residue protein product (AlphaFold model, mean pLDDT 77.31). Approximately how much of the protein is lost downstream of the truncation? | NM_000249.4(MLH1):c.386_392dup (p.Asp132fs) VARIANT_IN_GENE MLH1 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000249.4(MLH1):c.386_392dup (p.Asp132fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000249.4(MLH1):c.386_392dup (p.Asp132fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confiden... | A | [
"A. more than half the protein (>50%)",
"B. a small C-terminal portion (<25%)",
"C. a substantial portion (25-50%)"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "MLH1",
"source_db": "UniProt",
"payload": {
"accession": "P40692",
"sequence": "MSFVAGVIRRLDETVVNRIAAGEVIQRPANAIKEMIENCLDAKSTSIQVIVKEGGLKLIQIQDNGTGIRKEDLDIVCERFTTSKLQSFEDLASISTYGFRGEALASISHVAHVTITTKTADGKCAYRASYSDGK... | [
{
"source_db": "ClinVar",
"source_id": "MLH1",
"text": "NM_000249.4(MLH1):c.386_392dup (p.Asp132fs) VARIANT_IN_GENE MLH1",
"confidence": 1
}
] | {
"variant": "NM_000249.4(MLH1):c.386_392dup (p.Asp132fs)",
"gene": "MLH1",
"truncation_residue": 132,
"protein_length": 756,
"fraction_lost": 0.8250000000000001
} | 1 |
co_stru_00134 | structural_effect | coding_variant | easy | 1 | NM_032043.3(BRIP1):c.237del (p.Ala80fs) introduces a premature truncation at residue 80 of BRIP1's 1249-residue protein product (AlphaFold model, mean pLDDT 63.87). Approximately how much of the protein is lost downstream of the truncation? | NM_032043.3(BRIP1):c.237del (p.Ala80fs) VARIANT_IN_GENE BRIP1 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_032043.3(BRIP1):c.237del (p.Ala80fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_032043.3(BRIP1):c.237del (p.Ala80fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
... | A | [
"A. more than half the protein (>50%)",
"B. a substantial portion (25-50%)",
"C. a small C-terminal portion (<25%)"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "BRIP1",
"source_db": "UniProt",
"payload": {
"accession": "Q9BX63",
"sequence": "MSSMWSEYTIGGVKIYFPYKAYPSQLAMMNSILRGLNSKQHCLLESPTGSGKSLALLCSALAWQQSLSGKPADEGVSEKAEVQLSCCCACHSKDFTNNDMNQGTSRHFNYPSTPPSERNGTSSTCQDSPEKTT... | [
{
"source_db": "ClinVar",
"source_id": "BRIP1",
"text": "NM_032043.3(BRIP1):c.237del (p.Ala80fs) VARIANT_IN_GENE BRIP1",
"confidence": 1
}
] | {
"variant": "NM_032043.3(BRIP1):c.237del (p.Ala80fs)",
"gene": "BRIP1",
"truncation_residue": 80,
"protein_length": 1249,
"fraction_lost": 0.936
} | 1 |
co_stru_00135 | structural_effect | coding_variant | easy | 1 | NM_001008212.2(OPTN):c.1240G>T (p.Glu414Ter) introduces a premature truncation at residue 414 of OPTN's 577-residue protein product (AlphaFold model, mean pLDDT 77.26). Approximately how much of the protein is lost downstream of the truncation? | NM_001008212.2(OPTN):c.1240G>T (p.Glu414Ter) VARIANT_IN_GENE OPTN | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_001008212.2(OPTN):c.1240G>T (p.Glu414Ter)",
"source_node_type": "VARIANT",
"source_node_label": "NM_001008212.2(OPTN):c.1240G>T (p.Glu414Ter)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confid... | C | [
"A. more than half the protein (>50%)",
"B. a small C-terminal portion (<25%)",
"C. a substantial portion (25-50%)"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "OPTN",
"source_db": "UniProt",
"payload": {
"accession": "Q96CV9",
"sequence": "MSHQPLSCLTEKEDSPSESTGNGPPHLAHPNLDTFTPEELLQQMKELLTENHQLKEAMKLNNQAMKGRFEELSAWTEKQKEERQFFEIQSKEAKERLMALSHENEKLKEELGKLKGKSERSSEDPTDDSRLPRA... | [
{
"source_db": "ClinVar",
"source_id": "OPTN",
"text": "NM_001008212.2(OPTN):c.1240G>T (p.Glu414Ter) VARIANT_IN_GENE OPTN",
"confidence": 1
}
] | {
"variant": "NM_001008212.2(OPTN):c.1240G>T (p.Glu414Ter)",
"gene": "OPTN",
"truncation_residue": 414,
"protein_length": 577,
"fraction_lost": 0.28200000000000003
} | 1 |
co_stru_00136 | structural_effect | coding_variant | easy | 1 | NM_203446.3(SYNJ1):c.2791_2795delATAAG (p.Arg932fs) introduces a premature truncation at residue 932 of SYNJ1's 1573-residue protein product (AlphaFold model, mean pLDDT 67.05). Approximately how much of the protein is lost downstream of the truncation? | NM_203446.3(SYNJ1):c.2791_2795delATAAG (p.Arg932fs) VARIANT_IN_GENE SYNJ1 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_203446.3(SYNJ1):c.2791_2795delATAAG (p.Arg932fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_203446.3(SYNJ1):c.2791_2795delATAAG (p.Arg932fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
... | A | [
"A. a substantial portion (25-50%)",
"B. a small C-terminal portion (<25%)",
"C. more than half the protein (>50%)"
] | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "NM_203446.3(SYNJ1):c.2791_2795delATAAG (p.Arg932fs)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr21",
"pos": 32656687,
"track": "phyloP100way",
"window": 20,
"scores": [
-0.0451... | [
{
"source_db": "ClinVar",
"source_id": "SYNJ1",
"text": "NM_203446.3(SYNJ1):c.2791_2795delATAAG (p.Arg932fs) VARIANT_IN_GENE SYNJ1",
"confidence": 1
}
] | {
"variant": "NM_203446.3(SYNJ1):c.2791_2795delATAAG (p.Arg932fs)",
"gene": "SYNJ1",
"truncation_residue": 932,
"protein_length": 1573,
"fraction_lost": 0.40800000000000003
} | 1 |
co_stru_00137 | structural_effect | coding_variant | easy | 1 | NM_013254.4(TBK1):c.1382del (p.Lys461fs) introduces a premature truncation at residue 461 of TBK1's 729-residue protein product (AlphaFold model, mean pLDDT 89.7). Approximately how much of the protein is lost downstream of the truncation? | NM_013254.4(TBK1):c.1382del (p.Lys461fs) VARIANT_IN_GENE TBK1 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_013254.4(TBK1):c.1382del (p.Lys461fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_013254.4(TBK1):c.1382del (p.Lys461fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1... | A | [
"A. a substantial portion (25-50%)",
"B. more than half the protein (>50%)",
"C. a small C-terminal portion (<25%)"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "TBK1",
"source_db": "UniProt",
"payload": {
"accession": "Q9UHD2",
"sequence": "MQSTSNHLWLLSDILGQGATANVFRGRHKKTGDLFAIKVFNNISFLRPVDVQMREFEVLKKLNHKNIVKLFAIEEETTTRHKVLIMEFCPCGSLYTVLEEPSNAYGLPESEFLIVLRDVVGGMNHLRENGIVHR... | [
{
"source_db": "ClinVar",
"source_id": "TBK1",
"text": "NM_013254.4(TBK1):c.1382del (p.Lys461fs) VARIANT_IN_GENE TBK1",
"confidence": 1
}
] | {
"variant": "NM_013254.4(TBK1):c.1382del (p.Lys461fs)",
"gene": "TBK1",
"truncation_residue": 461,
"protein_length": 729,
"fraction_lost": 0.368
} | 1 |
co_stru_00138 | structural_effect | coding_variant | easy | 1 | NM_001291415.2(KDM6A):c.1780C>T (p.Gln594Ter) introduces a premature truncation at residue 594 of KDM6A's 1401-residue protein product (AlphaFold model, mean pLDDT 69.89). Approximately how much of the protein is lost downstream of the truncation? | NM_001291415.2(KDM6A):c.1780C>T (p.Gln594Ter) VARIANT_IN_GENE KDM6A | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_001291415.2(KDM6A):c.1780C>T (p.Gln594Ter)",
"source_node_type": "VARIANT",
"source_node_label": "NM_001291415.2(KDM6A):c.1780C>T (p.Gln594Ter)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_conf... | C | [
"A. a small C-terminal portion (<25%)",
"B. a substantial portion (25-50%)",
"C. more than half the protein (>50%)"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "KDM6A",
"source_db": "UniProt",
"payload": {
"accession": "O15550",
"sequence": "MKSCGVSLATAAAAAAAFGDEEKKMAAGKASGESEEASPSLTAEEREALGGLDSRLFGFVRFHEDGARTKALLGKAVRCYESLILKAEGKVESDFFCQLGHFNLLLEDYPKALSAYQRYYSLQSDYWKNAAFL... | [
{
"source_db": "ClinVar",
"source_id": "KDM6A",
"text": "NM_001291415.2(KDM6A):c.1780C>T (p.Gln594Ter) VARIANT_IN_GENE KDM6A",
"confidence": 1
}
] | {
"variant": "NM_001291415.2(KDM6A):c.1780C>T (p.Gln594Ter)",
"gene": "KDM6A",
"truncation_residue": 594,
"protein_length": 1401,
"fraction_lost": 0.5760000000000001
} | 1 |
co_stru_00139 | structural_effect | coding_variant | easy | 1 | NM_017617.5(NOTCH1):c.763_773del (p.Glu255fs) introduces a premature truncation at residue 255 of NOTCH1's 2555-residue protein product (AlphaFold model, mean pLDDT 59.6). Approximately how much of the protein is lost downstream of the truncation? | NM_017617.5(NOTCH1):c.763_773del (p.Glu255fs) VARIANT_IN_GENE NOTCH1 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_017617.5(NOTCH1):c.763_773del (p.Glu255fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_017617.5(NOTCH1):c.763_773del (p.Glu255fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_conf... | A | [
"A. more than half the protein (>50%)",
"B. a substantial portion (25-50%)",
"C. a small C-terminal portion (<25%)"
] | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "NM_017617.5(NOTCH1):c.763_773del (p.Glu255fs)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr9",
"pos": 136519535,
"track": "phyloP100way",
"window": 20,
"scores": [
0.76274000000... | [
{
"source_db": "ClinVar",
"source_id": "NOTCH1",
"text": "NM_017617.5(NOTCH1):c.763_773del (p.Glu255fs) VARIANT_IN_GENE NOTCH1",
"confidence": 1
}
] | {
"variant": "NM_017617.5(NOTCH1):c.763_773del (p.Glu255fs)",
"gene": "NOTCH1",
"truncation_residue": 255,
"protein_length": 2555,
"fraction_lost": 0.9
} | 1 |
co_stru_00140 | structural_effect | coding_variant | easy | 1 | NM_015338.6(ASXL1):c.2791del (p.Glu931fs) introduces a premature truncation at residue 931 of ASXL1's 1541-residue protein product (AlphaFold model, mean pLDDT 42.21). Approximately how much of the protein is lost downstream of the truncation? | NM_015338.6(ASXL1):c.2791del (p.Glu931fs) VARIANT_IN_GENE ASXL1 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_015338.6(ASXL1):c.2791del (p.Glu931fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_015338.6(ASXL1):c.2791del (p.Glu931fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence":... | C | [
"A. a small C-terminal portion (<25%)",
"B. more than half the protein (>50%)",
"C. a substantial portion (25-50%)"
] | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "NM_015338.6(ASXL1):c.2791del (p.Glu931fs)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr20",
"pos": 32435501,
"track": "phyloP100way",
"window": 20,
"scores": [
1.72512,
... | [
{
"source_db": "ClinVar",
"source_id": "ASXL1",
"text": "NM_015338.6(ASXL1):c.2791del (p.Glu931fs) VARIANT_IN_GENE ASXL1",
"confidence": 1
}
] | {
"variant": "NM_015338.6(ASXL1):c.2791del (p.Glu931fs)",
"gene": "ASXL1",
"truncation_residue": 931,
"protein_length": 1541,
"fraction_lost": 0.396
} | 1 |
co_stru_00141 | structural_effect | coding_variant | easy | 1 | NM_012179.4(FBXO7):c.1344T>A (p.Tyr448Ter) introduces a premature truncation at residue 448 of FBXO7's 522-residue protein product (AlphaFold model, mean pLDDT 66.43). Approximately how much of the protein is lost downstream of the truncation? | NM_012179.4(FBXO7):c.1344T>A (p.Tyr448Ter) VARIANT_IN_GENE FBXO7 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_012179.4(FBXO7):c.1344T>A (p.Tyr448Ter)",
"source_node_type": "VARIANT",
"source_node_label": "NM_012179.4(FBXO7):c.1344T>A (p.Tyr448Ter)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence... | C | [
"A. more than half the protein (>50%)",
"B. a substantial portion (25-50%)",
"C. a small C-terminal portion (<25%)"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "FBXO7",
"source_db": "UniProt",
"payload": {
"accession": "Q9Y3I1",
"sequence": "MRLRVRLLKRTWPLEVPETEPTLGHLRSHLRQSLLCTWGYSSNTRFTITLNYKDPLTGDEETLASYGIVSGDLICLILQDDIPAPNIPSSTDSEHSSLQNNEQPSLATSSNQTSMQDEQPSDSFQGQAAQSGV... | [
{
"source_db": "ClinVar",
"source_id": "FBXO7",
"text": "NM_012179.4(FBXO7):c.1344T>A (p.Tyr448Ter) VARIANT_IN_GENE FBXO7",
"confidence": 1
}
] | {
"variant": "NM_012179.4(FBXO7):c.1344T>A (p.Tyr448Ter)",
"gene": "FBXO7",
"truncation_residue": 448,
"protein_length": 522,
"fraction_lost": 0.14200000000000002
} | 1 |
co_stru_00142 | structural_effect | coding_variant | easy | 1 | NM_007294.4(BRCA1):c.409_418del (p.Leu137fs) introduces a premature truncation at residue 137 of BRCA1's 1863-residue protein product (AlphaFold model, mean pLDDT 41.59). Approximately how much of the protein is lost downstream of the truncation? | NM_007294.4(BRCA1):c.409_418del (p.Leu137fs) VARIANT_IN_GENE BRCA1 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_007294.4(BRCA1):c.409_418del (p.Leu137fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_007294.4(BRCA1):c.409_418del (p.Leu137fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confid... | C | [
"A. a substantial portion (25-50%)",
"B. a small C-terminal portion (<25%)",
"C. more than half the protein (>50%)"
] | [
"expression",
"intercell_role",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "BRCA1",
"source_db": "UniProt",
"payload": {
"accession": "P38398",
"sequence": "MDLSALRVEEVQNVINAMQKILECPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRSLQESTRFSQLVEELLKIICAFQLDTGLEYANSYNFAKKENNSPEHLKDEVSIIQSMGYRNR... | [
{
"source_db": "ClinVar",
"source_id": "BRCA1",
"text": "NM_007294.4(BRCA1):c.409_418del (p.Leu137fs) VARIANT_IN_GENE BRCA1",
"confidence": 1
}
] | {
"variant": "NM_007294.4(BRCA1):c.409_418del (p.Leu137fs)",
"gene": "BRCA1",
"truncation_residue": 137,
"protein_length": 1863,
"fraction_lost": 0.926
} | 1 |
co_stru_00143 | structural_effect | coding_variant | easy | 1 | NM_002878.4(RAD51D):c.486_532del (p.Glu162fs) introduces a premature truncation at residue 162 of RAD51D's 328-residue protein product (AlphaFold model, mean pLDDT 88.06). Approximately how much of the protein is lost downstream of the truncation? | NM_002878.4(RAD51D):c.486_532del (p.Glu162fs) VARIANT_IN_GENE RAD51D | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_002878.4(RAD51D):c.486_532del (p.Glu162fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_002878.4(RAD51D):c.486_532del (p.Glu162fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_conf... | A | [
"A. more than half the protein (>50%)",
"B. a small C-terminal portion (<25%)",
"C. a substantial portion (25-50%)"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "RAD51D",
"source_db": "UniProt",
"payload": {
"accession": "O75771",
"sequence": "MGVLRVGLCPGLTEEMIQLLRSHRIKTVVDLVSADLEEVAQKCGLSYKALVALRRVLLAQFSAFPVNGADLYEELKTSTAILSTGIGSLDKLLDAGLYTGEVTEIVGGPGSGKTQVCLCMAANVAHGLQQNV... | [
{
"source_db": "ClinVar",
"source_id": "RAD51D",
"text": "NM_002878.4(RAD51D):c.486_532del (p.Glu162fs) VARIANT_IN_GENE RAD51D",
"confidence": 1
}
] | {
"variant": "NM_002878.4(RAD51D):c.486_532del (p.Glu162fs)",
"gene": "RAD51D",
"truncation_residue": 162,
"protein_length": 328,
"fraction_lost": 0.506
} | 1 |
co_stru_00144 | structural_effect | coding_variant | easy | 1 | NM_007194.4(CHEK2):c.464_465del (p.Ser155fs) introduces a premature truncation at residue 155 of CHEK2's 543-residue protein product (AlphaFold model, mean pLDDT 76.18). Approximately how much of the protein is lost downstream of the truncation? | NM_007194.4(CHEK2):c.464_465del (p.Ser155fs) VARIANT_IN_GENE CHEK2 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_007194.4(CHEK2):c.464_465del (p.Ser155fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_007194.4(CHEK2):c.464_465del (p.Ser155fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confid... | C | [
"A. a small C-terminal portion (<25%)",
"B. a substantial portion (25-50%)",
"C. more than half the protein (>50%)"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CHEK2",
"source_db": "UniProt",
"payload": {
"accession": "O96017",
"sequence": "MSRESDVEAQQSHGSSACSQPHGSVTQSQGSSSQSQGISSSSTSTMPNSSQSSHSSSGTLSSLETVSTQELYSIPEDQEPEDQEPEEPTPAPWARLWALQDGFANLECVNDNYWFGRDKSCEYCFDEPLLKRT... | [
{
"source_db": "ClinVar",
"source_id": "CHEK2",
"text": "NM_007194.4(CHEK2):c.464_465del (p.Ser155fs) VARIANT_IN_GENE CHEK2",
"confidence": 1
}
] | {
"variant": "NM_007194.4(CHEK2):c.464_465del (p.Ser155fs)",
"gene": "CHEK2",
"truncation_residue": 155,
"protein_length": 543,
"fraction_lost": 0.715
} | 1 |
co_stru_00145 | structural_effect | coding_variant | easy | 1 | NM_013254.4(TBK1):c.1856G>A (p.Trp619Ter) introduces a premature truncation at residue 619 of TBK1's 729-residue protein product (AlphaFold model, mean pLDDT 89.7). Approximately how much of the protein is lost downstream of the truncation? | NM_013254.4(TBK1):c.1856G>A (p.Trp619Ter) VARIANT_IN_GENE TBK1 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_013254.4(TBK1):c.1856G>A (p.Trp619Ter)",
"source_node_type": "VARIANT",
"source_node_label": "NM_013254.4(TBK1):c.1856G>A (p.Trp619Ter)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence":... | C | [
"A. more than half the protein (>50%)",
"B. a substantial portion (25-50%)",
"C. a small C-terminal portion (<25%)"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "TBK1",
"source_db": "UniProt",
"payload": {
"accession": "Q9UHD2",
"sequence": "MQSTSNHLWLLSDILGQGATANVFRGRHKKTGDLFAIKVFNNISFLRPVDVQMREFEVLKKLNHKNIVKLFAIEEETTTRHKVLIMEFCPCGSLYTVLEEPSNAYGLPESEFLIVLRDVVGGMNHLRENGIVHR... | [
{
"source_db": "ClinVar",
"source_id": "TBK1",
"text": "NM_013254.4(TBK1):c.1856G>A (p.Trp619Ter) VARIANT_IN_GENE TBK1",
"confidence": 1
}
] | {
"variant": "NM_013254.4(TBK1):c.1856G>A (p.Trp619Ter)",
"gene": "TBK1",
"truncation_residue": 619,
"protein_length": 729,
"fraction_lost": 0.151
} | 1 |
co_stru_00146 | structural_effect | coding_variant | easy | 1 | NM_000535.7(PMS2):c.512del (p.Lys171fs) introduces a premature truncation at residue 171 of PMS2's 862-residue protein product (AlphaFold model, mean pLDDT 70.97). Approximately how much of the protein is lost downstream of the truncation? | NM_000535.7(PMS2):c.512del (p.Lys171fs) VARIANT_IN_GENE PMS2 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000535.7(PMS2):c.512del (p.Lys171fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000535.7(PMS2):c.512del (p.Lys171fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
... | B | [
"A. a substantial portion (25-50%)",
"B. more than half the protein (>50%)",
"C. a small C-terminal portion (<25%)"
] | [
"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": "PMS2",
"text": "NM_000535.7(PMS2):c.512del (p.Lys171fs) VARIANT_IN_GENE PMS2",
"confidence": 1
}
] | {
"variant": "NM_000535.7(PMS2):c.512del (p.Lys171fs)",
"gene": "PMS2",
"truncation_residue": 171,
"protein_length": 862,
"fraction_lost": 0.802
} | 1 |
co_stru_00147 | structural_effect | coding_variant | easy | 1 | NM_007194.4(CHEK2):c.883G>T (p.Glu295Ter) introduces a premature truncation at residue 295 of CHEK2's 543-residue protein product (AlphaFold model, mean pLDDT 76.18). Approximately how much of the protein is lost downstream of the truncation? | NM_007194.4(CHEK2):c.883G>T (p.Glu295Ter) VARIANT_IN_GENE CHEK2 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_007194.4(CHEK2):c.883G>T (p.Glu295Ter)",
"source_node_type": "VARIANT",
"source_node_label": "NM_007194.4(CHEK2):c.883G>T (p.Glu295Ter)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence":... | A | [
"A. a substantial portion (25-50%)",
"B. a small C-terminal portion (<25%)",
"C. more than half the protein (>50%)"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CHEK2",
"source_db": "UniProt",
"payload": {
"accession": "O96017",
"sequence": "MSRESDVEAQQSHGSSACSQPHGSVTQSQGSSSQSQGISSSSTSTMPNSSQSSHSSSGTLSSLETVSTQELYSIPEDQEPEDQEPEEPTPAPWARLWALQDGFANLECVNDNYWFGRDKSCEYCFDEPLLKRT... | [
{
"source_db": "ClinVar",
"source_id": "CHEK2",
"text": "NM_007194.4(CHEK2):c.883G>T (p.Glu295Ter) VARIANT_IN_GENE CHEK2",
"confidence": 1
}
] | {
"variant": "NM_007194.4(CHEK2):c.883G>T (p.Glu295Ter)",
"gene": "CHEK2",
"truncation_residue": 295,
"protein_length": 543,
"fraction_lost": 0.457
} | 1 |
co_stru_00148 | structural_effect | coding_variant | easy | 1 | NM_032409.3(PINK1):c.774C>A (p.Tyr258Ter) introduces a premature truncation at residue 258 of PINK1's 581-residue protein product (AlphaFold model, mean pLDDT 77.25). Approximately how much of the protein is lost downstream of the truncation? | NM_032409.3(PINK1):c.774C>A (p.Tyr258Ter) VARIANT_IN_GENE PINK1 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_032409.3(PINK1):c.774C>A (p.Tyr258Ter)",
"source_node_type": "VARIANT",
"source_node_label": "NM_032409.3(PINK1):c.774C>A (p.Tyr258Ter)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence":... | C | [
"A. a substantial portion (25-50%)",
"B. a small C-terminal portion (<25%)",
"C. more than half the protein (>50%)"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "PINK1",
"source_db": "UniProt",
"payload": {
"accession": "Q9BXM7",
"sequence": "MAVRQALGRGLQLGRALLLRFTGKPGRAYGLGRPGPAAGCVRGERPGWAAGPGAEPRRVGLGLPNRLRFFRQSVAGLAARLQRQFVVRAWGCAGPCGRAVFLAFGLGLGLIEEKQAESRRAVSACQEIQAIFT... | [
{
"source_db": "ClinVar",
"source_id": "PINK1",
"text": "NM_032409.3(PINK1):c.774C>A (p.Tyr258Ter) VARIANT_IN_GENE PINK1",
"confidence": 1
}
] | {
"variant": "NM_032409.3(PINK1):c.774C>A (p.Tyr258Ter)",
"gene": "PINK1",
"truncation_residue": 258,
"protein_length": 581,
"fraction_lost": 0.556
} | 1 |
co_stru_00149 | structural_effect | coding_variant | easy | 1 | NM_004360.5(CDH1):c.888C>G (p.Tyr296Ter) introduces a premature truncation at residue 296 of CDH1's 882-residue protein product (AlphaFold model, mean pLDDT 79.16). Approximately how much of the protein is lost downstream of the truncation? | NM_004360.5(CDH1):c.888C>G (p.Tyr296Ter) VARIANT_IN_GENE CDH1 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_004360.5(CDH1):c.888C>G (p.Tyr296Ter)",
"source_node_type": "VARIANT",
"source_node_label": "NM_004360.5(CDH1):c.888C>G (p.Tyr296Ter)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1... | C | [
"A. a small C-terminal portion (<25%)",
"B. a substantial portion (25-50%)",
"C. more than half the protein (>50%)"
] | [
"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": "CDH1",
"text": "NM_004360.5(CDH1):c.888C>G (p.Tyr296Ter) VARIANT_IN_GENE CDH1",
"confidence": 1
}
] | {
"variant": "NM_004360.5(CDH1):c.888C>G (p.Tyr296Ter)",
"gene": "CDH1",
"truncation_residue": 296,
"protein_length": 882,
"fraction_lost": 0.664
} | 1 |
co_stru_00150 | structural_effect | coding_variant | easy | 1 | NM_020919.4(ALS2):c.2104G>T (p.Glu702Ter) introduces a premature truncation at residue 702 of ALS2's 1657-residue protein product (AlphaFold model, mean pLDDT 74.05). Approximately how much of the protein is lost downstream of the truncation? | NM_020919.4(ALS2):c.2104G>T (p.Glu702Ter) VARIANT_IN_GENE ALS2 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_020919.4(ALS2):c.2104G>T (p.Glu702Ter)",
"source_node_type": "VARIANT",
"source_node_label": "NM_020919.4(ALS2):c.2104G>T (p.Glu702Ter)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence":... | B | [
"A. a small C-terminal portion (<25%)",
"B. more than half the protein (>50%)",
"C. a substantial portion (25-50%)"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ALS2",
"source_db": "UniProt",
"payload": {
"accession": "Q96Q42",
"sequence": "MDSKKRSSTEAEGSKERGLVHIWQAGSFPITPERLPGWGGKTVLQAALGVKHGVLLTEDGEVYSFGTLPWRSGPVEICPSSPILENALVGQYVITVATGSFHSGAVTDNGVAYMWGENSAGQCAVANQQYVPEP... | [
{
"source_db": "ClinVar",
"source_id": "ALS2",
"text": "NM_020919.4(ALS2):c.2104G>T (p.Glu702Ter) VARIANT_IN_GENE ALS2",
"confidence": 1
}
] | {
"variant": "NM_020919.4(ALS2):c.2104G>T (p.Glu702Ter)",
"gene": "ALS2",
"truncation_residue": 702,
"protein_length": 1657,
"fraction_lost": 0.5760000000000001
} | 1 |
co_stru_00151 | structural_effect | coding_variant | easy | 1 | NM_014845.6(FIG4):c.1149_1150delinsT (p.Lys383fs) introduces a premature truncation at residue 383 of FIG4's 907-residue protein product (AlphaFold model, mean pLDDT 79.96). Approximately how much of the protein is lost downstream of the truncation? | NM_014845.6(FIG4):c.1149_1150delinsT (p.Lys383fs) VARIANT_IN_GENE FIG4 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_014845.6(FIG4):c.1149_1150delinsT (p.Lys383fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_014845.6(FIG4):c.1149_1150delinsT (p.Lys383fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"e... | A | [
"A. more than half the protein (>50%)",
"B. a substantial portion (25-50%)",
"C. a small C-terminal portion (<25%)"
] | [
"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": "FIG4",
"text": "NM_014845.6(FIG4):c.1149_1150delinsT (p.Lys383fs) VARIANT_IN_GENE FIG4",
"confidence": 1
}
] | {
"variant": "NM_014845.6(FIG4):c.1149_1150delinsT (p.Lys383fs)",
"gene": "FIG4",
"truncation_residue": 383,
"protein_length": 907,
"fraction_lost": 0.578
} | 1 |
co_stru_00152 | structural_effect | coding_variant | easy | 1 | NM_177924.5(ASAH1):c.53dup (p.Cys18fs) introduces a premature truncation at residue 18 of ASAH1's 395-residue protein product (AlphaFold model, mean pLDDT 91.52). Approximately how much of the protein is lost downstream of the truncation? | NM_177924.5(ASAH1):c.53dup (p.Cys18fs) VARIANT_IN_GENE ASAH1 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_177924.5(ASAH1):c.53dup (p.Cys18fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_177924.5(ASAH1):c.53dup (p.Cys18fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
... | B | [
"A. a small C-terminal portion (<25%)",
"B. more than half the protein (>50%)",
"C. a substantial portion (25-50%)"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ASAH1",
"source_db": "UniProt",
"payload": {
"accession": "Q13510",
"sequence": "MPGRSCVALVLLAAAVSCAVAQHAPPWTEDCRKSTYPPSGPTYRGAVPWYTINLDLPPYKRWHELMLDKAPVLKVIVNSLKNMINTFVPSGKIMQVVDEKLPGLLGNFPGPFEEEMKGIAAVTDIPLGEIISF... | [
{
"source_db": "ClinVar",
"source_id": "ASAH1",
"text": "NM_177924.5(ASAH1):c.53dup (p.Cys18fs) VARIANT_IN_GENE ASAH1",
"confidence": 1
}
] | {
"variant": "NM_177924.5(ASAH1):c.53dup (p.Cys18fs)",
"gene": "ASAH1",
"truncation_residue": 18,
"protein_length": 395,
"fraction_lost": 0.9540000000000001
} | 1 |
co_stru_00153 | structural_effect | coding_variant | easy | 1 | NM_001040108.2(MLH3):c.3023dup (p.Val1009fs) introduces a premature truncation at residue 1009 of MLH3's 1453-residue protein product (AlphaFold model, mean pLDDT 55.82). Approximately how much of the protein is lost downstream of the truncation? | NM_001040108.2(MLH3):c.3023dup (p.Val1009fs) VARIANT_IN_GENE MLH3 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_001040108.2(MLH3):c.3023dup (p.Val1009fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_001040108.2(MLH3):c.3023dup (p.Val1009fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confid... | B | [
"A. more than half the protein (>50%)",
"B. a substantial portion (25-50%)",
"C. a small C-terminal portion (<25%)"
] | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "NM_001040108.2(MLH3):c.3023dup (p.Val1009fs)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr14",
"pos": 75046632,
"track": "phyloP100way",
"window": 20,
"scores": [
0.271543,
... | [
{
"source_db": "ClinVar",
"source_id": "MLH3",
"text": "NM_001040108.2(MLH3):c.3023dup (p.Val1009fs) VARIANT_IN_GENE MLH3",
"confidence": 1
}
] | {
"variant": "NM_001040108.2(MLH3):c.3023dup (p.Val1009fs)",
"gene": "MLH3",
"truncation_residue": 1009,
"protein_length": 1453,
"fraction_lost": 0.306
} | 1 |
co_stru_00154 | structural_effect | coding_variant | easy | 1 | NM_004562.3(PRKN):c.992T>G (p.Leu331Ter) introduces a premature truncation at residue 331 of PRKN's 465-residue protein product (AlphaFold model, mean pLDDT 78.07). Approximately how much of the protein is lost downstream of the truncation? | NM_004562.3(PRKN):c.992T>G (p.Leu331Ter) VARIANT_IN_GENE PRKN | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_004562.3(PRKN):c.992T>G (p.Leu331Ter)",
"source_node_type": "VARIANT",
"source_node_label": "NM_004562.3(PRKN):c.992T>G (p.Leu331Ter)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1... | A | [
"A. a substantial portion (25-50%)",
"B. a small C-terminal portion (<25%)",
"C. more than half the protein (>50%)"
] | [
"conservation",
"protein_sequence",
"protein_structure"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "NM_004562.3(PRKN):c.992T>G (p.Leu331Ter)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr6",
"pos": 161548945,
"track": "phyloP100way",
"window": 20,
"scores": [
6.19867,
-... | [
{
"source_db": "ClinVar",
"source_id": "PRKN",
"text": "NM_004562.3(PRKN):c.992T>G (p.Leu331Ter) VARIANT_IN_GENE PRKN",
"confidence": 1
}
] | {
"variant": "NM_004562.3(PRKN):c.992T>G (p.Leu331Ter)",
"gene": "PRKN",
"truncation_residue": 331,
"protein_length": 465,
"fraction_lost": 0.28800000000000003
} | 1 |
co_stru_00155 | structural_effect | coding_variant | easy | 1 | NM_000789.4(ACE):c.2062C>T (p.Gln688Ter) introduces a premature truncation at residue 688 of ACE's 1306-residue protein product (AlphaFold model, mean pLDDT 90.94). Approximately how much of the protein is lost downstream of the truncation? | NM_000789.4(ACE):c.2062C>T (p.Gln688Ter) VARIANT_IN_GENE ACE | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000789.4(ACE):c.2062C>T (p.Gln688Ter)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000789.4(ACE):c.2062C>T (p.Gln688Ter)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1... | A | [
"A. a substantial portion (25-50%)",
"B. more than half the protein (>50%)",
"C. a small C-terminal portion (<25%)"
] | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "NM_000789.4(ACE):c.2062C>T (p.Gln688Ter)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr17",
"pos": 63486560,
"track": "phyloP100way",
"window": 20,
"scores": [
-1.06983,
... | [
{
"source_db": "ClinVar",
"source_id": "ACE",
"text": "NM_000789.4(ACE):c.2062C>T (p.Gln688Ter) VARIANT_IN_GENE ACE",
"confidence": 1
}
] | {
"variant": "NM_000789.4(ACE):c.2062C>T (p.Gln688Ter)",
"gene": "ACE",
"truncation_residue": 688,
"protein_length": 1306,
"fraction_lost": 0.47300000000000003
} | 1 |
co_stru_00156 | structural_effect | coding_variant | easy | 1 | NM_001008212.2(OPTN):c.1078_1079del (p.Lys360fs) introduces a premature truncation at residue 360 of OPTN's 577-residue protein product (AlphaFold model, mean pLDDT 77.26). Approximately how much of the protein is lost downstream of the truncation? | NM_001008212.2(OPTN):c.1078_1079del (p.Lys360fs) VARIANT_IN_GENE OPTN | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_001008212.2(OPTN):c.1078_1079del (p.Lys360fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_001008212.2(OPTN):c.1078_1079del (p.Lys360fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edg... | B | [
"A. more than half the protein (>50%)",
"B. a substantial portion (25-50%)",
"C. a small C-terminal portion (<25%)"
] | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "NM_001008212.2(OPTN):c.1078_1079del (p.Lys360fs)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr10",
"pos": 13125494,
"track": "phyloP100way",
"window": 20,
"scores": [
2.07424,
... | [
{
"source_db": "ClinVar",
"source_id": "OPTN",
"text": "NM_001008212.2(OPTN):c.1078_1079del (p.Lys360fs) VARIANT_IN_GENE OPTN",
"confidence": 1
}
] | {
"variant": "NM_001008212.2(OPTN):c.1078_1079del (p.Lys360fs)",
"gene": "OPTN",
"truncation_residue": 360,
"protein_length": 577,
"fraction_lost": 0.376
} | 1 |
co_stru_00157 | structural_effect | coding_variant | easy | 1 | NM_000249.4(MLH1):c.984_997del (p.His329fs) introduces a premature truncation at residue 329 of MLH1's 756-residue protein product (AlphaFold model, mean pLDDT 77.31). Approximately how much of the protein is lost downstream of the truncation? | NM_000249.4(MLH1):c.984_997del (p.His329fs) VARIANT_IN_GENE MLH1 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000249.4(MLH1):c.984_997del (p.His329fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000249.4(MLH1):c.984_997del (p.His329fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confiden... | C | [
"A. a small C-terminal portion (<25%)",
"B. a substantial portion (25-50%)",
"C. more than half the protein (>50%)"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "MLH1",
"source_db": "UniProt",
"payload": {
"accession": "P40692",
"sequence": "MSFVAGVIRRLDETVVNRIAAGEVIQRPANAIKEMIENCLDAKSTSIQVIVKEGGLKLIQIQDNGTGIRKEDLDIVCERFTTSKLQSFEDLASISTYGFRGEALASISHVAHVTITTKTADGKCAYRASYSDGK... | [
{
"source_db": "ClinVar",
"source_id": "MLH1",
"text": "NM_000249.4(MLH1):c.984_997del (p.His329fs) VARIANT_IN_GENE MLH1",
"confidence": 1
}
] | {
"variant": "NM_000249.4(MLH1):c.984_997del (p.His329fs)",
"gene": "MLH1",
"truncation_residue": 329,
"protein_length": 756,
"fraction_lost": 0.5650000000000001
} | 1 |
co_stru_00158 | structural_effect | coding_variant | easy | 1 | NM_000535.7(PMS2):c.740del (p.Pro247fs) introduces a premature truncation at residue 247 of PMS2's 862-residue protein product (AlphaFold model, mean pLDDT 70.97). Approximately how much of the protein is lost downstream of the truncation? | NM_000535.7(PMS2):c.740del (p.Pro247fs) VARIANT_IN_GENE PMS2 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000535.7(PMS2):c.740del (p.Pro247fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000535.7(PMS2):c.740del (p.Pro247fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
... | A | [
"A. more than half the protein (>50%)",
"B. a substantial portion (25-50%)",
"C. a small C-terminal portion (<25%)"
] | [
"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": "PMS2",
"text": "NM_000535.7(PMS2):c.740del (p.Pro247fs) VARIANT_IN_GENE PMS2",
"confidence": 1
}
] | {
"variant": "NM_000535.7(PMS2):c.740del (p.Pro247fs)",
"gene": "PMS2",
"truncation_residue": 247,
"protein_length": 862,
"fraction_lost": 0.713
} | 1 |
co_stru_00159 | structural_effect | coding_variant | easy | 1 | NM_014845.6(FIG4):c.490del (p.Tyr164fs) introduces a premature truncation at residue 164 of FIG4's 907-residue protein product (AlphaFold model, mean pLDDT 79.96). Approximately how much of the protein is lost downstream of the truncation? | NM_014845.6(FIG4):c.490del (p.Tyr164fs) VARIANT_IN_GENE FIG4 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_014845.6(FIG4):c.490del (p.Tyr164fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_014845.6(FIG4):c.490del (p.Tyr164fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
... | C | [
"A. a substantial portion (25-50%)",
"B. a small C-terminal portion (<25%)",
"C. more than half the protein (>50%)"
] | [
"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": "FIG4",
"text": "NM_014845.6(FIG4):c.490del (p.Tyr164fs) VARIANT_IN_GENE FIG4",
"confidence": 1
}
] | {
"variant": "NM_014845.6(FIG4):c.490del (p.Tyr164fs)",
"gene": "FIG4",
"truncation_residue": 164,
"protein_length": 907,
"fraction_lost": 0.8190000000000001
} | 1 |
co_stru_00160 | structural_effect | coding_variant | easy | 1 | NM_017617.5(NOTCH1):c.2380G>T (p.Glu794Ter) introduces a premature truncation at residue 794 of NOTCH1's 2555-residue protein product (AlphaFold model, mean pLDDT 59.6). Approximately how much of the protein is lost downstream of the truncation? | NM_017617.5(NOTCH1):c.2380G>T (p.Glu794Ter) VARIANT_IN_GENE NOTCH1 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_017617.5(NOTCH1):c.2380G>T (p.Glu794Ter)",
"source_node_type": "VARIANT",
"source_node_label": "NM_017617.5(NOTCH1):c.2380G>T (p.Glu794Ter)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confiden... | A | [
"A. more than half the protein (>50%)",
"B. a small C-terminal portion (<25%)",
"C. a substantial portion (25-50%)"
] | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "NM_017617.5(NOTCH1):c.2380G>T (p.Glu794Ter)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr9",
"pos": 136513108,
"track": "phyloP100way",
"window": 20,
"scores": [
2.10934,
... | [
{
"source_db": "ClinVar",
"source_id": "NOTCH1",
"text": "NM_017617.5(NOTCH1):c.2380G>T (p.Glu794Ter) VARIANT_IN_GENE NOTCH1",
"confidence": 1
}
] | {
"variant": "NM_017617.5(NOTCH1):c.2380G>T (p.Glu794Ter)",
"gene": "NOTCH1",
"truncation_residue": 794,
"protein_length": 2555,
"fraction_lost": 0.6890000000000001
} | 1 |
co_stru_00161 | structural_effect | coding_variant | easy | 1 | NM_014845.6(FIG4):c.837dup (p.Ala280fs) introduces a premature truncation at residue 280 of FIG4's 907-residue protein product (AlphaFold model, mean pLDDT 79.96). Approximately how much of the protein is lost downstream of the truncation? | NM_014845.6(FIG4):c.837dup (p.Ala280fs) VARIANT_IN_GENE FIG4 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_014845.6(FIG4):c.837dup (p.Ala280fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_014845.6(FIG4):c.837dup (p.Ala280fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
... | B | [
"A. a substantial portion (25-50%)",
"B. more than half the protein (>50%)",
"C. a small C-terminal portion (<25%)"
] | [
"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": "FIG4",
"text": "NM_014845.6(FIG4):c.837dup (p.Ala280fs) VARIANT_IN_GENE FIG4",
"confidence": 1
}
] | {
"variant": "NM_014845.6(FIG4):c.837dup (p.Ala280fs)",
"gene": "FIG4",
"truncation_residue": 280,
"protein_length": 907,
"fraction_lost": 0.6910000000000001
} | 1 |
co_stru_00162 | structural_effect | coding_variant | easy | 1 | NM_032043.3(BRIP1):c.1004G>A (p.Trp335Ter) introduces a premature truncation at residue 335 of BRIP1's 1249-residue protein product (AlphaFold model, mean pLDDT 63.87). Approximately how much of the protein is lost downstream of the truncation? | NM_032043.3(BRIP1):c.1004G>A (p.Trp335Ter) VARIANT_IN_GENE BRIP1 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_032043.3(BRIP1):c.1004G>A (p.Trp335Ter)",
"source_node_type": "VARIANT",
"source_node_label": "NM_032043.3(BRIP1):c.1004G>A (p.Trp335Ter)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence... | C | [
"A. a substantial portion (25-50%)",
"B. a small C-terminal portion (<25%)",
"C. more than half the protein (>50%)"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "BRIP1",
"source_db": "UniProt",
"payload": {
"accession": "Q9BX63",
"sequence": "MSSMWSEYTIGGVKIYFPYKAYPSQLAMMNSILRGLNSKQHCLLESPTGSGKSLALLCSALAWQQSLSGKPADEGVSEKAEVQLSCCCACHSKDFTNNDMNQGTSRHFNYPSTPPSERNGTSSTCQDSPEKTT... | [
{
"source_db": "ClinVar",
"source_id": "BRIP1",
"text": "NM_032043.3(BRIP1):c.1004G>A (p.Trp335Ter) VARIANT_IN_GENE BRIP1",
"confidence": 1
}
] | {
"variant": "NM_032043.3(BRIP1):c.1004G>A (p.Trp335Ter)",
"gene": "BRIP1",
"truncation_residue": 335,
"protein_length": 1249,
"fraction_lost": 0.732
} | 1 |
co_stru_00163 | structural_effect | coding_variant | easy | 1 | NM_024675.4(PALB2):c.1033_1034insCTTT (p.Leu345fs) introduces a premature truncation at residue 345 of PALB2's 1186-residue protein product (AlphaFold model, mean pLDDT 53.81). Approximately how much of the protein is lost downstream of the truncation? | NM_024675.4(PALB2):c.1033_1034insCTTT (p.Leu345fs) VARIANT_IN_GENE PALB2 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_024675.4(PALB2):c.1033_1034insCTTT (p.Leu345fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_024675.4(PALB2):c.1033_1034insCTTT (p.Leu345fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
... | A | [
"A. more than half the protein (>50%)",
"B. a small C-terminal portion (<25%)",
"C. a substantial portion (25-50%)"
] | [
"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": "PALB2",
"text": "NM_024675.4(PALB2):c.1033_1034insCTTT (p.Leu345fs) VARIANT_IN_GENE PALB2",
"confidence": 1
}
] | {
"variant": "NM_024675.4(PALB2):c.1033_1034insCTTT (p.Leu345fs)",
"gene": "PALB2",
"truncation_residue": 345,
"protein_length": 1186,
"fraction_lost": 0.709
} | 1 |
co_stru_00164 | structural_effect | coding_variant | easy | 1 | NM_000179.3(MSH6):c.3733_3737dup (p.Thr1247fs) introduces a premature truncation at residue 1247 of MSH6's 1360-residue protein product (AlphaFold model, mean pLDDT 77.09). Approximately how much of the protein is lost downstream of the truncation? | NM_000179.3(MSH6):c.3733_3737dup (p.Thr1247fs) VARIANT_IN_GENE MSH6 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000179.3(MSH6):c.3733_3737dup (p.Thr1247fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000179.3(MSH6):c.3733_3737dup (p.Thr1247fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_co... | B | [
"A. more than half the protein (>50%)",
"B. a small C-terminal portion (<25%)",
"C. a substantial portion (25-50%)"
] | [
"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": "MSH6",
"text": "NM_000179.3(MSH6):c.3733_3737dup (p.Thr1247fs) VARIANT_IN_GENE MSH6",
"confidence": 1
}
] | {
"variant": "NM_000179.3(MSH6):c.3733_3737dup (p.Thr1247fs)",
"gene": "MSH6",
"truncation_residue": 1247,
"protein_length": 1360,
"fraction_lost": 0.083
} | 1 |
co_stru_00165 | structural_effect | coding_variant | easy | 1 | NM_000465.4(BARD1):c.2203C>T (p.Gln735Ter) introduces a premature truncation at residue 735 of BARD1's 777-residue protein product (AlphaFold model, mean pLDDT 64.16). Approximately how much of the protein is lost downstream of the truncation? | NM_000465.4(BARD1):c.2203C>T (p.Gln735Ter) VARIANT_IN_GENE BARD1 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000465.4(BARD1):c.2203C>T (p.Gln735Ter)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000465.4(BARD1):c.2203C>T (p.Gln735Ter)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence... | C | [
"A. more than half the protein (>50%)",
"B. a substantial portion (25-50%)",
"C. a small C-terminal portion (<25%)"
] | [
"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": "BARD1",
"text": "NM_000465.4(BARD1):c.2203C>T (p.Gln735Ter) VARIANT_IN_GENE BARD1",
"confidence": 1
}
] | {
"variant": "NM_000465.4(BARD1):c.2203C>T (p.Gln735Ter)",
"gene": "BARD1",
"truncation_residue": 735,
"protein_length": 777,
"fraction_lost": 0.054
} | 1 |
co_stru_00166 | structural_effect | coding_variant | easy | 1 | NM_006231.4(POLE):c.2175_2179del (p.Asp725fs) introduces a premature truncation at residue 725 of POLE's 2286-residue protein product (AlphaFold model, mean pLDDT 79.72). Approximately how much of the protein is lost downstream of the truncation? | NM_006231.4(POLE):c.2175_2179del (p.Asp725fs) VARIANT_IN_GENE POLE | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_006231.4(POLE):c.2175_2179del (p.Asp725fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_006231.4(POLE):c.2175_2179del (p.Asp725fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_conf... | A | [
"A. more than half the protein (>50%)",
"B. a substantial portion (25-50%)",
"C. a small C-terminal portion (<25%)"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "POLE",
"source_db": "UniProt",
"payload": {
"accession": "Q07864",
"sequence": "MSLRSGGRRRADPGADGEASRDDGATSSVSALKRLERSQWTDKMDLRFGFERLKEPGEKTGWLINMHPTEILDEDKRLGSAVDYYFIQDDGSRFKVALPYKPYFYIATRKGCEREVSSFLSKKFQGKIAKVETV... | [
{
"source_db": "ClinVar",
"source_id": "POLE",
"text": "NM_006231.4(POLE):c.2175_2179del (p.Asp725fs) VARIANT_IN_GENE POLE",
"confidence": 1
}
] | {
"variant": "NM_006231.4(POLE):c.2175_2179del (p.Asp725fs)",
"gene": "POLE",
"truncation_residue": 725,
"protein_length": 2286,
"fraction_lost": 0.683
} | 1 |
co_stru_00167 | structural_effect | coding_variant | easy | 1 | NM_001903.5(CTNNA1):c.926_936del (p.Leu309fs) introduces a premature truncation at residue 309 of CTNNA1's 906-residue protein product (AlphaFold model, mean pLDDT 82.94). Approximately how much of the protein is lost downstream of the truncation? | NM_001903.5(CTNNA1):c.926_936del (p.Leu309fs) VARIANT_IN_GENE CTNNA1 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_001903.5(CTNNA1):c.926_936del (p.Leu309fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_001903.5(CTNNA1):c.926_936del (p.Leu309fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_conf... | B | [
"A. a small C-terminal portion (<25%)",
"B. more than half the protein (>50%)",
"C. a substantial portion (25-50%)"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CTNNA1",
"source_db": "UniProt",
"payload": {
"accession": "P35221",
"sequence": "MTAVHAGNINFKWDPKSLEIRTLAVERLLEPLVTQVTTLVNTNSKGPSNKKRGRSKKAHVLAASVEQATENFLEKGDKIAKESQFLKEELVAAVEDVRKQGDLMKAAAGEFADDPCSSVKRGNMVRAARALL... | [
{
"source_db": "ClinVar",
"source_id": "CTNNA1",
"text": "NM_001903.5(CTNNA1):c.926_936del (p.Leu309fs) VARIANT_IN_GENE CTNNA1",
"confidence": 1
}
] | {
"variant": "NM_001903.5(CTNNA1):c.926_936del (p.Leu309fs)",
"gene": "CTNNA1",
"truncation_residue": 309,
"protein_length": 906,
"fraction_lost": 0.659
} | 1 |
co_stru_00168 | structural_effect | coding_variant | easy | 1 | NM_000179.3(MSH6):c.2036T>A (p.Leu679Ter) introduces a premature truncation at residue 679 of MSH6's 1360-residue protein product (AlphaFold model, mean pLDDT 77.09). Approximately how much of the protein is lost downstream of the truncation? | NM_000179.3(MSH6):c.2036T>A (p.Leu679Ter) VARIANT_IN_GENE MSH6 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000179.3(MSH6):c.2036T>A (p.Leu679Ter)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000179.3(MSH6):c.2036T>A (p.Leu679Ter)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence":... | A | [
"A. more than half the protein (>50%)",
"B. a small C-terminal portion (<25%)",
"C. a substantial portion (25-50%)"
] | [
"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": "MSH6",
"text": "NM_000179.3(MSH6):c.2036T>A (p.Leu679Ter) VARIANT_IN_GENE MSH6",
"confidence": 1
}
] | {
"variant": "NM_000179.3(MSH6):c.2036T>A (p.Leu679Ter)",
"gene": "MSH6",
"truncation_residue": 679,
"protein_length": 1360,
"fraction_lost": 0.501
} | 1 |
co_stru_00169 | structural_effect | coding_variant | easy | 1 | NM_000249.4(MLH1):c.1659del (p.Lys554fs) introduces a premature truncation at residue 554 of MLH1's 756-residue protein product (AlphaFold model, mean pLDDT 77.31). Approximately how much of the protein is lost downstream of the truncation? | NM_000249.4(MLH1):c.1659del (p.Lys554fs) VARIANT_IN_GENE MLH1 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000249.4(MLH1):c.1659del (p.Lys554fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000249.4(MLH1):c.1659del (p.Lys554fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1... | A | [
"A. a substantial portion (25-50%)",
"B. more than half the protein (>50%)",
"C. a small C-terminal portion (<25%)"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "MLH1",
"source_db": "UniProt",
"payload": {
"accession": "P40692",
"sequence": "MSFVAGVIRRLDETVVNRIAAGEVIQRPANAIKEMIENCLDAKSTSIQVIVKEGGLKLIQIQDNGTGIRKEDLDIVCERFTTSKLQSFEDLASISTYGFRGEALASISHVAHVTITTKTADGKCAYRASYSDGK... | [
{
"source_db": "ClinVar",
"source_id": "MLH1",
"text": "NM_000249.4(MLH1):c.1659del (p.Lys554fs) VARIANT_IN_GENE MLH1",
"confidence": 1
}
] | {
"variant": "NM_000249.4(MLH1):c.1659del (p.Lys554fs)",
"gene": "MLH1",
"truncation_residue": 554,
"protein_length": 756,
"fraction_lost": 0.267
} | 1 |
co_stru_00170 | structural_effect | coding_variant | easy | 1 | NM_000535.7(PMS2):c.375C>A (p.Cys125Ter) introduces a premature truncation at residue 125 of PMS2's 862-residue protein product (AlphaFold model, mean pLDDT 70.97). Approximately how much of the protein is lost downstream of the truncation? | NM_000535.7(PMS2):c.375C>A (p.Cys125Ter) VARIANT_IN_GENE PMS2 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000535.7(PMS2):c.375C>A (p.Cys125Ter)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000535.7(PMS2):c.375C>A (p.Cys125Ter)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1... | C | [
"A. a substantial portion (25-50%)",
"B. a small C-terminal portion (<25%)",
"C. more than half the protein (>50%)"
] | [
"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": "PMS2",
"text": "NM_000535.7(PMS2):c.375C>A (p.Cys125Ter) VARIANT_IN_GENE PMS2",
"confidence": 1
}
] | {
"variant": "NM_000535.7(PMS2):c.375C>A (p.Cys125Ter)",
"gene": "PMS2",
"truncation_residue": 125,
"protein_length": 862,
"fraction_lost": 0.855
} | 1 |
co_stru_00171 | structural_effect | coding_variant | easy | 1 | NM_000535.7(PMS2):c.232G>T (p.Glu78Ter) introduces a premature truncation at residue 78 of PMS2's 862-residue protein product (AlphaFold model, mean pLDDT 70.97). Approximately how much of the protein is lost downstream of the truncation? | NM_000535.7(PMS2):c.232G>T (p.Glu78Ter) VARIANT_IN_GENE PMS2 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000535.7(PMS2):c.232G>T (p.Glu78Ter)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000535.7(PMS2):c.232G>T (p.Glu78Ter)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
... | B | [
"A. a small C-terminal portion (<25%)",
"B. more than half the protein (>50%)",
"C. a substantial portion (25-50%)"
] | [
"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": "PMS2",
"text": "NM_000535.7(PMS2):c.232G>T (p.Glu78Ter) VARIANT_IN_GENE PMS2",
"confidence": 1
}
] | {
"variant": "NM_000535.7(PMS2):c.232G>T (p.Glu78Ter)",
"gene": "PMS2",
"truncation_residue": 78,
"protein_length": 862,
"fraction_lost": 0.91
} | 1 |
co_stru_00172 | structural_effect | coding_variant | easy | 1 | NM_004360.5(CDH1):c.617_623dup (p.Glu208delinsAspTyrTer) introduces a premature truncation at residue 208 of CDH1's 882-residue protein product (AlphaFold model, mean pLDDT 79.16). Approximately how much of the protein is lost downstream of the truncation? | NM_004360.5(CDH1):c.617_623dup (p.Glu208delinsAspTyrTer) VARIANT_IN_GENE CDH1 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_004360.5(CDH1):c.617_623dup (p.Glu208delinsAspTyrTer)",
"source_node_type": "VARIANT",
"source_node_label": "NM_004360.5(CDH1):c.617_623dup (p.Glu208delinsAspTyrTer)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "cura... | A | [
"A. more than half the protein (>50%)",
"B. a substantial portion (25-50%)",
"C. a small C-terminal portion (<25%)"
] | [
"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": "CDH1",
"text": "NM_004360.5(CDH1):c.617_623dup (p.Glu208delinsAspTyrTer) VARIANT_IN_GENE CDH1",
"confidence": 1
}
] | {
"variant": "NM_004360.5(CDH1):c.617_623dup (p.Glu208delinsAspTyrTer)",
"gene": "CDH1",
"truncation_residue": 208,
"protein_length": 882,
"fraction_lost": 0.764
} | 1 |
co_stru_00173 | structural_effect | coding_variant | easy | 1 | NM_007294.4(BRCA1):c.4410del (p.Gly1471fs) introduces a premature truncation at residue 1471 of BRCA1's 1863-residue protein product (AlphaFold model, mean pLDDT 41.59). Approximately how much of the protein is lost downstream of the truncation? | NM_007294.4(BRCA1):c.4410del (p.Gly1471fs) VARIANT_IN_GENE BRCA1 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_007294.4(BRCA1):c.4410del (p.Gly1471fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_007294.4(BRCA1):c.4410del (p.Gly1471fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence... | B | [
"A. a substantial portion (25-50%)",
"B. a small C-terminal portion (<25%)",
"C. more than half the protein (>50%)"
] | [
"expression",
"intercell_role",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "BRCA1",
"source_db": "UniProt",
"payload": {
"accession": "P38398",
"sequence": "MDLSALRVEEVQNVINAMQKILECPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRSLQESTRFSQLVEELLKIICAFQLDTGLEYANSYNFAKKENNSPEHLKDEVSIIQSMGYRNR... | [
{
"source_db": "ClinVar",
"source_id": "BRCA1",
"text": "NM_007294.4(BRCA1):c.4410del (p.Gly1471fs) VARIANT_IN_GENE BRCA1",
"confidence": 1
}
] | {
"variant": "NM_007294.4(BRCA1):c.4410del (p.Gly1471fs)",
"gene": "BRCA1",
"truncation_residue": 1471,
"protein_length": 1863,
"fraction_lost": 0.21
} | 1 |
co_stru_00174 | structural_effect | coding_variant | easy | 1 | NM_006231.4(POLE):c.4830del (p.Ile1611fs) introduces a premature truncation at residue 1611 of POLE's 2286-residue protein product (AlphaFold model, mean pLDDT 79.72). Approximately how much of the protein is lost downstream of the truncation? | NM_006231.4(POLE):c.4830del (p.Ile1611fs) VARIANT_IN_GENE POLE | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_006231.4(POLE):c.4830del (p.Ile1611fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_006231.4(POLE):c.4830del (p.Ile1611fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence":... | A | [
"A. a substantial portion (25-50%)",
"B. more than half the protein (>50%)",
"C. a small C-terminal portion (<25%)"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "POLE",
"source_db": "UniProt",
"payload": {
"accession": "Q07864",
"sequence": "MSLRSGGRRRADPGADGEASRDDGATSSVSALKRLERSQWTDKMDLRFGFERLKEPGEKTGWLINMHPTEILDEDKRLGSAVDYYFIQDDGSRFKVALPYKPYFYIATRKGCEREVSSFLSKKFQGKIAKVETV... | [
{
"source_db": "ClinVar",
"source_id": "POLE",
"text": "NM_006231.4(POLE):c.4830del (p.Ile1611fs) VARIANT_IN_GENE POLE",
"confidence": 1
}
] | {
"variant": "NM_006231.4(POLE):c.4830del (p.Ile1611fs)",
"gene": "POLE",
"truncation_residue": 1611,
"protein_length": 2286,
"fraction_lost": 0.295
} | 1 |
co_stru_00175 | structural_effect | coding_variant | easy | 1 | NM_007194.4(CHEK2):c.743del (p.Ile248fs) introduces a premature truncation at residue 248 of CHEK2's 543-residue protein product (AlphaFold model, mean pLDDT 76.18). Approximately how much of the protein is lost downstream of the truncation? | NM_007194.4(CHEK2):c.743del (p.Ile248fs) VARIANT_IN_GENE CHEK2 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_007194.4(CHEK2):c.743del (p.Ile248fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_007194.4(CHEK2):c.743del (p.Ile248fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1... | B | [
"A. a small C-terminal portion (<25%)",
"B. more than half the protein (>50%)",
"C. a substantial portion (25-50%)"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CHEK2",
"source_db": "UniProt",
"payload": {
"accession": "O96017",
"sequence": "MSRESDVEAQQSHGSSACSQPHGSVTQSQGSSSQSQGISSSSTSTMPNSSQSSHSSSGTLSSLETVSTQELYSIPEDQEPEDQEPEEPTPAPWARLWALQDGFANLECVNDNYWFGRDKSCEYCFDEPLLKRT... | [
{
"source_db": "ClinVar",
"source_id": "CHEK2",
"text": "NM_007194.4(CHEK2):c.743del (p.Ile248fs) VARIANT_IN_GENE CHEK2",
"confidence": 1
}
] | {
"variant": "NM_007194.4(CHEK2):c.743del (p.Ile248fs)",
"gene": "CHEK2",
"truncation_residue": 248,
"protein_length": 543,
"fraction_lost": 0.543
} | 1 |
co_stru_00176 | structural_effect | coding_variant | easy | 1 | NM_000535.7(PMS2):c.2341C>T (p.Gln781Ter) introduces a premature truncation at residue 781 of PMS2's 862-residue protein product (AlphaFold model, mean pLDDT 70.97). Approximately how much of the protein is lost downstream of the truncation? | NM_000535.7(PMS2):c.2341C>T (p.Gln781Ter) VARIANT_IN_GENE PMS2 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000535.7(PMS2):c.2341C>T (p.Gln781Ter)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000535.7(PMS2):c.2341C>T (p.Gln781Ter)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence":... | A | [
"A. a small C-terminal portion (<25%)",
"B. a substantial portion (25-50%)",
"C. more than half the protein (>50%)"
] | [
"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": "PMS2",
"text": "NM_000535.7(PMS2):c.2341C>T (p.Gln781Ter) VARIANT_IN_GENE PMS2",
"confidence": 1
}
] | {
"variant": "NM_000535.7(PMS2):c.2341C>T (p.Gln781Ter)",
"gene": "PMS2",
"truncation_residue": 781,
"protein_length": 862,
"fraction_lost": 0.094
} | 1 |
co_stru_00177 | structural_effect | coding_variant | easy | 1 | NM_007294.4(BRCA1):c.3755dup (p.Ser1253fs) introduces a premature truncation at residue 1253 of BRCA1's 1863-residue protein product (AlphaFold model, mean pLDDT 41.59). Approximately how much of the protein is lost downstream of the truncation? | NM_007294.4(BRCA1):c.3755dup (p.Ser1253fs) VARIANT_IN_GENE BRCA1 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_007294.4(BRCA1):c.3755dup (p.Ser1253fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_007294.4(BRCA1):c.3755dup (p.Ser1253fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence... | B | [
"A. more than half the protein (>50%)",
"B. a substantial portion (25-50%)",
"C. a small C-terminal portion (<25%)"
] | [
"expression",
"intercell_role",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "BRCA1",
"source_db": "UniProt",
"payload": {
"accession": "P38398",
"sequence": "MDLSALRVEEVQNVINAMQKILECPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRSLQESTRFSQLVEELLKIICAFQLDTGLEYANSYNFAKKENNSPEHLKDEVSIIQSMGYRNR... | [
{
"source_db": "ClinVar",
"source_id": "BRCA1",
"text": "NM_007294.4(BRCA1):c.3755dup (p.Ser1253fs) VARIANT_IN_GENE BRCA1",
"confidence": 1
}
] | {
"variant": "NM_007294.4(BRCA1):c.3755dup (p.Ser1253fs)",
"gene": "BRCA1",
"truncation_residue": 1253,
"protein_length": 1863,
"fraction_lost": 0.327
} | 1 |
co_stru_00178 | structural_effect | coding_variant | easy | 1 | NM_032043.3(BRIP1):c.243del (p.Val82fs) introduces a premature truncation at residue 82 of BRIP1's 1249-residue protein product (AlphaFold model, mean pLDDT 63.87). Approximately how much of the protein is lost downstream of the truncation? | NM_032043.3(BRIP1):c.243del (p.Val82fs) VARIANT_IN_GENE BRIP1 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_032043.3(BRIP1):c.243del (p.Val82fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_032043.3(BRIP1):c.243del (p.Val82fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
... | A | [
"A. more than half the protein (>50%)",
"B. a small C-terminal portion (<25%)",
"C. a substantial portion (25-50%)"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "BRIP1",
"source_db": "UniProt",
"payload": {
"accession": "Q9BX63",
"sequence": "MSSMWSEYTIGGVKIYFPYKAYPSQLAMMNSILRGLNSKQHCLLESPTGSGKSLALLCSALAWQQSLSGKPADEGVSEKAEVQLSCCCACHSKDFTNNDMNQGTSRHFNYPSTPPSERNGTSSTCQDSPEKTT... | [
{
"source_db": "ClinVar",
"source_id": "BRIP1",
"text": "NM_032043.3(BRIP1):c.243del (p.Val82fs) VARIANT_IN_GENE BRIP1",
"confidence": 1
}
] | {
"variant": "NM_032043.3(BRIP1):c.243del (p.Val82fs)",
"gene": "BRIP1",
"truncation_residue": 82,
"protein_length": 1249,
"fraction_lost": 0.934
} | 1 |
co_stru_00179 | structural_effect | coding_variant | easy | 1 | NM_138576.4(BCL11B):c.2443del (p.Arg815fs) introduces a premature truncation at residue 815 of BCL11B's 894-residue protein product (AlphaFold model, mean pLDDT 50.82). Approximately how much of the protein is lost downstream of the truncation? | NM_138576.4(BCL11B):c.2443del (p.Arg815fs) VARIANT_IN_GENE BCL11B | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_138576.4(BCL11B):c.2443del (p.Arg815fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_138576.4(BCL11B):c.2443del (p.Arg815fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence... | A | [
"A. a small C-terminal portion (<25%)",
"B. a substantial portion (25-50%)",
"C. more than half the protein (>50%)"
] | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "NM_138576.4(BCL11B):c.2443del (p.Arg815fs)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr14",
"pos": 99174393,
"track": "phyloP100way",
"window": 20,
"scores": [
1.96465000000000... | [
{
"source_db": "ClinVar",
"source_id": "BCL11B",
"text": "NM_138576.4(BCL11B):c.2443del (p.Arg815fs) VARIANT_IN_GENE BCL11B",
"confidence": 1
}
] | {
"variant": "NM_138576.4(BCL11B):c.2443del (p.Arg815fs)",
"gene": "BCL11B",
"truncation_residue": 815,
"protein_length": 894,
"fraction_lost": 0.088
} | 1 |
co_stru_00180 | structural_effect | coding_variant | easy | 1 | NM_006231.4(POLE):c.3912dup (p.Gly1305fs) introduces a premature truncation at residue 1305 of POLE's 2286-residue protein product (AlphaFold model, mean pLDDT 79.72). Approximately how much of the protein is lost downstream of the truncation? | NM_006231.4(POLE):c.3912dup (p.Gly1305fs) VARIANT_IN_GENE POLE | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_006231.4(POLE):c.3912dup (p.Gly1305fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_006231.4(POLE):c.3912dup (p.Gly1305fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence":... | C | [
"A. more than half the protein (>50%)",
"B. a small C-terminal portion (<25%)",
"C. a substantial portion (25-50%)"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "POLE",
"source_db": "UniProt",
"payload": {
"accession": "Q07864",
"sequence": "MSLRSGGRRRADPGADGEASRDDGATSSVSALKRLERSQWTDKMDLRFGFERLKEPGEKTGWLINMHPTEILDEDKRLGSAVDYYFIQDDGSRFKVALPYKPYFYIATRKGCEREVSSFLSKKFQGKIAKVETV... | [
{
"source_db": "ClinVar",
"source_id": "POLE",
"text": "NM_006231.4(POLE):c.3912dup (p.Gly1305fs) VARIANT_IN_GENE POLE",
"confidence": 1
}
] | {
"variant": "NM_006231.4(POLE):c.3912dup (p.Gly1305fs)",
"gene": "POLE",
"truncation_residue": 1305,
"protein_length": 2286,
"fraction_lost": 0.429
} | 1 |
co_stru_00181 | structural_effect | coding_variant | easy | 1 | NM_007294.4(BRCA1):c.4387dup (p.Tyr1463fs) introduces a premature truncation at residue 1463 of BRCA1's 1863-residue protein product (AlphaFold model, mean pLDDT 41.59). Approximately how much of the protein is lost downstream of the truncation? | NM_007294.4(BRCA1):c.4387dup (p.Tyr1463fs) VARIANT_IN_GENE BRCA1 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_007294.4(BRCA1):c.4387dup (p.Tyr1463fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_007294.4(BRCA1):c.4387dup (p.Tyr1463fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence... | A | [
"A. a small C-terminal portion (<25%)",
"B. a substantial portion (25-50%)",
"C. more than half the protein (>50%)"
] | [
"expression",
"intercell_role",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "BRCA1",
"source_db": "UniProt",
"payload": {
"accession": "P38398",
"sequence": "MDLSALRVEEVQNVINAMQKILECPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRSLQESTRFSQLVEELLKIICAFQLDTGLEYANSYNFAKKENNSPEHLKDEVSIIQSMGYRNR... | [
{
"source_db": "ClinVar",
"source_id": "BRCA1",
"text": "NM_007294.4(BRCA1):c.4387dup (p.Tyr1463fs) VARIANT_IN_GENE BRCA1",
"confidence": 1
}
] | {
"variant": "NM_007294.4(BRCA1):c.4387dup (p.Tyr1463fs)",
"gene": "BRCA1",
"truncation_residue": 1463,
"protein_length": 1863,
"fraction_lost": 0.215
} | 1 |
co_stru_00182 | structural_effect | coding_variant | easy | 1 | NM_007194.4(CHEK2):c.504del (p.Phe169fs) introduces a premature truncation at residue 169 of CHEK2's 543-residue protein product (AlphaFold model, mean pLDDT 76.18). Approximately how much of the protein is lost downstream of the truncation? | NM_007194.4(CHEK2):c.504del (p.Phe169fs) VARIANT_IN_GENE CHEK2 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_007194.4(CHEK2):c.504del (p.Phe169fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_007194.4(CHEK2):c.504del (p.Phe169fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1... | B | [
"A. a small C-terminal portion (<25%)",
"B. more than half the protein (>50%)",
"C. a substantial portion (25-50%)"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CHEK2",
"source_db": "UniProt",
"payload": {
"accession": "O96017",
"sequence": "MSRESDVEAQQSHGSSACSQPHGSVTQSQGSSSQSQGISSSSTSTMPNSSQSSHSSSGTLSSLETVSTQELYSIPEDQEPEDQEPEEPTPAPWARLWALQDGFANLECVNDNYWFGRDKSCEYCFDEPLLKRT... | [
{
"source_db": "ClinVar",
"source_id": "CHEK2",
"text": "NM_007194.4(CHEK2):c.504del (p.Phe169fs) VARIANT_IN_GENE CHEK2",
"confidence": 1
}
] | {
"variant": "NM_007194.4(CHEK2):c.504del (p.Phe169fs)",
"gene": "CHEK2",
"truncation_residue": 169,
"protein_length": 543,
"fraction_lost": 0.6890000000000001
} | 1 |
co_stru_00183 | structural_effect | coding_variant | easy | 1 | NM_006158.5(NEFL):c.760del (p.Leu254fs) introduces a premature truncation at residue 254 of NEFL's 543-residue protein product (AlphaFold model, mean pLDDT 73.03). Approximately how much of the protein is lost downstream of the truncation? | NM_006158.5(NEFL):c.760del (p.Leu254fs) VARIANT_IN_GENE NEFL | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_006158.5(NEFL):c.760del (p.Leu254fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_006158.5(NEFL):c.760del (p.Leu254fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
... | C | [
"A. a substantial portion (25-50%)",
"B. a small C-terminal portion (<25%)",
"C. more than half the protein (>50%)"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "NEFL",
"source_db": "UniProt",
"payload": {
"accession": "P07196",
"sequence": "MSSFSYEPYYSTSYKRRYVETPRVHISSVRSGYSTARSAYSSYSAPVSSSLSVRRSYSSSSGSLMPSLENLDLSQVAAISNDLKSIRTQEKAQLQDLNDRFASFIERVHELEQQNKVLEAELLVLRQKHSEPSR... | [
{
"source_db": "ClinVar",
"source_id": "NEFL",
"text": "NM_006158.5(NEFL):c.760del (p.Leu254fs) VARIANT_IN_GENE NEFL",
"confidence": 1
}
] | {
"variant": "NM_006158.5(NEFL):c.760del (p.Leu254fs)",
"gene": "NEFL",
"truncation_residue": 254,
"protein_length": 543,
"fraction_lost": 0.532
} | 1 |
co_stru_00184 | structural_effect | coding_variant | easy | 1 | NM_000455.5(STK11):c.884_888del (p.Ala295fs) introduces a premature truncation at residue 295 of STK11's 433-residue protein product (AlphaFold model, mean pLDDT 78.79). Approximately how much of the protein is lost downstream of the truncation? | NM_000455.5(STK11):c.884_888del (p.Ala295fs) VARIANT_IN_GENE STK11 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000455.5(STK11):c.884_888del (p.Ala295fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000455.5(STK11):c.884_888del (p.Ala295fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confid... | C | [
"A. a small C-terminal portion (<25%)",
"B. more than half the protein (>50%)",
"C. a substantial portion (25-50%)"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "STK11",
"source_db": "UniProt",
"payload": {
"accession": "Q15831",
"sequence": "MEVVDPQQLGMFTEGELMSVGMDTFIHRIDSTEVIYQPRRKRAKLIGKYLMGDLLGEGSYGKVKEVLDSETLCRRAVKILKKKKLRRIPNGEANVKKEIQLLRRLRHKNVIQLVDVLYNEEKQKMYMVMEYCV... | [
{
"source_db": "ClinVar",
"source_id": "STK11",
"text": "NM_000455.5(STK11):c.884_888del (p.Ala295fs) VARIANT_IN_GENE STK11",
"confidence": 1
}
] | {
"variant": "NM_000455.5(STK11):c.884_888del (p.Ala295fs)",
"gene": "STK11",
"truncation_residue": 295,
"protein_length": 433,
"fraction_lost": 0.319
} | 1 |
co_stru_00185 | structural_effect | coding_variant | easy | 1 | NM_007294.4(BRCA1):c.3752_3753del (p.Cys1251fs) introduces a premature truncation at residue 1251 of BRCA1's 1863-residue protein product (AlphaFold model, mean pLDDT 41.59). Approximately how much of the protein is lost downstream of the truncation? | NM_007294.4(BRCA1):c.3752_3753del (p.Cys1251fs) VARIANT_IN_GENE BRCA1 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_007294.4(BRCA1):c.3752_3753del (p.Cys1251fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_007294.4(BRCA1):c.3752_3753del (p.Cys1251fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_... | B | [
"A. more than half the protein (>50%)",
"B. a substantial portion (25-50%)",
"C. a small C-terminal portion (<25%)"
] | [
"expression",
"intercell_role",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "BRCA1",
"source_db": "UniProt",
"payload": {
"accession": "P38398",
"sequence": "MDLSALRVEEVQNVINAMQKILECPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRSLQESTRFSQLVEELLKIICAFQLDTGLEYANSYNFAKKENNSPEHLKDEVSIIQSMGYRNR... | [
{
"source_db": "ClinVar",
"source_id": "BRCA1",
"text": "NM_007294.4(BRCA1):c.3752_3753del (p.Cys1251fs) VARIANT_IN_GENE BRCA1",
"confidence": 1
}
] | {
"variant": "NM_007294.4(BRCA1):c.3752_3753del (p.Cys1251fs)",
"gene": "BRCA1",
"truncation_residue": 1251,
"protein_length": 1863,
"fraction_lost": 0.329
} | 1 |
co_stru_00186 | structural_effect | coding_variant | easy | 1 | NM_000546.6(TP53):c.783_794delinsG (p.Ser261fs) introduces a premature truncation at residue 261 of TP53's 393-residue protein product (AlphaFold model, mean pLDDT 75.05). Approximately how much of the protein is lost downstream of the truncation? | NM_000546.6(TP53):c.783_794delinsG (p.Ser261fs) VARIANT_IN_GENE TP53 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000546.6(TP53):c.783_794delinsG (p.Ser261fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000546.6(TP53):c.783_794delinsG (p.Ser261fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_... | C | [
"A. more than half the protein (>50%)",
"B. a small C-terminal portion (<25%)",
"C. a substantial portion (25-50%)"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "TP53",
"source_db": "UniProt",
"payload": {
"accession": "P04637",
"sequence": "MEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPGPDEAPRMPEAAPPVAPAPAAPTPAAPAPAPSWPLSSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMF... | [
{
"source_db": "ClinVar",
"source_id": "TP53",
"text": "NM_000546.6(TP53):c.783_794delinsG (p.Ser261fs) VARIANT_IN_GENE TP53",
"confidence": 1
}
] | {
"variant": "NM_000546.6(TP53):c.783_794delinsG (p.Ser261fs)",
"gene": "TP53",
"truncation_residue": 261,
"protein_length": 393,
"fraction_lost": 0.336
} | 1 |
co_stru_00187 | structural_effect | coding_variant | easy | 1 | NM_058216.3(RAD51C):c.561_562del (p.His187fs) introduces a premature truncation at residue 187 of RAD51C's 376-residue protein product (AlphaFold model, mean pLDDT 84.36). Approximately how much of the protein is lost downstream of the truncation? | NM_058216.3(RAD51C):c.561_562del (p.His187fs) VARIANT_IN_GENE RAD51C | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_058216.3(RAD51C):c.561_562del (p.His187fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_058216.3(RAD51C):c.561_562del (p.His187fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_conf... | B | [
"A. a small C-terminal portion (<25%)",
"B. more than half the protein (>50%)",
"C. a substantial portion (25-50%)"
] | [
"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": "RAD51C",
"text": "NM_058216.3(RAD51C):c.561_562del (p.His187fs) VARIANT_IN_GENE RAD51C",
"confidence": 1
}
] | {
"variant": "NM_058216.3(RAD51C):c.561_562del (p.His187fs)",
"gene": "RAD51C",
"truncation_residue": 187,
"protein_length": 376,
"fraction_lost": 0.503
} | 1 |
co_stru_00188 | structural_effect | coding_variant | easy | 1 | NM_001903.5(CTNNA1):c.1369_1370dup (p.Leu457fs) introduces a premature truncation at residue 457 of CTNNA1's 906-residue protein product (AlphaFold model, mean pLDDT 82.94). Approximately how much of the protein is lost downstream of the truncation? | NM_001903.5(CTNNA1):c.1369_1370dup (p.Leu457fs) VARIANT_IN_GENE CTNNA1 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_001903.5(CTNNA1):c.1369_1370dup (p.Leu457fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_001903.5(CTNNA1):c.1369_1370dup (p.Leu457fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_... | C | [
"A. a small C-terminal portion (<25%)",
"B. more than half the protein (>50%)",
"C. a substantial portion (25-50%)"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CTNNA1",
"source_db": "UniProt",
"payload": {
"accession": "P35221",
"sequence": "MTAVHAGNINFKWDPKSLEIRTLAVERLLEPLVTQVTTLVNTNSKGPSNKKRGRSKKAHVLAASVEQATENFLEKGDKIAKESQFLKEELVAAVEDVRKQGDLMKAAAGEFADDPCSSVKRGNMVRAARALL... | [
{
"source_db": "ClinVar",
"source_id": "CTNNA1",
"text": "NM_001903.5(CTNNA1):c.1369_1370dup (p.Leu457fs) VARIANT_IN_GENE CTNNA1",
"confidence": 1
}
] | {
"variant": "NM_001903.5(CTNNA1):c.1369_1370dup (p.Leu457fs)",
"gene": "CTNNA1",
"truncation_residue": 457,
"protein_length": 906,
"fraction_lost": 0.496
} | 1 |
co_stru_00189 | structural_effect | coding_variant | easy | 1 | NM_001199397.3(NEK1):c.3337G>T (p.Glu1113Ter) introduces a premature truncation at residue 1113 of NEK1's 1258-residue protein product (AlphaFold model, mean pLDDT 56.86). Approximately how much of the protein is lost downstream of the truncation? | NM_001199397.3(NEK1):c.3337G>T (p.Glu1113Ter) VARIANT_IN_GENE NEK1 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_001199397.3(NEK1):c.3337G>T (p.Glu1113Ter)",
"source_node_type": "VARIANT",
"source_node_label": "NM_001199397.3(NEK1):c.3337G>T (p.Glu1113Ter)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_conf... | A | [
"A. a small C-terminal portion (<25%)",
"B. a substantial portion (25-50%)",
"C. more than half the protein (>50%)"
] | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "NM_001199397.3(NEK1):c.3337G>T (p.Glu1113Ter)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr4",
"pos": 169406633,
"track": "phyloP100way",
"window": 20,
"scores": [
0.0730236,
... | [
{
"source_db": "ClinVar",
"source_id": "NEK1",
"text": "NM_001199397.3(NEK1):c.3337G>T (p.Glu1113Ter) VARIANT_IN_GENE NEK1",
"confidence": 1
}
] | {
"variant": "NM_001199397.3(NEK1):c.3337G>T (p.Glu1113Ter)",
"gene": "NEK1",
"truncation_residue": 1113,
"protein_length": 1258,
"fraction_lost": 0.115
} | 1 |
co_stru_00190 | structural_effect | coding_variant | easy | 1 | NM_004655.4(AXIN2):c.1396_1447del (p.Ser466fs) introduces a premature truncation at residue 466 of AXIN2's 843-residue protein product (AlphaFold model, mean pLDDT 60.5). Approximately how much of the protein is lost downstream of the truncation? | NM_004655.4(AXIN2):c.1396_1447del (p.Ser466fs) VARIANT_IN_GENE AXIN2 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_004655.4(AXIN2):c.1396_1447del (p.Ser466fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_004655.4(AXIN2):c.1396_1447del (p.Ser466fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_co... | A | [
"A. a substantial portion (25-50%)",
"B. more than half the protein (>50%)",
"C. a small C-terminal portion (<25%)"
] | [
"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": "AXIN2",
"text": "NM_004655.4(AXIN2):c.1396_1447del (p.Ser466fs) VARIANT_IN_GENE AXIN2",
"confidence": 1
}
] | {
"variant": "NM_004655.4(AXIN2):c.1396_1447del (p.Ser466fs)",
"gene": "AXIN2",
"truncation_residue": 466,
"protein_length": 843,
"fraction_lost": 0.447
} | 1 |
co_stru_00191 | structural_effect | coding_variant | easy | 1 | NM_000314.8(PTEN):c.888del (p.Cys296fs) introduces a premature truncation at residue 296 of PTEN's 403-residue protein product (AlphaFold model, mean pLDDT 83.03). Approximately how much of the protein is lost downstream of the truncation? | NM_000314.8(PTEN):c.888del (p.Cys296fs) VARIANT_IN_GENE PTEN | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000314.8(PTEN):c.888del (p.Cys296fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000314.8(PTEN):c.888del (p.Cys296fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
... | B | [
"A. more than half the protein (>50%)",
"B. a substantial portion (25-50%)",
"C. a small C-terminal portion (<25%)"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "PTEN",
"source_db": "UniProt",
"payload": {
"accession": "P60484",
"sequence": "MTAIIKEIVSRNKRRYQEDGFDLDLTYIYPNIIAMGFPAERLEGVYRNNIDDVVRFLDSKHKNHYKIYNLCAERHYDTAKFNCRVAQYPFEDHNPPQLELIKPFCEDLDQWLSEDDNHVAAIHCKAGKGRTGVM... | [
{
"source_db": "ClinVar",
"source_id": "PTEN",
"text": "NM_000314.8(PTEN):c.888del (p.Cys296fs) VARIANT_IN_GENE PTEN",
"confidence": 1
}
] | {
"variant": "NM_000314.8(PTEN):c.888del (p.Cys296fs)",
"gene": "PTEN",
"truncation_residue": 296,
"protein_length": 403,
"fraction_lost": 0.266
} | 1 |
co_stru_00192 | structural_effect | coding_variant | easy | 1 | NM_004380.3(CREBBP):c.5991del (p.Pro1997_Val1998insTer) introduces a premature truncation at residue 1997 of CREBBP's 2442-residue protein product (AlphaFold model, mean pLDDT 52.52). Approximately how much of the protein is lost downstream of the truncation? | NM_004380.3(CREBBP):c.5991del (p.Pro1997_Val1998insTer) VARIANT_IN_GENE CREBBP | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_004380.3(CREBBP):c.5991del (p.Pro1997_Val1998insTer)",
"source_node_type": "VARIANT",
"source_node_label": "NM_004380.3(CREBBP):c.5991del (p.Pro1997_Val1998insTer)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curate... | C | [
"A. a substantial portion (25-50%)",
"B. more than half the protein (>50%)",
"C. a small C-terminal portion (<25%)"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CREBBP",
"source_db": "UniProt",
"payload": {
"accession": "Q92793",
"sequence": "MAENLLDGPPNPKRAKLSSPGFSANDSTDFGSLFDLENDLPDELIPNGGELGLLNSGNLVPDAASKHKQLSELLRGGSGSSINPGIGNVSASSPVQQGLGGQAQGQPNSANMASLSAMGKSPLSQGDSSAPS... | [
{
"source_db": "ClinVar",
"source_id": "CREBBP",
"text": "NM_004380.3(CREBBP):c.5991del (p.Pro1997_Val1998insTer) VARIANT_IN_GENE CREBBP",
"confidence": 1
}
] | {
"variant": "NM_004380.3(CREBBP):c.5991del (p.Pro1997_Val1998insTer)",
"gene": "CREBBP",
"truncation_residue": 1997,
"protein_length": 2442,
"fraction_lost": 0.182
} | 1 |
co_stru_00193 | structural_effect | coding_variant | easy | 1 | NM_000179.3(MSH6):c.1510A>T (p.Lys504Ter) introduces a premature truncation at residue 504 of MSH6's 1360-residue protein product (AlphaFold model, mean pLDDT 77.09). Approximately how much of the protein is lost downstream of the truncation? | NM_000179.3(MSH6):c.1510A>T (p.Lys504Ter) VARIANT_IN_GENE MSH6 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000179.3(MSH6):c.1510A>T (p.Lys504Ter)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000179.3(MSH6):c.1510A>T (p.Lys504Ter)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence":... | C | [
"A. a small C-terminal portion (<25%)",
"B. a substantial portion (25-50%)",
"C. more than half the protein (>50%)"
] | [
"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": "MSH6",
"text": "NM_000179.3(MSH6):c.1510A>T (p.Lys504Ter) VARIANT_IN_GENE MSH6",
"confidence": 1
}
] | {
"variant": "NM_000179.3(MSH6):c.1510A>T (p.Lys504Ter)",
"gene": "MSH6",
"truncation_residue": 504,
"protein_length": 1360,
"fraction_lost": 0.629
} | 1 |
co_stru_00194 | structural_effect | coding_variant | easy | 1 | NM_000249.4(MLH1):c.770_771insGTCC (p.Ile257fs) introduces a premature truncation at residue 257 of MLH1's 756-residue protein product (AlphaFold model, mean pLDDT 77.31). Approximately how much of the protein is lost downstream of the truncation? | NM_000249.4(MLH1):c.770_771insGTCC (p.Ile257fs) VARIANT_IN_GENE MLH1 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000249.4(MLH1):c.770_771insGTCC (p.Ile257fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000249.4(MLH1):c.770_771insGTCC (p.Ile257fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_... | A | [
"A. more than half the protein (>50%)",
"B. a substantial portion (25-50%)",
"C. a small C-terminal portion (<25%)"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "MLH1",
"source_db": "UniProt",
"payload": {
"accession": "P40692",
"sequence": "MSFVAGVIRRLDETVVNRIAAGEVIQRPANAIKEMIENCLDAKSTSIQVIVKEGGLKLIQIQDNGTGIRKEDLDIVCERFTTSKLQSFEDLASISTYGFRGEALASISHVAHVTITTKTADGKCAYRASYSDGK... | [
{
"source_db": "ClinVar",
"source_id": "MLH1",
"text": "NM_000249.4(MLH1):c.770_771insGTCC (p.Ile257fs) VARIANT_IN_GENE MLH1",
"confidence": 1
}
] | {
"variant": "NM_000249.4(MLH1):c.770_771insGTCC (p.Ile257fs)",
"gene": "MLH1",
"truncation_residue": 257,
"protein_length": 756,
"fraction_lost": 0.66
} | 1 |
co_stru_00195 | structural_effect | coding_variant | easy | 1 | NM_000044.6(AR):c.463G>T (p.Glu155Ter) introduces a premature truncation at residue 155 of AR's 920-residue protein product (AlphaFold model, mean pLDDT 57.25). Approximately how much of the protein is lost downstream of the truncation? | NM_000044.6(AR):c.463G>T (p.Glu155Ter) VARIANT_IN_GENE AR | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000044.6(AR):c.463G>T (p.Glu155Ter)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000044.6(AR):c.463G>T (p.Glu155Ter)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
... | B | [
"A. a small C-terminal portion (<25%)",
"B. more than half the protein (>50%)",
"C. a substantial portion (25-50%)"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "AR",
"source_db": "UniProt",
"payload": {
"accession": "P10275",
"sequence": "MEVQLGLGRVYPRPPSKTYRGAFQNLFQSVREVIQNPGPRHPEAASAAPPGASLLLLQQQQQQQQQQQQQQQQQQQQQQQETSPRQQQQQQGEDGSPQAHRRGPTGYLVLDEEQQPSQPQSALECHPERGCVPEPG... | [
{
"source_db": "ClinVar",
"source_id": "AR",
"text": "NM_000044.6(AR):c.463G>T (p.Glu155Ter) VARIANT_IN_GENE AR",
"confidence": 1
}
] | {
"variant": "NM_000044.6(AR):c.463G>T (p.Glu155Ter)",
"gene": "AR",
"truncation_residue": 155,
"protein_length": 920,
"fraction_lost": 0.8320000000000001
} | 1 |
co_stru_00196 | structural_effect | coding_variant | easy | 1 | NM_000546.6(TP53):c.490A>T (p.Lys164Ter) introduces a premature truncation at residue 164 of TP53's 393-residue protein product (AlphaFold model, mean pLDDT 75.05). Approximately how much of the protein is lost downstream of the truncation? | NM_000546.6(TP53):c.490A>T (p.Lys164Ter) VARIANT_IN_GENE TP53 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000546.6(TP53):c.490A>T (p.Lys164Ter)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000546.6(TP53):c.490A>T (p.Lys164Ter)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1... | B | [
"A. a substantial portion (25-50%)",
"B. more than half the protein (>50%)",
"C. a small C-terminal portion (<25%)"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "TP53",
"source_db": "UniProt",
"payload": {
"accession": "P04637",
"sequence": "MEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPGPDEAPRMPEAAPPVAPAPAAPTPAAPAPAPSWPLSSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMF... | [
{
"source_db": "ClinVar",
"source_id": "TP53",
"text": "NM_000546.6(TP53):c.490A>T (p.Lys164Ter) VARIANT_IN_GENE TP53",
"confidence": 1
}
] | {
"variant": "NM_000546.6(TP53):c.490A>T (p.Lys164Ter)",
"gene": "TP53",
"truncation_residue": 164,
"protein_length": 393,
"fraction_lost": 0.583
} | 1 |
co_stru_00197 | structural_effect | coding_variant | easy | 1 | NM_000546.6(TP53):c.406C>T (p.Gln136Ter) introduces a premature truncation at residue 136 of TP53's 393-residue protein product (AlphaFold model, mean pLDDT 75.05). Approximately how much of the protein is lost downstream of the truncation? | NM_000546.6(TP53):c.406C>T (p.Gln136Ter) VARIANT_IN_GENE TP53 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000546.6(TP53):c.406C>T (p.Gln136Ter)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000546.6(TP53):c.406C>T (p.Gln136Ter)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1... | A | [
"A. more than half the protein (>50%)",
"B. a small C-terminal portion (<25%)",
"C. a substantial portion (25-50%)"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "TP53",
"source_db": "UniProt",
"payload": {
"accession": "P04637",
"sequence": "MEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPGPDEAPRMPEAAPPVAPAPAAPTPAAPAPAPSWPLSSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMF... | [
{
"source_db": "ClinVar",
"source_id": "TP53",
"text": "NM_000546.6(TP53):c.406C>T (p.Gln136Ter) VARIANT_IN_GENE TP53",
"confidence": 1
}
] | {
"variant": "NM_000546.6(TP53):c.406C>T (p.Gln136Ter)",
"gene": "TP53",
"truncation_residue": 136,
"protein_length": 393,
"fraction_lost": 0.654
} | 1 |
co_stru_00198 | structural_effect | coding_variant | easy | 1 | NM_024675.4(PALB2):c.3156del (p.Asp1052fs) introduces a premature truncation at residue 1052 of PALB2's 1186-residue protein product (AlphaFold model, mean pLDDT 53.81). Approximately how much of the protein is lost downstream of the truncation? | NM_024675.4(PALB2):c.3156del (p.Asp1052fs) VARIANT_IN_GENE PALB2 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_024675.4(PALB2):c.3156del (p.Asp1052fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_024675.4(PALB2):c.3156del (p.Asp1052fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence... | C | [
"A. more than half the protein (>50%)",
"B. a substantial portion (25-50%)",
"C. a small C-terminal portion (<25%)"
] | [
"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": "PALB2",
"text": "NM_024675.4(PALB2):c.3156del (p.Asp1052fs) VARIANT_IN_GENE PALB2",
"confidence": 1
}
] | {
"variant": "NM_024675.4(PALB2):c.3156del (p.Asp1052fs)",
"gene": "PALB2",
"truncation_residue": 1052,
"protein_length": 1186,
"fraction_lost": 0.113
} | 1 |
co_stru_00199 | structural_effect | coding_variant | easy | 1 | NM_001123385.2(BCOR):c.1634del (p.Pro545fs) introduces a premature truncation at residue 545 of BCOR's 1755-residue protein product (AlphaFold model, mean pLDDT 39.64). Approximately how much of the protein is lost downstream of the truncation? | NM_001123385.2(BCOR):c.1634del (p.Pro545fs) VARIANT_IN_GENE BCOR | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_001123385.2(BCOR):c.1634del (p.Pro545fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_001123385.2(BCOR):c.1634del (p.Pro545fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confiden... | C | [
"A. a substantial portion (25-50%)",
"B. a small C-terminal portion (<25%)",
"C. more than half the protein (>50%)"
] | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "NM_001123385.2(BCOR):c.1634del (p.Pro545fs)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chrX",
"pos": 40073712,
"track": "phyloP100way",
"window": 20,
"scores": [
0.08674019999999... | [
{
"source_db": "ClinVar",
"source_id": "BCOR",
"text": "NM_001123385.2(BCOR):c.1634del (p.Pro545fs) VARIANT_IN_GENE BCOR",
"confidence": 1
}
] | {
"variant": "NM_001123385.2(BCOR):c.1634del (p.Pro545fs)",
"gene": "BCOR",
"truncation_residue": 545,
"protein_length": 1755,
"fraction_lost": 0.6890000000000001
} | 1 |
co_stru_00200 | structural_effect | coding_variant | easy | 1 | NM_001904.4(CTNNB1):c.1870dup (p.Asp624fs) introduces a premature truncation at residue 624 of CTNNB1's 781-residue protein product (AlphaFold model, mean pLDDT 81.06). Approximately how much of the protein is lost downstream of the truncation? | NM_001904.4(CTNNB1):c.1870dup (p.Asp624fs) VARIANT_IN_GENE CTNNB1 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_001904.4(CTNNB1):c.1870dup (p.Asp624fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_001904.4(CTNNB1):c.1870dup (p.Asp624fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence... | A | [
"A. a small C-terminal portion (<25%)",
"B. a substantial portion (25-50%)",
"C. more than half the protein (>50%)"
] | [
"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": "CTNNB1",
"text": "NM_001904.4(CTNNB1):c.1870dup (p.Asp624fs) VARIANT_IN_GENE CTNNB1",
"confidence": 1
}
] | {
"variant": "NM_001904.4(CTNNB1):c.1870dup (p.Asp624fs)",
"gene": "CTNNB1",
"truncation_residue": 624,
"protein_length": 781,
"fraction_lost": 0.201
} | 1 |
co_stru_00201 | structural_effect | coding_variant | easy | 1 | NM_032043.3(BRIP1):c.1007_1031del (p.Asp336fs) introduces a premature truncation at residue 336 of BRIP1's 1249-residue protein product (AlphaFold model, mean pLDDT 63.87). Approximately how much of the protein is lost downstream of the truncation? | NM_032043.3(BRIP1):c.1007_1031del (p.Asp336fs) VARIANT_IN_GENE BRIP1 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_032043.3(BRIP1):c.1007_1031del (p.Asp336fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_032043.3(BRIP1):c.1007_1031del (p.Asp336fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_co... | C | [
"A. a small C-terminal portion (<25%)",
"B. a substantial portion (25-50%)",
"C. more than half the protein (>50%)"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "BRIP1",
"source_db": "UniProt",
"payload": {
"accession": "Q9BX63",
"sequence": "MSSMWSEYTIGGVKIYFPYKAYPSQLAMMNSILRGLNSKQHCLLESPTGSGKSLALLCSALAWQQSLSGKPADEGVSEKAEVQLSCCCACHSKDFTNNDMNQGTSRHFNYPSTPPSERNGTSSTCQDSPEKTT... | [
{
"source_db": "ClinVar",
"source_id": "BRIP1",
"text": "NM_032043.3(BRIP1):c.1007_1031del (p.Asp336fs) VARIANT_IN_GENE BRIP1",
"confidence": 1
}
] | {
"variant": "NM_032043.3(BRIP1):c.1007_1031del (p.Asp336fs)",
"gene": "BRIP1",
"truncation_residue": 336,
"protein_length": 1249,
"fraction_lost": 0.731
} | 1 |
co_stru_00202 | structural_effect | coding_variant | easy | 1 | NM_000251.3(MSH2):c.2163dup (p.Val722fs) introduces a premature truncation at residue 722 of MSH2's 934-residue protein product (AlphaFold model, mean pLDDT 85.29). Approximately how much of the protein is lost downstream of the truncation? | NM_000251.3(MSH2):c.2163dup (p.Val722fs) VARIANT_IN_GENE MSH2 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000251.3(MSH2):c.2163dup (p.Val722fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000251.3(MSH2):c.2163dup (p.Val722fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1... | A | [
"A. a small C-terminal portion (<25%)",
"B. more than half the protein (>50%)",
"C. a substantial portion (25-50%)"
] | [
"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": "MSH2",
"text": "NM_000251.3(MSH2):c.2163dup (p.Val722fs) VARIANT_IN_GENE MSH2",
"confidence": 1
}
] | {
"variant": "NM_000251.3(MSH2):c.2163dup (p.Val722fs)",
"gene": "MSH2",
"truncation_residue": 722,
"protein_length": 934,
"fraction_lost": 0.227
} | 1 |
co_stru_00203 | structural_effect | coding_variant | easy | 1 | NM_004360.5(CDH1):c.2355_2356insCAACCCTCATGGT (p.Asp786delinsGlnProSerTrpTer) introduces a premature truncation at residue 786 of CDH1's 882-residue protein product (AlphaFold model, mean pLDDT 79.16). Approximately how much of the protein is lost downstream of the truncation? | NM_004360.5(CDH1):c.2355_2356insCAACCCTCATGGT (p.Asp786delinsGlnProSerTrpTer) VARIANT_IN_GENE CDH1 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_004360.5(CDH1):c.2355_2356insCAACCCTCATGGT (p.Asp786delinsGlnProSerTrpTer)",
"source_node_type": "VARIANT",
"source_node_label": "NM_004360.5(CDH1):c.2355_2356insCAACCCTCATGGT (p.Asp786delinsGlnProSerTrpTer)",
"edge_relation": "VARIANT_I... | A | [
"A. a small C-terminal portion (<25%)",
"B. more than half the protein (>50%)",
"C. a substantial portion (25-50%)"
] | [
"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": "CDH1",
"text": "NM_004360.5(CDH1):c.2355_2356insCAACCCTCATGGT (p.Asp786delinsGlnProSerTrpTer) VARIANT_IN_GENE CDH1",
"confidence": 1
}
] | {
"variant": "NM_004360.5(CDH1):c.2355_2356insCAACCCTCATGGT (p.Asp786delinsGlnProSerTrpTer)",
"gene": "CDH1",
"truncation_residue": 786,
"protein_length": 882,
"fraction_lost": 0.109
} | 1 |
co_stru_00204 | structural_effect | coding_variant | easy | 1 | NM_000789.4(ACE):c.3262C>T (p.Gln1088Ter) introduces a premature truncation at residue 1088 of ACE's 1306-residue protein product (AlphaFold model, mean pLDDT 90.94). Approximately how much of the protein is lost downstream of the truncation? | NM_000789.4(ACE):c.3262C>T (p.Gln1088Ter) VARIANT_IN_GENE ACE | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000789.4(ACE):c.3262C>T (p.Gln1088Ter)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000789.4(ACE):c.3262C>T (p.Gln1088Ter)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence":... | B | [
"A. more than half the protein (>50%)",
"B. a small C-terminal portion (<25%)",
"C. a substantial portion (25-50%)"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ACE",
"source_db": "UniProt",
"payload": {
"accession": "P12821",
"sequence": "MGAASGRRGPGLLLPLPLLLLLPPQPALALDPGLQPGNFSADEAGAQLFAQSYNSSAEQVLFQSVAASWAHDTNITAENARRQEEAALLSQEFAEAWGQKAKELYEPIWQNFTDPQLRRIIGAVRTLGSANLPLA... | [
{
"source_db": "ClinVar",
"source_id": "ACE",
"text": "NM_000789.4(ACE):c.3262C>T (p.Gln1088Ter) VARIANT_IN_GENE ACE",
"confidence": 1
}
] | {
"variant": "NM_000789.4(ACE):c.3262C>T (p.Gln1088Ter)",
"gene": "ACE",
"truncation_residue": 1088,
"protein_length": 1306,
"fraction_lost": 0.167
} | 1 |
co_stru_00205 | structural_effect | coding_variant | easy | 1 | NM_001903.5(CTNNA1):c.660_666del (p.Tyr222fs) introduces a premature truncation at residue 222 of CTNNA1's 906-residue protein product (AlphaFold model, mean pLDDT 82.94). Approximately how much of the protein is lost downstream of the truncation? | NM_001903.5(CTNNA1):c.660_666del (p.Tyr222fs) VARIANT_IN_GENE CTNNA1 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_001903.5(CTNNA1):c.660_666del (p.Tyr222fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_001903.5(CTNNA1):c.660_666del (p.Tyr222fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_conf... | C | [
"A. a substantial portion (25-50%)",
"B. a small C-terminal portion (<25%)",
"C. more than half the protein (>50%)"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CTNNA1",
"source_db": "UniProt",
"payload": {
"accession": "P35221",
"sequence": "MTAVHAGNINFKWDPKSLEIRTLAVERLLEPLVTQVTTLVNTNSKGPSNKKRGRSKKAHVLAASVEQATENFLEKGDKIAKESQFLKEELVAAVEDVRKQGDLMKAAAGEFADDPCSSVKRGNMVRAARALL... | [
{
"source_db": "ClinVar",
"source_id": "CTNNA1",
"text": "NM_001903.5(CTNNA1):c.660_666del (p.Tyr222fs) VARIANT_IN_GENE CTNNA1",
"confidence": 1
}
] | {
"variant": "NM_001903.5(CTNNA1):c.660_666del (p.Tyr222fs)",
"gene": "CTNNA1",
"truncation_residue": 222,
"protein_length": 906,
"fraction_lost": 0.755
} | 1 |
co_stru_00206 | structural_effect | coding_variant | easy | 1 | NM_000314.8(PTEN):c.969del (p.Asn323fs) introduces a premature truncation at residue 323 of PTEN's 403-residue protein product (AlphaFold model, mean pLDDT 83.03). Approximately how much of the protein is lost downstream of the truncation? | NM_000314.8(PTEN):c.969del (p.Asn323fs) VARIANT_IN_GENE PTEN | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000314.8(PTEN):c.969del (p.Asn323fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000314.8(PTEN):c.969del (p.Asn323fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
... | A | [
"A. a small C-terminal portion (<25%)",
"B. a substantial portion (25-50%)",
"C. more than half the protein (>50%)"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "PTEN",
"source_db": "UniProt",
"payload": {
"accession": "P60484",
"sequence": "MTAIIKEIVSRNKRRYQEDGFDLDLTYIYPNIIAMGFPAERLEGVYRNNIDDVVRFLDSKHKNHYKIYNLCAERHYDTAKFNCRVAQYPFEDHNPPQLELIKPFCEDLDQWLSEDDNHVAAIHCKAGKGRTGVM... | [
{
"source_db": "ClinVar",
"source_id": "PTEN",
"text": "NM_000314.8(PTEN):c.969del (p.Asn323fs) VARIANT_IN_GENE PTEN",
"confidence": 1
}
] | {
"variant": "NM_000314.8(PTEN):c.969del (p.Asn323fs)",
"gene": "PTEN",
"truncation_residue": 323,
"protein_length": 403,
"fraction_lost": 0.199
} | 1 |
co_stru_00207 | structural_effect | coding_variant | easy | 1 | NM_006231.4(POLE):c.4658del (p.Phe1553fs) introduces a premature truncation at residue 1553 of POLE's 2286-residue protein product (AlphaFold model, mean pLDDT 79.72). Approximately how much of the protein is lost downstream of the truncation? | NM_006231.4(POLE):c.4658del (p.Phe1553fs) VARIANT_IN_GENE POLE | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_006231.4(POLE):c.4658del (p.Phe1553fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_006231.4(POLE):c.4658del (p.Phe1553fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence":... | C | [
"A. more than half the protein (>50%)",
"B. a small C-terminal portion (<25%)",
"C. a substantial portion (25-50%)"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "POLE",
"source_db": "UniProt",
"payload": {
"accession": "Q07864",
"sequence": "MSLRSGGRRRADPGADGEASRDDGATSSVSALKRLERSQWTDKMDLRFGFERLKEPGEKTGWLINMHPTEILDEDKRLGSAVDYYFIQDDGSRFKVALPYKPYFYIATRKGCEREVSSFLSKKFQGKIAKVETV... | [
{
"source_db": "ClinVar",
"source_id": "POLE",
"text": "NM_006231.4(POLE):c.4658del (p.Phe1553fs) VARIANT_IN_GENE POLE",
"confidence": 1
}
] | {
"variant": "NM_006231.4(POLE):c.4658del (p.Phe1553fs)",
"gene": "POLE",
"truncation_residue": 1553,
"protein_length": 2286,
"fraction_lost": 0.321
} | 1 |
co_stru_00208 | structural_effect | coding_variant | easy | 1 | NM_001904.4(CTNNB1):c.923del (p.Asn308fs) introduces a premature truncation at residue 308 of CTNNB1's 781-residue protein product (AlphaFold model, mean pLDDT 81.06). Approximately how much of the protein is lost downstream of the truncation? | NM_001904.4(CTNNB1):c.923del (p.Asn308fs) VARIANT_IN_GENE CTNNB1 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_001904.4(CTNNB1):c.923del (p.Asn308fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_001904.4(CTNNB1):c.923del (p.Asn308fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence":... | A | [
"A. more than half the protein (>50%)",
"B. a small C-terminal portion (<25%)",
"C. a substantial portion (25-50%)"
] | [
"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": "CTNNB1",
"text": "NM_001904.4(CTNNB1):c.923del (p.Asn308fs) VARIANT_IN_GENE CTNNB1",
"confidence": 1
}
] | {
"variant": "NM_001904.4(CTNNB1):c.923del (p.Asn308fs)",
"gene": "CTNNB1",
"truncation_residue": 308,
"protein_length": 781,
"fraction_lost": 0.606
} | 1 |
co_stru_00209 | structural_effect | coding_variant | easy | 1 | NM_000251.3(MSH2):c.1933del (p.Gln645fs) introduces a premature truncation at residue 645 of MSH2's 934-residue protein product (AlphaFold model, mean pLDDT 85.29). Approximately how much of the protein is lost downstream of the truncation? | NM_000251.3(MSH2):c.1933del (p.Gln645fs) VARIANT_IN_GENE MSH2 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000251.3(MSH2):c.1933del (p.Gln645fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000251.3(MSH2):c.1933del (p.Gln645fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1... | A | [
"A. a substantial portion (25-50%)",
"B. more than half the protein (>50%)",
"C. a small C-terminal portion (<25%)"
] | [
"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": "MSH2",
"text": "NM_000251.3(MSH2):c.1933del (p.Gln645fs) VARIANT_IN_GENE MSH2",
"confidence": 1
}
] | {
"variant": "NM_000251.3(MSH2):c.1933del (p.Gln645fs)",
"gene": "MSH2",
"truncation_residue": 645,
"protein_length": 934,
"fraction_lost": 0.309
} | 1 |
co_stru_00210 | structural_effect | coding_variant | easy | 1 | NM_000314.8(PTEN):c.329_401del (p.Gln110fs) introduces a premature truncation at residue 110 of PTEN's 403-residue protein product (AlphaFold model, mean pLDDT 83.03). Approximately how much of the protein is lost downstream of the truncation? | NM_000314.8(PTEN):c.329_401del (p.Gln110fs) VARIANT_IN_GENE PTEN | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000314.8(PTEN):c.329_401del (p.Gln110fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000314.8(PTEN):c.329_401del (p.Gln110fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confiden... | A | [
"A. more than half the protein (>50%)",
"B. a substantial portion (25-50%)",
"C. a small C-terminal portion (<25%)"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "PTEN",
"source_db": "UniProt",
"payload": {
"accession": "P60484",
"sequence": "MTAIIKEIVSRNKRRYQEDGFDLDLTYIYPNIIAMGFPAERLEGVYRNNIDDVVRFLDSKHKNHYKIYNLCAERHYDTAKFNCRVAQYPFEDHNPPQLELIKPFCEDLDQWLSEDDNHVAAIHCKAGKGRTGVM... | [
{
"source_db": "ClinVar",
"source_id": "PTEN",
"text": "NM_000314.8(PTEN):c.329_401del (p.Gln110fs) VARIANT_IN_GENE PTEN",
"confidence": 1
}
] | {
"variant": "NM_000314.8(PTEN):c.329_401del (p.Gln110fs)",
"gene": "PTEN",
"truncation_residue": 110,
"protein_length": 403,
"fraction_lost": 0.727
} | 1 |
co_stru_00211 | structural_effect | coding_variant | easy | 1 | NM_007194.4(CHEK2):c.1274dup (p.Pro426fs) introduces a premature truncation at residue 426 of CHEK2's 543-residue protein product (AlphaFold model, mean pLDDT 76.18). Approximately how much of the protein is lost downstream of the truncation? | NM_007194.4(CHEK2):c.1274dup (p.Pro426fs) VARIANT_IN_GENE CHEK2 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_007194.4(CHEK2):c.1274dup (p.Pro426fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_007194.4(CHEK2):c.1274dup (p.Pro426fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence":... | C | [
"A. more than half the protein (>50%)",
"B. a substantial portion (25-50%)",
"C. a small C-terminal portion (<25%)"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CHEK2",
"source_db": "UniProt",
"payload": {
"accession": "O96017",
"sequence": "MSRESDVEAQQSHGSSACSQPHGSVTQSQGSSSQSQGISSSSTSTMPNSSQSSHSSSGTLSSLETVSTQELYSIPEDQEPEDQEPEEPTPAPWARLWALQDGFANLECVNDNYWFGRDKSCEYCFDEPLLKRT... | [
{
"source_db": "ClinVar",
"source_id": "CHEK2",
"text": "NM_007194.4(CHEK2):c.1274dup (p.Pro426fs) VARIANT_IN_GENE CHEK2",
"confidence": 1
}
] | {
"variant": "NM_007194.4(CHEK2):c.1274dup (p.Pro426fs)",
"gene": "CHEK2",
"truncation_residue": 426,
"protein_length": 543,
"fraction_lost": 0.215
} | 1 |
co_stru_00212 | structural_effect | coding_variant | easy | 1 | NM_004928.3(CFAP410):c.436_466del (p.Glu146fs) introduces a premature truncation at residue 146 of CFAP410's 256-residue protein product (AlphaFold model, mean pLDDT 77.65). Approximately how much of the protein is lost downstream of the truncation? | NM_004928.3(CFAP410):c.436_466del (p.Glu146fs) VARIANT_IN_GENE CFAP410 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_004928.3(CFAP410):c.436_466del (p.Glu146fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_004928.3(CFAP410):c.436_466del (p.Glu146fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_co... | A | [
"A. a substantial portion (25-50%)",
"B. more than half the protein (>50%)",
"C. a small C-terminal portion (<25%)"
] | [
"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": "CFAP410",
"text": "NM_004928.3(CFAP410):c.436_466del (p.Glu146fs) VARIANT_IN_GENE CFAP410",
"confidence": 1
}
] | {
"variant": "NM_004928.3(CFAP410):c.436_466del (p.Glu146fs)",
"gene": "CFAP410",
"truncation_residue": 146,
"protein_length": 256,
"fraction_lost": 0.43
} | 1 |
co_stru_00213 | structural_effect | coding_variant | easy | 1 | NM_004364.5(CEBPA):c.273_309delinsGGCCAGGGTCT (p.Lys92fs) introduces a premature truncation at residue 92 of CEBPA's 358-residue protein product (AlphaFold model, mean pLDDT 61.7). Approximately how much of the protein is lost downstream of the truncation? | NM_004364.5(CEBPA):c.273_309delinsGGCCAGGGTCT (p.Lys92fs) VARIANT_IN_GENE CEBPA | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_004364.5(CEBPA):c.273_309delinsGGCCAGGGTCT (p.Lys92fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_004364.5(CEBPA):c.273_309delinsGGCCAGGGTCT (p.Lys92fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "cu... | B | [
"A. a small C-terminal portion (<25%)",
"B. more than half the protein (>50%)",
"C. a substantial portion (25-50%)"
] | [
"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": "CEBPA",
"text": "NM_004364.5(CEBPA):c.273_309delinsGGCCAGGGTCT (p.Lys92fs) VARIANT_IN_GENE CEBPA",
"confidence": 1
}
] | {
"variant": "NM_004364.5(CEBPA):c.273_309delinsGGCCAGGGTCT (p.Lys92fs)",
"gene": "CEBPA",
"truncation_residue": 92,
"protein_length": 358,
"fraction_lost": 0.743
} | 1 |
co_stru_00214 | structural_effect | coding_variant | easy | 1 | NM_007194.4(CHEK2):c.953del (p.Arg318fs) introduces a premature truncation at residue 318 of CHEK2's 543-residue protein product (AlphaFold model, mean pLDDT 76.18). Approximately how much of the protein is lost downstream of the truncation? | NM_007194.4(CHEK2):c.953del (p.Arg318fs) VARIANT_IN_GENE CHEK2 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_007194.4(CHEK2):c.953del (p.Arg318fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_007194.4(CHEK2):c.953del (p.Arg318fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1... | C | [
"A. more than half the protein (>50%)",
"B. a small C-terminal portion (<25%)",
"C. a substantial portion (25-50%)"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CHEK2",
"source_db": "UniProt",
"payload": {
"accession": "O96017",
"sequence": "MSRESDVEAQQSHGSSACSQPHGSVTQSQGSSSQSQGISSSSTSTMPNSSQSSHSSSGTLSSLETVSTQELYSIPEDQEPEDQEPEEPTPAPWARLWALQDGFANLECVNDNYWFGRDKSCEYCFDEPLLKRT... | [
{
"source_db": "ClinVar",
"source_id": "CHEK2",
"text": "NM_007194.4(CHEK2):c.953del (p.Arg318fs) VARIANT_IN_GENE CHEK2",
"confidence": 1
}
] | {
"variant": "NM_007194.4(CHEK2):c.953del (p.Arg318fs)",
"gene": "CHEK2",
"truncation_residue": 318,
"protein_length": 543,
"fraction_lost": 0.41400000000000003
} | 1 |
co_stru_00215 | structural_effect | coding_variant | easy | 1 | NM_006231.4(POLE):c.4651_4652insTG (p.His1551fs) introduces a premature truncation at residue 1551 of POLE's 2286-residue protein product (AlphaFold model, mean pLDDT 79.72). Approximately how much of the protein is lost downstream of the truncation? | NM_006231.4(POLE):c.4651_4652insTG (p.His1551fs) VARIANT_IN_GENE POLE | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_006231.4(POLE):c.4651_4652insTG (p.His1551fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_006231.4(POLE):c.4651_4652insTG (p.His1551fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edg... | A | [
"A. a substantial portion (25-50%)",
"B. a small C-terminal portion (<25%)",
"C. more than half the protein (>50%)"
] | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "NM_006231.4(POLE):c.4651_4652insTG (p.His1551fs)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr12",
"pos": 132642896,
"track": "phyloP100way",
"window": 20,
"scores": [
7.75888,
... | [
{
"source_db": "ClinVar",
"source_id": "POLE",
"text": "NM_006231.4(POLE):c.4651_4652insTG (p.His1551fs) VARIANT_IN_GENE POLE",
"confidence": 1
}
] | {
"variant": "NM_006231.4(POLE):c.4651_4652insTG (p.His1551fs)",
"gene": "POLE",
"truncation_residue": 1551,
"protein_length": 2286,
"fraction_lost": 0.322
} | 1 |
co_stru_00216 | structural_effect | coding_variant | easy | 1 | NM_002087.4(GRN):c.424dup (p.Met142fs) introduces a premature truncation at residue 142 of GRN's 593-residue protein product (AlphaFold model, mean pLDDT 77.01). Approximately how much of the protein is lost downstream of the truncation? | NM_002087.4(GRN):c.424dup (p.Met142fs) VARIANT_IN_GENE GRN | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_002087.4(GRN):c.424dup (p.Met142fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_002087.4(GRN):c.424dup (p.Met142fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
... | C | [
"A. a small C-terminal portion (<25%)",
"B. a substantial portion (25-50%)",
"C. more than half the protein (>50%)"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "GRN",
"source_db": "UniProt",
"payload": {
"accession": "P28799",
"sequence": "MWTLVSWVALTAGLVAGTRCPDGQFCPVACCLDPGGASYSCCRPLLDKWPTTLSRHLGGPCQVDAHCSAGHSCIFTVSGTSSCCPFPEAVACGDGHHCCPRGFHCSADGRSCFQRSGNNSVGAIQCPDSQFECPD... | [
{
"source_db": "ClinVar",
"source_id": "GRN",
"text": "NM_002087.4(GRN):c.424dup (p.Met142fs) VARIANT_IN_GENE GRN",
"confidence": 1
}
] | {
"variant": "NM_002087.4(GRN):c.424dup (p.Met142fs)",
"gene": "GRN",
"truncation_residue": 142,
"protein_length": 593,
"fraction_lost": 0.761
} | 1 |
co_stru_00217 | structural_effect | coding_variant | easy | 1 | NM_000314.8(PTEN):c.170dup (p.Leu57fs) introduces a premature truncation at residue 57 of PTEN's 403-residue protein product (AlphaFold model, mean pLDDT 83.03). Approximately how much of the protein is lost downstream of the truncation? | NM_000314.8(PTEN):c.170dup (p.Leu57fs) VARIANT_IN_GENE PTEN | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000314.8(PTEN):c.170dup (p.Leu57fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000314.8(PTEN):c.170dup (p.Leu57fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
... | C | [
"A. a small C-terminal portion (<25%)",
"B. a substantial portion (25-50%)",
"C. more than half the protein (>50%)"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "PTEN",
"source_db": "UniProt",
"payload": {
"accession": "P60484",
"sequence": "MTAIIKEIVSRNKRRYQEDGFDLDLTYIYPNIIAMGFPAERLEGVYRNNIDDVVRFLDSKHKNHYKIYNLCAERHYDTAKFNCRVAQYPFEDHNPPQLELIKPFCEDLDQWLSEDDNHVAAIHCKAGKGRTGVM... | [
{
"source_db": "ClinVar",
"source_id": "PTEN",
"text": "NM_000314.8(PTEN):c.170dup (p.Leu57fs) VARIANT_IN_GENE PTEN",
"confidence": 1
}
] | {
"variant": "NM_000314.8(PTEN):c.170dup (p.Leu57fs)",
"gene": "PTEN",
"truncation_residue": 57,
"protein_length": 403,
"fraction_lost": 0.859
} | 1 |
co_stru_00218 | structural_effect | coding_variant | easy | 1 | NM_000535.7(PMS2):c.1918G>T (p.Glu640Ter) introduces a premature truncation at residue 640 of PMS2's 862-residue protein product (AlphaFold model, mean pLDDT 70.97). Approximately how much of the protein is lost downstream of the truncation? | NM_000535.7(PMS2):c.1918G>T (p.Glu640Ter) VARIANT_IN_GENE PMS2 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000535.7(PMS2):c.1918G>T (p.Glu640Ter)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000535.7(PMS2):c.1918G>T (p.Glu640Ter)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence":... | A | [
"A. a substantial portion (25-50%)",
"B. more than half the protein (>50%)",
"C. a small C-terminal portion (<25%)"
] | [
"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": "PMS2",
"text": "NM_000535.7(PMS2):c.1918G>T (p.Glu640Ter) VARIANT_IN_GENE PMS2",
"confidence": 1
}
] | {
"variant": "NM_000535.7(PMS2):c.1918G>T (p.Glu640Ter)",
"gene": "PMS2",
"truncation_residue": 640,
"protein_length": 862,
"fraction_lost": 0.258
} | 1 |
co_stru_00219 | structural_effect | coding_variant | easy | 1 | NM_001903.5(CTNNA1):c.149dup (p.Lys51fs) introduces a premature truncation at residue 51 of CTNNA1's 906-residue protein product (AlphaFold model, mean pLDDT 82.94). Approximately how much of the protein is lost downstream of the truncation? | NM_001903.5(CTNNA1):c.149dup (p.Lys51fs) VARIANT_IN_GENE CTNNA1 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_001903.5(CTNNA1):c.149dup (p.Lys51fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_001903.5(CTNNA1):c.149dup (p.Lys51fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1... | A | [
"A. more than half the protein (>50%)",
"B. a small C-terminal portion (<25%)",
"C. a substantial portion (25-50%)"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CTNNA1",
"source_db": "UniProt",
"payload": {
"accession": "P35221",
"sequence": "MTAVHAGNINFKWDPKSLEIRTLAVERLLEPLVTQVTTLVNTNSKGPSNKKRGRSKKAHVLAASVEQATENFLEKGDKIAKESQFLKEELVAAVEDVRKQGDLMKAAAGEFADDPCSSVKRGNMVRAARALL... | [
{
"source_db": "ClinVar",
"source_id": "CTNNA1",
"text": "NM_001903.5(CTNNA1):c.149dup (p.Lys51fs) VARIANT_IN_GENE CTNNA1",
"confidence": 1
}
] | {
"variant": "NM_001903.5(CTNNA1):c.149dup (p.Lys51fs)",
"gene": "CTNNA1",
"truncation_residue": 51,
"protein_length": 906,
"fraction_lost": 0.9440000000000001
} | 1 |
co_stru_00220 | structural_effect | coding_variant | easy | 1 | NM_000057.4(BLM):c.2797A>T (p.Lys933Ter) introduces a premature truncation at residue 933 of BLM's 1417-residue protein product (AlphaFold model, mean pLDDT 60.54). Approximately how much of the protein is lost downstream of the truncation? | NM_000057.4(BLM):c.2797A>T (p.Lys933Ter) VARIANT_IN_GENE BLM | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000057.4(BLM):c.2797A>T (p.Lys933Ter)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000057.4(BLM):c.2797A>T (p.Lys933Ter)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1... | A | [
"A. a substantial portion (25-50%)",
"B. a small C-terminal portion (<25%)",
"C. more than half the protein (>50%)"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "BLM",
"source_db": "UniProt",
"payload": {
"accession": "P54132",
"sequence": "MAAVPQNNLQEQLERHSARTLNNKLSLSKPKFSGFTFKKKTSSDNNVSVTNVSVAKTPVLRNKDVNVTEDFSFSEPLPNTTNQQRVKDFFKNAPAGQETQRGGSKSLLPDFLQTPKEVVCTTQNTPTVKKSRDTA... | [
{
"source_db": "ClinVar",
"source_id": "BLM",
"text": "NM_000057.4(BLM):c.2797A>T (p.Lys933Ter) VARIANT_IN_GENE BLM",
"confidence": 1
}
] | {
"variant": "NM_000057.4(BLM):c.2797A>T (p.Lys933Ter)",
"gene": "BLM",
"truncation_residue": 933,
"protein_length": 1417,
"fraction_lost": 0.342
} | 1 |
co_stru_00221 | structural_effect | coding_variant | easy | 1 | NM_000057.4(BLM):c.3442A>T (p.Lys1148Ter) introduces a premature truncation at residue 1148 of BLM's 1417-residue protein product (AlphaFold model, mean pLDDT 60.54). Approximately how much of the protein is lost downstream of the truncation? | NM_000057.4(BLM):c.3442A>T (p.Lys1148Ter) VARIANT_IN_GENE BLM | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000057.4(BLM):c.3442A>T (p.Lys1148Ter)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000057.4(BLM):c.3442A>T (p.Lys1148Ter)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence":... | B | [
"A. a substantial portion (25-50%)",
"B. a small C-terminal portion (<25%)",
"C. more than half the protein (>50%)"
] | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "NM_000057.4(BLM):c.3442A>T (p.Lys1148Ter)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr15",
"pos": 90803604,
"track": "phyloP100way",
"window": 20,
"scores": [
8.47583,
... | [
{
"source_db": "ClinVar",
"source_id": "BLM",
"text": "NM_000057.4(BLM):c.3442A>T (p.Lys1148Ter) VARIANT_IN_GENE BLM",
"confidence": 1
}
] | {
"variant": "NM_000057.4(BLM):c.3442A>T (p.Lys1148Ter)",
"gene": "BLM",
"truncation_residue": 1148,
"protein_length": 1417,
"fraction_lost": 0.19
} | 1 |
co_stru_00222 | structural_effect | coding_variant | easy | 1 | NM_000546.6(TP53):c.814_826del (p.Val272fs) introduces a premature truncation at residue 272 of TP53's 393-residue protein product (AlphaFold model, mean pLDDT 75.05). Approximately how much of the protein is lost downstream of the truncation? | NM_000546.6(TP53):c.814_826del (p.Val272fs) VARIANT_IN_GENE TP53 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000546.6(TP53):c.814_826del (p.Val272fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000546.6(TP53):c.814_826del (p.Val272fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confiden... | A | [
"A. a substantial portion (25-50%)",
"B. a small C-terminal portion (<25%)",
"C. more than half the protein (>50%)"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "TP53",
"source_db": "UniProt",
"payload": {
"accession": "P04637",
"sequence": "MEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPGPDEAPRMPEAAPPVAPAPAAPTPAAPAPAPSWPLSSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMF... | [
{
"source_db": "ClinVar",
"source_id": "TP53",
"text": "NM_000546.6(TP53):c.814_826del (p.Val272fs) VARIANT_IN_GENE TP53",
"confidence": 1
}
] | {
"variant": "NM_000546.6(TP53):c.814_826del (p.Val272fs)",
"gene": "TP53",
"truncation_residue": 272,
"protein_length": 393,
"fraction_lost": 0.308
} | 1 |
co_stru_00223 | structural_effect | coding_variant | easy | 1 | NM_000455.5(STK11):c.561_562dup (p.Gly188fs) introduces a premature truncation at residue 188 of STK11's 433-residue protein product (AlphaFold model, mean pLDDT 78.79). Approximately how much of the protein is lost downstream of the truncation? | NM_000455.5(STK11):c.561_562dup (p.Gly188fs) VARIANT_IN_GENE STK11 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000455.5(STK11):c.561_562dup (p.Gly188fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000455.5(STK11):c.561_562dup (p.Gly188fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confid... | B | [
"A. a substantial portion (25-50%)",
"B. more than half the protein (>50%)",
"C. a small C-terminal portion (<25%)"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "STK11",
"source_db": "UniProt",
"payload": {
"accession": "Q15831",
"sequence": "MEVVDPQQLGMFTEGELMSVGMDTFIHRIDSTEVIYQPRRKRAKLIGKYLMGDLLGEGSYGKVKEVLDSETLCRRAVKILKKKKLRRIPNGEANVKKEIQLLRRLRHKNVIQLVDVLYNEEKQKMYMVMEYCV... | [
{
"source_db": "ClinVar",
"source_id": "STK11",
"text": "NM_000455.5(STK11):c.561_562dup (p.Gly188fs) VARIANT_IN_GENE STK11",
"confidence": 1
}
] | {
"variant": "NM_000455.5(STK11):c.561_562dup (p.Gly188fs)",
"gene": "STK11",
"truncation_residue": 188,
"protein_length": 433,
"fraction_lost": 0.5660000000000001
} | 1 |
co_stru_00224 | structural_effect | coding_variant | easy | 1 | NM_004380.3(CREBBP):c.4078C>T (p.Arg1360Ter) introduces a premature truncation at residue 1360 of CREBBP's 2442-residue protein product (AlphaFold model, mean pLDDT 52.52). Approximately how much of the protein is lost downstream of the truncation? | NM_004380.3(CREBBP):c.4078C>T (p.Arg1360Ter) VARIANT_IN_GENE CREBBP | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_004380.3(CREBBP):c.4078C>T (p.Arg1360Ter)",
"source_node_type": "VARIANT",
"source_node_label": "NM_004380.3(CREBBP):c.4078C>T (p.Arg1360Ter)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confid... | A | [
"A. a substantial portion (25-50%)",
"B. a small C-terminal portion (<25%)",
"C. more than half the protein (>50%)"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CREBBP",
"source_db": "UniProt",
"payload": {
"accession": "Q92793",
"sequence": "MAENLLDGPPNPKRAKLSSPGFSANDSTDFGSLFDLENDLPDELIPNGGELGLLNSGNLVPDAASKHKQLSELLRGGSGSSINPGIGNVSASSPVQQGLGGQAQGQPNSANMASLSAMGKSPLSQGDSSAPS... | [
{
"source_db": "ClinVar",
"source_id": "CREBBP",
"text": "NM_004380.3(CREBBP):c.4078C>T (p.Arg1360Ter) VARIANT_IN_GENE CREBBP",
"confidence": 1
}
] | {
"variant": "NM_004380.3(CREBBP):c.4078C>T (p.Arg1360Ter)",
"gene": "CREBBP",
"truncation_residue": 1360,
"protein_length": 2442,
"fraction_lost": 0.443
} | 1 |
co_stru_00225 | structural_effect | coding_variant | easy | 1 | NM_004380.3(CREBBP):c.2524del (p.Gln842fs) introduces a premature truncation at residue 842 of CREBBP's 2442-residue protein product (AlphaFold model, mean pLDDT 52.52). Approximately how much of the protein is lost downstream of the truncation? | NM_004380.3(CREBBP):c.2524del (p.Gln842fs) VARIANT_IN_GENE CREBBP | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_004380.3(CREBBP):c.2524del (p.Gln842fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_004380.3(CREBBP):c.2524del (p.Gln842fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence... | B | [
"A. a substantial portion (25-50%)",
"B. more than half the protein (>50%)",
"C. a small C-terminal portion (<25%)"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CREBBP",
"source_db": "UniProt",
"payload": {
"accession": "Q92793",
"sequence": "MAENLLDGPPNPKRAKLSSPGFSANDSTDFGSLFDLENDLPDELIPNGGELGLLNSGNLVPDAASKHKQLSELLRGGSGSSINPGIGNVSASSPVQQGLGGQAQGQPNSANMASLSAMGKSPLSQGDSSAPS... | [
{
"source_db": "ClinVar",
"source_id": "CREBBP",
"text": "NM_004380.3(CREBBP):c.2524del (p.Gln842fs) VARIANT_IN_GENE CREBBP",
"confidence": 1
}
] | {
"variant": "NM_004380.3(CREBBP):c.2524del (p.Gln842fs)",
"gene": "CREBBP",
"truncation_residue": 842,
"protein_length": 2442,
"fraction_lost": 0.655
} | 1 |
co_stru_00226 | structural_effect | coding_variant | easy | 1 | NM_002087.4(GRN):c.775_778del (p.Lys259fs) introduces a premature truncation at residue 259 of GRN's 593-residue protein product (AlphaFold model, mean pLDDT 77.01). Approximately how much of the protein is lost downstream of the truncation? | NM_002087.4(GRN):c.775_778del (p.Lys259fs) VARIANT_IN_GENE GRN | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_002087.4(GRN):c.775_778del (p.Lys259fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_002087.4(GRN):c.775_778del (p.Lys259fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence... | B | [
"A. a substantial portion (25-50%)",
"B. more than half the protein (>50%)",
"C. a small C-terminal portion (<25%)"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "GRN",
"source_db": "UniProt",
"payload": {
"accession": "P28799",
"sequence": "MWTLVSWVALTAGLVAGTRCPDGQFCPVACCLDPGGASYSCCRPLLDKWPTTLSRHLGGPCQVDAHCSAGHSCIFTVSGTSSCCPFPEAVACGDGHHCCPRGFHCSADGRSCFQRSGNNSVGAIQCPDSQFECPD... | [
{
"source_db": "ClinVar",
"source_id": "GRN",
"text": "NM_002087.4(GRN):c.775_778del (p.Lys259fs) VARIANT_IN_GENE GRN",
"confidence": 1
}
] | {
"variant": "NM_002087.4(GRN):c.775_778del (p.Lys259fs)",
"gene": "GRN",
"truncation_residue": 259,
"protein_length": 593,
"fraction_lost": 0.5630000000000001
} | 1 |
co_stru_00227 | structural_effect | coding_variant | easy | 1 | NM_001904.4(CTNNB1):c.1838_1842dup (p.Ala615Ter) introduces a premature truncation at residue 615 of CTNNB1's 781-residue protein product (AlphaFold model, mean pLDDT 81.06). Approximately how much of the protein is lost downstream of the truncation? | NM_001904.4(CTNNB1):c.1838_1842dup (p.Ala615Ter) VARIANT_IN_GENE CTNNB1 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_001904.4(CTNNB1):c.1838_1842dup (p.Ala615Ter)",
"source_node_type": "VARIANT",
"source_node_label": "NM_001904.4(CTNNB1):c.1838_1842dup (p.Ala615Ter)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edg... | B | [
"A. more than half the protein (>50%)",
"B. a small C-terminal portion (<25%)",
"C. a substantial portion (25-50%)"
] | [
"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": "CTNNB1",
"text": "NM_001904.4(CTNNB1):c.1838_1842dup (p.Ala615Ter) VARIANT_IN_GENE CTNNB1",
"confidence": 1
}
] | {
"variant": "NM_001904.4(CTNNB1):c.1838_1842dup (p.Ala615Ter)",
"gene": "CTNNB1",
"truncation_residue": 615,
"protein_length": 781,
"fraction_lost": 0.213
} | 1 |
co_stru_00228 | structural_effect | coding_variant | easy | 1 | NM_022552.5(DNMT3A):c.2086C>T (p.Gln696Ter) introduces a premature truncation at residue 696 of DNMT3A's 912-residue protein product (AlphaFold model, mean pLDDT 72.94). Approximately how much of the protein is lost downstream of the truncation? | NM_022552.5(DNMT3A):c.2086C>T (p.Gln696Ter) VARIANT_IN_GENE DNMT3A | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_022552.5(DNMT3A):c.2086C>T (p.Gln696Ter)",
"source_node_type": "VARIANT",
"source_node_label": "NM_022552.5(DNMT3A):c.2086C>T (p.Gln696Ter)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confiden... | B | [
"A. a substantial portion (25-50%)",
"B. a small C-terminal portion (<25%)",
"C. more than half the protein (>50%)"
] | [
"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": "DNMT3A",
"text": "NM_022552.5(DNMT3A):c.2086C>T (p.Gln696Ter) VARIANT_IN_GENE DNMT3A",
"confidence": 1
}
] | {
"variant": "NM_022552.5(DNMT3A):c.2086C>T (p.Gln696Ter)",
"gene": "DNMT3A",
"truncation_residue": 696,
"protein_length": 912,
"fraction_lost": 0.23700000000000002
} | 1 |
co_stru_00229 | structural_effect | coding_variant | easy | 1 | NM_000179.3(MSH6):c.1686_1687dup (p.Thr563fs) introduces a premature truncation at residue 563 of MSH6's 1360-residue protein product (AlphaFold model, mean pLDDT 77.09). Approximately how much of the protein is lost downstream of the truncation? | NM_000179.3(MSH6):c.1686_1687dup (p.Thr563fs) VARIANT_IN_GENE MSH6 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000179.3(MSH6):c.1686_1687dup (p.Thr563fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000179.3(MSH6):c.1686_1687dup (p.Thr563fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_conf... | B | [
"A. a substantial portion (25-50%)",
"B. more than half the protein (>50%)",
"C. a small C-terminal portion (<25%)"
] | [
"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": "MSH6",
"text": "NM_000179.3(MSH6):c.1686_1687dup (p.Thr563fs) VARIANT_IN_GENE MSH6",
"confidence": 1
}
] | {
"variant": "NM_000179.3(MSH6):c.1686_1687dup (p.Thr563fs)",
"gene": "MSH6",
"truncation_residue": 563,
"protein_length": 1360,
"fraction_lost": 0.586
} | 1 |
co_stru_00230 | structural_effect | coding_variant | easy | 1 | NM_024675.4(PALB2):c.1384G>T (p.Glu462Ter) introduces a premature truncation at residue 462 of PALB2's 1186-residue protein product (AlphaFold model, mean pLDDT 53.81). Approximately how much of the protein is lost downstream of the truncation? | NM_024675.4(PALB2):c.1384G>T (p.Glu462Ter) VARIANT_IN_GENE PALB2 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_024675.4(PALB2):c.1384G>T (p.Glu462Ter)",
"source_node_type": "VARIANT",
"source_node_label": "NM_024675.4(PALB2):c.1384G>T (p.Glu462Ter)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence... | A | [
"A. more than half the protein (>50%)",
"B. a small C-terminal portion (<25%)",
"C. a substantial portion (25-50%)"
] | [
"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": "PALB2",
"text": "NM_024675.4(PALB2):c.1384G>T (p.Glu462Ter) VARIANT_IN_GENE PALB2",
"confidence": 1
}
] | {
"variant": "NM_024675.4(PALB2):c.1384G>T (p.Glu462Ter)",
"gene": "PALB2",
"truncation_residue": 462,
"protein_length": 1186,
"fraction_lost": 0.61
} | 1 |
co_stru_00231 | structural_effect | coding_variant | easy | 1 | NM_004655.4(AXIN2):c.880_881del (p.Ala294fs) introduces a premature truncation at residue 294 of AXIN2's 843-residue protein product (AlphaFold model, mean pLDDT 60.5). Approximately how much of the protein is lost downstream of the truncation? | NM_004655.4(AXIN2):c.880_881del (p.Ala294fs) VARIANT_IN_GENE AXIN2 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_004655.4(AXIN2):c.880_881del (p.Ala294fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_004655.4(AXIN2):c.880_881del (p.Ala294fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confid... | A | [
"A. more than half the protein (>50%)",
"B. a substantial portion (25-50%)",
"C. a small C-terminal portion (<25%)"
] | [
"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": "AXIN2",
"text": "NM_004655.4(AXIN2):c.880_881del (p.Ala294fs) VARIANT_IN_GENE AXIN2",
"confidence": 1
}
] | {
"variant": "NM_004655.4(AXIN2):c.880_881del (p.Ala294fs)",
"gene": "AXIN2",
"truncation_residue": 294,
"protein_length": 843,
"fraction_lost": 0.651
} | 1 |
co_stru_00232 | structural_effect | coding_variant | easy | 1 | NM_004360.5(CDH1):c.628G>T (p.Glu210Ter) introduces a premature truncation at residue 210 of CDH1's 882-residue protein product (AlphaFold model, mean pLDDT 79.16). Approximately how much of the protein is lost downstream of the truncation? | NM_004360.5(CDH1):c.628G>T (p.Glu210Ter) VARIANT_IN_GENE CDH1 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_004360.5(CDH1):c.628G>T (p.Glu210Ter)",
"source_node_type": "VARIANT",
"source_node_label": "NM_004360.5(CDH1):c.628G>T (p.Glu210Ter)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1... | C | [
"A. a substantial portion (25-50%)",
"B. a small C-terminal portion (<25%)",
"C. more than half the protein (>50%)"
] | [
"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": "CDH1",
"text": "NM_004360.5(CDH1):c.628G>T (p.Glu210Ter) VARIANT_IN_GENE CDH1",
"confidence": 1
}
] | {
"variant": "NM_004360.5(CDH1):c.628G>T (p.Glu210Ter)",
"gene": "CDH1",
"truncation_residue": 210,
"protein_length": 882,
"fraction_lost": 0.762
} | 1 |
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