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_00033 | structural_effect | coding_variant | easy | 1 | NM_000455.5(STK11):c.641_662del (p.Gln214fs) introduces a premature truncation at residue 214 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.641_662del (p.Gln214fs) VARIANT_IN_GENE STK11 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000455.5(STK11):c.641_662del (p.Gln214fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000455.5(STK11):c.641_662del (p.Gln214fs)",
"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.641_662del (p.Gln214fs) VARIANT_IN_GENE STK11",
"confidence": 1
}
] | {
"variant": "NM_000455.5(STK11):c.641_662del (p.Gln214fs)",
"gene": "STK11",
"truncation_residue": 214,
"protein_length": 433,
"fraction_lost": 0.506
} | 1 |
co_stru_00034 | structural_effect | coding_variant | easy | 1 | NM_007194.4(CHEK2):c.934A>T (p.Lys312Ter) introduces a premature truncation at residue 312 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.934A>T (p.Lys312Ter) VARIANT_IN_GENE CHEK2 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_007194.4(CHEK2):c.934A>T (p.Lys312Ter)",
"source_node_type": "VARIANT",
"source_node_label": "NM_007194.4(CHEK2):c.934A>T (p.Lys312Ter)",
"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": "CHEK2",
"source_db": "UniProt",
"payload": {
"accession": "O96017",
"sequence": "MSRESDVEAQQSHGSSACSQPHGSVTQSQGSSSQSQGISSSSTSTMPNSSQSSHSSSGTLSSLETVSTQELYSIPEDQEPEDQEPEEPTPAPWARLWALQDGFANLECVNDNYWFGRDKSCEYCFDEPLLKRT... | [
{
"source_db": "ClinVar",
"source_id": "CHEK2",
"text": "NM_007194.4(CHEK2):c.934A>T (p.Lys312Ter) VARIANT_IN_GENE CHEK2",
"confidence": 1
}
] | {
"variant": "NM_007194.4(CHEK2):c.934A>T (p.Lys312Ter)",
"gene": "CHEK2",
"truncation_residue": 312,
"protein_length": 543,
"fraction_lost": 0.425
} | 1 |
co_stru_00035 | structural_effect | coding_variant | easy | 1 | NM_000057.4(BLM):c.1108C>T (p.Gln370Ter) introduces a premature truncation at residue 370 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.1108C>T (p.Gln370Ter) VARIANT_IN_GENE BLM | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000057.4(BLM):c.1108C>T (p.Gln370Ter)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000057.4(BLM):c.1108C>T (p.Gln370Ter)",
"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%)"
] | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "NM_000057.4(BLM):c.1108C>T (p.Gln370Ter)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr15",
"pos": 90760167,
"track": "phyloP100way",
"window": 20,
"scores": [
-0.513016,
... | [
{
"source_db": "ClinVar",
"source_id": "BLM",
"text": "NM_000057.4(BLM):c.1108C>T (p.Gln370Ter) VARIANT_IN_GENE BLM",
"confidence": 1
}
] | {
"variant": "NM_000057.4(BLM):c.1108C>T (p.Gln370Ter)",
"gene": "BLM",
"truncation_residue": 370,
"protein_length": 1417,
"fraction_lost": 0.739
} | 1 |
co_stru_00036 | structural_effect | coding_variant | easy | 1 | NM_015338.6(ASXL1):c.2477del (p.Gly826fs) introduces a premature truncation at residue 826 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.2477del (p.Gly826fs) VARIANT_IN_GENE ASXL1 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_015338.6(ASXL1):c.2477del (p.Gly826fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_015338.6(ASXL1):c.2477del (p.Gly826fs)",
"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%)"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ASXL1",
"source_db": "UniProt",
"payload": {
"accession": "Q8IXJ9",
"sequence": "MKDKQKKKKERTWAEAARLVLENYSDAPMTPKQILQVIEAEGLKEMRSGTSPLACLNAMLHSNSRGGEGLFYKLPGRISLFTLKKDALQWSRHPATVEGEEPEDTADVESCGSNEASTVSGENDVSLDETSSN... | [
{
"source_db": "ClinVar",
"source_id": "ASXL1",
"text": "NM_015338.6(ASXL1):c.2477del (p.Gly826fs) VARIANT_IN_GENE ASXL1",
"confidence": 1
}
] | {
"variant": "NM_015338.6(ASXL1):c.2477del (p.Gly826fs)",
"gene": "ASXL1",
"truncation_residue": 826,
"protein_length": 1541,
"fraction_lost": 0.464
} | 1 |
co_stru_00037 | structural_effect | coding_variant | easy | 1 | NM_000179.3(MSH6):c.1055_1056insC (p.Val352_Ser353insTer) introduces a premature truncation at residue 352 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.1055_1056insC (p.Val352_Ser353insTer) VARIANT_IN_GENE MSH6 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000179.3(MSH6):c.1055_1056insC (p.Val352_Ser353insTer)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000179.3(MSH6):c.1055_1056insC (p.Val352_Ser353insTer)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "cu... | 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.1055_1056insC (p.Val352_Ser353insTer) VARIANT_IN_GENE MSH6",
"confidence": 1
}
] | {
"variant": "NM_000179.3(MSH6):c.1055_1056insC (p.Val352_Ser353insTer)",
"gene": "MSH6",
"truncation_residue": 352,
"protein_length": 1360,
"fraction_lost": 0.741
} | 1 |
co_stru_00038 | structural_effect | coding_variant | easy | 1 | NM_004360.5(CDH1):c.326del (p.Lys109fs) introduces a premature truncation at residue 109 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.326del (p.Lys109fs) VARIANT_IN_GENE CDH1 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_004360.5(CDH1):c.326del (p.Lys109fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_004360.5(CDH1):c.326del (p.Lys109fs)",
"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": "CDH1",
"source_db": "UniProt",
"payload": {
"accession": "P12830",
"sequence": "MGPWSRSLSALLLLLQVSSWLCQEPEPCHPGFDAESYTFTVPRRHLERGRVLGRVNFEDCTGRQRTAYFSLDTRFKVGTDGVITVKRPLRFHNPQIHFLVYAWDSTYRKFSTKVTLNTVGHHHRPPPHQASVSG... | [
{
"source_db": "ClinVar",
"source_id": "CDH1",
"text": "NM_004360.5(CDH1):c.326del (p.Lys109fs) VARIANT_IN_GENE CDH1",
"confidence": 1
}
] | {
"variant": "NM_004360.5(CDH1):c.326del (p.Lys109fs)",
"gene": "CDH1",
"truncation_residue": 109,
"protein_length": 882,
"fraction_lost": 0.876
} | 1 |
co_stru_00039 | structural_effect | coding_variant | easy | 1 | NM_000465.4(BARD1):c.2036T>A (p.Leu679Ter) introduces a premature truncation at residue 679 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.2036T>A (p.Leu679Ter) VARIANT_IN_GENE BARD1 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000465.4(BARD1):c.2036T>A (p.Leu679Ter)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000465.4(BARD1):c.2036T>A (p.Leu679Ter)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence... | 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": "BARD1",
"source_db": "UniProt",
"payload": {
"accession": "Q99728",
"sequence": "MPDNRQPRNRQPRIRSGNEPRSAPAMEPDGRGAWAHSRAALDRLEKLLRCSRCTNILREPVCLGGCEHIFCSNCVSDCIGTGCPVCYTPAWIQDLKINRQLDSMIQLCSKLRNLLHDNELSDLKEDKPRKSLF... | [
{
"source_db": "ClinVar",
"source_id": "BARD1",
"text": "NM_000465.4(BARD1):c.2036T>A (p.Leu679Ter) VARIANT_IN_GENE BARD1",
"confidence": 1
}
] | {
"variant": "NM_000465.4(BARD1):c.2036T>A (p.Leu679Ter)",
"gene": "BARD1",
"truncation_residue": 679,
"protein_length": 777,
"fraction_lost": 0.126
} | 1 |
co_stru_00040 | structural_effect | coding_variant | easy | 1 | NM_001288705.3(CSF1R):c.828C>G (p.Tyr276Ter) introduces a premature truncation at residue 276 of CSF1R's 972-residue protein product (AlphaFold model, mean pLDDT 77.81). Approximately how much of the protein is lost downstream of the truncation? | NM_001288705.3(CSF1R):c.828C>G (p.Tyr276Ter) VARIANT_IN_GENE CSF1R | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_001288705.3(CSF1R):c.828C>G (p.Tyr276Ter)",
"source_node_type": "VARIANT",
"source_node_label": "NM_001288705.3(CSF1R):c.828C>G (p.Tyr276Ter)",
"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": "CSF1R",
"source_db": "UniProt",
"payload": {
"accession": "P07333",
"sequence": "MGPGVLLLLLVATAWHGQGIPVIEPSVPELVVKPGATVTLRCVGNGSVEWDGPPSPHWTLYSDGSSSILSTNNATFQNTGTYRCTEPGDPLGGSAAIHLYVKDPARPWNVLAQEVVVFEDQDALLPCLLTDPV... | [
{
"source_db": "ClinVar",
"source_id": "CSF1R",
"text": "NM_001288705.3(CSF1R):c.828C>G (p.Tyr276Ter) VARIANT_IN_GENE CSF1R",
"confidence": 1
}
] | {
"variant": "NM_001288705.3(CSF1R):c.828C>G (p.Tyr276Ter)",
"gene": "CSF1R",
"truncation_residue": 276,
"protein_length": 972,
"fraction_lost": 0.716
} | 1 |
co_stru_00041 | structural_effect | coding_variant | easy | 1 | NM_058216.3(RAD51C):c.160A>T (p.Lys54Ter) introduces a premature truncation at residue 54 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.160A>T (p.Lys54Ter) VARIANT_IN_GENE RAD51C | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_058216.3(RAD51C):c.160A>T (p.Lys54Ter)",
"source_node_type": "VARIANT",
"source_node_label": "NM_058216.3(RAD51C):c.160A>T (p.Lys54Ter)",
"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": "RAD51C",
"source_db": "UniProt",
"payload": {
"accession": "O43502",
"sequence": "MRGKTFRFEMQRDLVSFPLSPAVRVKLVSAGFQTAEELLEVKPSELSKEVGISKAEALETLQIIRRECLTNKPRYAGTSESHKKCTALELLEQEHTQGFIITFCSALDDILGGGVPLMKTTEICGAPGVGKT... | [
{
"source_db": "ClinVar",
"source_id": "RAD51C",
"text": "NM_058216.3(RAD51C):c.160A>T (p.Lys54Ter) VARIANT_IN_GENE RAD51C",
"confidence": 1
}
] | {
"variant": "NM_058216.3(RAD51C):c.160A>T (p.Lys54Ter)",
"gene": "RAD51C",
"truncation_residue": 54,
"protein_length": 376,
"fraction_lost": 0.856
} | 1 |
co_stru_00042 | structural_effect | coding_variant | easy | 1 | NM_015046.7(SETX):c.4890dup (p.Ile1631fs) introduces a premature truncation at residue 1631 of SETX's 2677-residue protein product (AlphaFold model, mean pLDDT 52.27). Approximately how much of the protein is lost downstream of the truncation? | NM_015046.7(SETX):c.4890dup (p.Ile1631fs) VARIANT_IN_GENE SETX | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_015046.7(SETX):c.4890dup (p.Ile1631fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_015046.7(SETX):c.4890dup (p.Ile1631fs)",
"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": "SETX",
"source_db": "UniProt",
"payload": {
"accession": "Q7Z333",
"sequence": "MSTCCWCTPGGASTIDFLKRYASNTPSGEFQTADEDLCYCLECVAEYHKARDELPFLHEVLWELETLRLINHFEKSMKAEIGDDDELYIVDNNGEMPLFDITGQDFENKLRVPLLEILKYPYLLLHERVNELCV... | [
{
"source_db": "ClinVar",
"source_id": "SETX",
"text": "NM_015046.7(SETX):c.4890dup (p.Ile1631fs) VARIANT_IN_GENE SETX",
"confidence": 1
}
] | {
"variant": "NM_015046.7(SETX):c.4890dup (p.Ile1631fs)",
"gene": "SETX",
"truncation_residue": 1631,
"protein_length": 2677,
"fraction_lost": 0.391
} | 1 |
co_stru_00043 | structural_effect | coding_variant | easy | 1 | NM_007194.4(CHEK2):c.1304C>A (p.Ser435Ter) introduces a premature truncation at residue 435 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.1304C>A (p.Ser435Ter) VARIANT_IN_GENE CHEK2 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_007194.4(CHEK2):c.1304C>A (p.Ser435Ter)",
"source_node_type": "VARIANT",
"source_node_label": "NM_007194.4(CHEK2):c.1304C>A (p.Ser435Ter)",
"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",
"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.1304C>A (p.Ser435Ter) VARIANT_IN_GENE CHEK2",
"confidence": 1
}
] | {
"variant": "NM_007194.4(CHEK2):c.1304C>A (p.Ser435Ter)",
"gene": "CHEK2",
"truncation_residue": 435,
"protein_length": 543,
"fraction_lost": 0.199
} | 1 |
co_stru_00044 | structural_effect | coding_variant | easy | 1 | NM_002878.4(RAD51D):c.76_77del (p.Lys26fs) introduces a premature truncation at residue 26 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.76_77del (p.Lys26fs) VARIANT_IN_GENE RAD51D | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_002878.4(RAD51D):c.76_77del (p.Lys26fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_002878.4(RAD51D):c.76_77del (p.Lys26fs)",
"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": "RAD51D",
"source_db": "UniProt",
"payload": {
"accession": "O75771",
"sequence": "MGVLRVGLCPGLTEEMIQLLRSHRIKTVVDLVSADLEEVAQKCGLSYKALVALRRVLLAQFSAFPVNGADLYEELKTSTAILSTGIGSLDKLLDAGLYTGEVTEIVGGPGSGKTQVCLCMAANVAHGLQQNV... | [
{
"source_db": "ClinVar",
"source_id": "RAD51D",
"text": "NM_002878.4(RAD51D):c.76_77del (p.Lys26fs) VARIANT_IN_GENE RAD51D",
"confidence": 1
}
] | {
"variant": "NM_002878.4(RAD51D):c.76_77del (p.Lys26fs)",
"gene": "RAD51D",
"truncation_residue": 26,
"protein_length": 328,
"fraction_lost": 0.921
} | 1 |
co_stru_00045 | structural_effect | coding_variant | easy | 1 | NM_058216.3(RAD51C):c.858_861dup (p.Thr288fs) introduces a premature truncation at residue 288 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.858_861dup (p.Thr288fs) VARIANT_IN_GENE RAD51C | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_058216.3(RAD51C):c.858_861dup (p.Thr288fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_058216.3(RAD51C):c.858_861dup (p.Thr288fs)",
"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%)"
] | [
"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.858_861dup (p.Thr288fs) VARIANT_IN_GENE RAD51C",
"confidence": 1
}
] | {
"variant": "NM_058216.3(RAD51C):c.858_861dup (p.Thr288fs)",
"gene": "RAD51C",
"truncation_residue": 288,
"protein_length": 376,
"fraction_lost": 0.234
} | 1 |
co_stru_00046 | structural_effect | coding_variant | easy | 1 | NM_000546.6(TP53):c.436_457del (p.Trp146fs) introduces a premature truncation at residue 146 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.436_457del (p.Trp146fs) VARIANT_IN_GENE TP53 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000546.6(TP53):c.436_457del (p.Trp146fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000546.6(TP53):c.436_457del (p.Trp146fs)",
"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": "TP53",
"source_db": "UniProt",
"payload": {
"accession": "P04637",
"sequence": "MEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPGPDEAPRMPEAAPPVAPAPAAPTPAAPAPAPSWPLSSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMF... | [
{
"source_db": "ClinVar",
"source_id": "TP53",
"text": "NM_000546.6(TP53):c.436_457del (p.Trp146fs) VARIANT_IN_GENE TP53",
"confidence": 1
}
] | {
"variant": "NM_000546.6(TP53):c.436_457del (p.Trp146fs)",
"gene": "TP53",
"truncation_residue": 146,
"protein_length": 393,
"fraction_lost": 0.628
} | 1 |
co_stru_00047 | structural_effect | coding_variant | easy | 1 | NM_024675.4(PALB2):c.3392del (p.Ile1131fs) introduces a premature truncation at residue 1131 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.3392del (p.Ile1131fs) VARIANT_IN_GENE PALB2 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_024675.4(PALB2):c.3392del (p.Ile1131fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_024675.4(PALB2):c.3392del (p.Ile1131fs)",
"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": "PALB2",
"source_db": "UniProt",
"payload": {
"accession": "Q86YC2",
"sequence": "MDEPPGKPLSCEEKEKLKEKLAFLKREYSKTLARLQRAQRAEKIKHSIKKTVEEQDCLSQQDLSPQLKHSEPKNKICVYDKLHIKTHLDEETGEKTSITLDVGPESFNPGDGPGGLPIQRTDDTQEHFPHRVS... | [
{
"source_db": "ClinVar",
"source_id": "PALB2",
"text": "NM_024675.4(PALB2):c.3392del (p.Ile1131fs) VARIANT_IN_GENE PALB2",
"confidence": 1
}
] | {
"variant": "NM_024675.4(PALB2):c.3392del (p.Ile1131fs)",
"gene": "PALB2",
"truncation_residue": 1131,
"protein_length": 1186,
"fraction_lost": 0.046
} | 1 |
co_stru_00048 | structural_effect | coding_variant | easy | 1 | NM_000465.4(BARD1):c.513del (p.Asp172fs) introduces a premature truncation at residue 172 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.513del (p.Asp172fs) VARIANT_IN_GENE BARD1 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000465.4(BARD1):c.513del (p.Asp172fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000465.4(BARD1):c.513del (p.Asp172fs)",
"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": "BARD1",
"source_db": "UniProt",
"payload": {
"accession": "Q99728",
"sequence": "MPDNRQPRNRQPRIRSGNEPRSAPAMEPDGRGAWAHSRAALDRLEKLLRCSRCTNILREPVCLGGCEHIFCSNCVSDCIGTGCPVCYTPAWIQDLKINRQLDSMIQLCSKLRNLLHDNELSDLKEDKPRKSLF... | [
{
"source_db": "ClinVar",
"source_id": "BARD1",
"text": "NM_000465.4(BARD1):c.513del (p.Asp172fs) VARIANT_IN_GENE BARD1",
"confidence": 1
}
] | {
"variant": "NM_000465.4(BARD1):c.513del (p.Asp172fs)",
"gene": "BARD1",
"truncation_residue": 172,
"protein_length": 777,
"fraction_lost": 0.779
} | 1 |
co_stru_00049 | structural_effect | coding_variant | easy | 1 | NM_000249.4(MLH1):c.597_598dup (p.Thr200fs) introduces a premature truncation at residue 200 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.597_598dup (p.Thr200fs) VARIANT_IN_GENE MLH1 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000249.4(MLH1):c.597_598dup (p.Thr200fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000249.4(MLH1):c.597_598dup (p.Thr200fs)",
"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.597_598dup (p.Thr200fs) VARIANT_IN_GENE MLH1",
"confidence": 1
}
] | {
"variant": "NM_000249.4(MLH1):c.597_598dup (p.Thr200fs)",
"gene": "MLH1",
"truncation_residue": 200,
"protein_length": 756,
"fraction_lost": 0.735
} | 1 |
co_stru_00050 | structural_effect | coding_variant | easy | 1 | NM_024675.4(PALB2):c.2889_2890del (p.Gly964fs) introduces a premature truncation at residue 964 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.2889_2890del (p.Gly964fs) VARIANT_IN_GENE PALB2 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_024675.4(PALB2):c.2889_2890del (p.Gly964fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_024675.4(PALB2):c.2889_2890del (p.Gly964fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_co... | 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": "PALB2",
"source_db": "UniProt",
"payload": {
"accession": "Q86YC2",
"sequence": "MDEPPGKPLSCEEKEKLKEKLAFLKREYSKTLARLQRAQRAEKIKHSIKKTVEEQDCLSQQDLSPQLKHSEPKNKICVYDKLHIKTHLDEETGEKTSITLDVGPESFNPGDGPGGLPIQRTDDTQEHFPHRVS... | [
{
"source_db": "ClinVar",
"source_id": "PALB2",
"text": "NM_024675.4(PALB2):c.2889_2890del (p.Gly964fs) VARIANT_IN_GENE PALB2",
"confidence": 1
}
] | {
"variant": "NM_024675.4(PALB2):c.2889_2890del (p.Gly964fs)",
"gene": "PALB2",
"truncation_residue": 964,
"protein_length": 1186,
"fraction_lost": 0.187
} | 1 |
co_stru_00051 | structural_effect | coding_variant | easy | 1 | NM_007194.4(CHEK2):c.233_239del (p.Gln78fs) introduces a premature truncation at residue 78 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.233_239del (p.Gln78fs) VARIANT_IN_GENE CHEK2 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_007194.4(CHEK2):c.233_239del (p.Gln78fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_007194.4(CHEK2):c.233_239del (p.Gln78fs)",
"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": "CHEK2",
"source_db": "UniProt",
"payload": {
"accession": "O96017",
"sequence": "MSRESDVEAQQSHGSSACSQPHGSVTQSQGSSSQSQGISSSSTSTMPNSSQSSHSSSGTLSSLETVSTQELYSIPEDQEPEDQEPEEPTPAPWARLWALQDGFANLECVNDNYWFGRDKSCEYCFDEPLLKRT... | [
{
"source_db": "ClinVar",
"source_id": "CHEK2",
"text": "NM_007194.4(CHEK2):c.233_239del (p.Gln78fs) VARIANT_IN_GENE CHEK2",
"confidence": 1
}
] | {
"variant": "NM_007194.4(CHEK2):c.233_239del (p.Gln78fs)",
"gene": "CHEK2",
"truncation_residue": 78,
"protein_length": 543,
"fraction_lost": 0.856
} | 1 |
co_stru_00052 | structural_effect | coding_variant | easy | 1 | NM_000314.8(PTEN):c.510_513del (p.Ser170fs) introduces a premature truncation at residue 170 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.510_513del (p.Ser170fs) VARIANT_IN_GENE PTEN | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000314.8(PTEN):c.510_513del (p.Ser170fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000314.8(PTEN):c.510_513del (p.Ser170fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confiden... | 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": "PTEN",
"source_db": "UniProt",
"payload": {
"accession": "P60484",
"sequence": "MTAIIKEIVSRNKRRYQEDGFDLDLTYIYPNIIAMGFPAERLEGVYRNNIDDVVRFLDSKHKNHYKIYNLCAERHYDTAKFNCRVAQYPFEDHNPPQLELIKPFCEDLDQWLSEDDNHVAAIHCKAGKGRTGVM... | [
{
"source_db": "ClinVar",
"source_id": "PTEN",
"text": "NM_000314.8(PTEN):c.510_513del (p.Ser170fs) VARIANT_IN_GENE PTEN",
"confidence": 1
}
] | {
"variant": "NM_000314.8(PTEN):c.510_513del (p.Ser170fs)",
"gene": "PTEN",
"truncation_residue": 170,
"protein_length": 403,
"fraction_lost": 0.578
} | 1 |
co_stru_00053 | structural_effect | coding_variant | easy | 1 | NM_000455.5(STK11):c.288_289dup (p.Lys97fs) introduces a premature truncation at residue 97 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.288_289dup (p.Lys97fs) VARIANT_IN_GENE STK11 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000455.5(STK11):c.288_289dup (p.Lys97fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000455.5(STK11):c.288_289dup (p.Lys97fs)",
"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": "STK11",
"source_db": "UniProt",
"payload": {
"accession": "Q15831",
"sequence": "MEVVDPQQLGMFTEGELMSVGMDTFIHRIDSTEVIYQPRRKRAKLIGKYLMGDLLGEGSYGKVKEVLDSETLCRRAVKILKKKKLRRIPNGEANVKKEIQLLRRLRHKNVIQLVDVLYNEEKQKMYMVMEYCV... | [
{
"source_db": "ClinVar",
"source_id": "STK11",
"text": "NM_000455.5(STK11):c.288_289dup (p.Lys97fs) VARIANT_IN_GENE STK11",
"confidence": 1
}
] | {
"variant": "NM_000455.5(STK11):c.288_289dup (p.Lys97fs)",
"gene": "STK11",
"truncation_residue": 97,
"protein_length": 433,
"fraction_lost": 0.776
} | 1 |
co_stru_00054 | structural_effect | coding_variant | easy | 1 | NM_004928.3(CFAP410):c.285_289del (p.Glu96fs) introduces a premature truncation at residue 96 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.285_289del (p.Glu96fs) VARIANT_IN_GENE CFAP410 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_004928.3(CFAP410):c.285_289del (p.Glu96fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_004928.3(CFAP410):c.285_289del (p.Glu96fs)",
"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%)"
] | [
"conservation",
"protein_sequence",
"protein_structure"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "NM_004928.3(CFAP410):c.285_289del (p.Glu96fs)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr21",
"pos": 44333117,
"track": "phyloP100way",
"window": 20,
"scores": [
1.60793,
... | [
{
"source_db": "ClinVar",
"source_id": "CFAP410",
"text": "NM_004928.3(CFAP410):c.285_289del (p.Glu96fs) VARIANT_IN_GENE CFAP410",
"confidence": 1
}
] | {
"variant": "NM_004928.3(CFAP410):c.285_289del (p.Glu96fs)",
"gene": "CFAP410",
"truncation_residue": 96,
"protein_length": 256,
"fraction_lost": 0.625
} | 1 |
co_stru_00055 | structural_effect | coding_variant | easy | 1 | NM_177924.5(ASAH1):c.605C>G (p.Ser202Ter) introduces a premature truncation at residue 202 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.605C>G (p.Ser202Ter) VARIANT_IN_GENE ASAH1 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_177924.5(ASAH1):c.605C>G (p.Ser202Ter)",
"source_node_type": "VARIANT",
"source_node_label": "NM_177924.5(ASAH1):c.605C>G (p.Ser202Ter)",
"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",
"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.605C>G (p.Ser202Ter) VARIANT_IN_GENE ASAH1",
"confidence": 1
}
] | {
"variant": "NM_177924.5(ASAH1):c.605C>G (p.Ser202Ter)",
"gene": "ASAH1",
"truncation_residue": 202,
"protein_length": 395,
"fraction_lost": 0.489
} | 1 |
co_stru_00056 | structural_effect | coding_variant | easy | 1 | NM_005235.3(ERBB4):c.29G>A (p.Trp10Ter) introduces a premature truncation at residue 10 of ERBB4's 1308-residue protein product (AlphaFold model, mean pLDDT 73.12). Approximately how much of the protein is lost downstream of the truncation? | NM_005235.3(ERBB4):c.29G>A (p.Trp10Ter) VARIANT_IN_GENE ERBB4 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_005235.3(ERBB4):c.29G>A (p.Trp10Ter)",
"source_node_type": "VARIANT",
"source_node_label": "NM_005235.3(ERBB4):c.29G>A (p.Trp10Ter)",
"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%)"
] | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "NM_005235.3(ERBB4):c.29G>A (p.Trp10Ter)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr2",
"pos": 212538502,
"track": "phyloP100way",
"window": 20,
"scores": [
0.512976,
-... | [
{
"source_db": "ClinVar",
"source_id": "ERBB4",
"text": "NM_005235.3(ERBB4):c.29G>A (p.Trp10Ter) VARIANT_IN_GENE ERBB4",
"confidence": 1
}
] | {
"variant": "NM_005235.3(ERBB4):c.29G>A (p.Trp10Ter)",
"gene": "ERBB4",
"truncation_residue": 10,
"protein_length": 1308,
"fraction_lost": 0.992
} | 1 |
co_stru_00057 | structural_effect | coding_variant | easy | 1 | NM_001903.5(CTNNA1):c.1636C>T (p.Arg546Ter) introduces a premature truncation at residue 546 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.1636C>T (p.Arg546Ter) VARIANT_IN_GENE CTNNA1 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_001903.5(CTNNA1):c.1636C>T (p.Arg546Ter)",
"source_node_type": "VARIANT",
"source_node_label": "NM_001903.5(CTNNA1):c.1636C>T (p.Arg546Ter)",
"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": "CTNNA1",
"source_db": "UniProt",
"payload": {
"accession": "P35221",
"sequence": "MTAVHAGNINFKWDPKSLEIRTLAVERLLEPLVTQVTTLVNTNSKGPSNKKRGRSKKAHVLAASVEQATENFLEKGDKIAKESQFLKEELVAAVEDVRKQGDLMKAAAGEFADDPCSSVKRGNMVRAARALL... | [
{
"source_db": "ClinVar",
"source_id": "CTNNA1",
"text": "NM_001903.5(CTNNA1):c.1636C>T (p.Arg546Ter) VARIANT_IN_GENE CTNNA1",
"confidence": 1
}
] | {
"variant": "NM_001903.5(CTNNA1):c.1636C>T (p.Arg546Ter)",
"gene": "CTNNA1",
"truncation_residue": 546,
"protein_length": 906,
"fraction_lost": 0.397
} | 1 |
co_stru_00058 | structural_effect | coding_variant | easy | 1 | NM_000179.3(MSH6):c.1263_1311dup (p.Met438Ter) introduces a premature truncation at residue 438 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.1263_1311dup (p.Met438Ter) VARIANT_IN_GENE MSH6 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000179.3(MSH6):c.1263_1311dup (p.Met438Ter)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000179.3(MSH6):c.1263_1311dup (p.Met438Ter)",
"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": "MSH6",
"source_db": "UniProt",
"payload": {
"accession": "P52701",
"sequence": "MSRQSTLYSFFPKSPALSDANKASARASREGGRAAAAPGASPSPGGDAAWSEAGPGPRPLARSASPPKAKNLNGGLRRSVAPAAPTSCDFSPGDLVWAKMEGYPWWPCLVYNHPFDGTFIREKGKSVRVHVQFF... | [
{
"source_db": "ClinVar",
"source_id": "MSH6",
"text": "NM_000179.3(MSH6):c.1263_1311dup (p.Met438Ter) VARIANT_IN_GENE MSH6",
"confidence": 1
}
] | {
"variant": "NM_000179.3(MSH6):c.1263_1311dup (p.Met438Ter)",
"gene": "MSH6",
"truncation_residue": 438,
"protein_length": 1360,
"fraction_lost": 0.678
} | 1 |
co_stru_00059 | structural_effect | coding_variant | easy | 1 | NM_058216.3(RAD51C):c.312T>A (p.Cys104Ter) introduces a premature truncation at residue 104 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.312T>A (p.Cys104Ter) VARIANT_IN_GENE RAD51C | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_058216.3(RAD51C):c.312T>A (p.Cys104Ter)",
"source_node_type": "VARIANT",
"source_node_label": "NM_058216.3(RAD51C):c.312T>A (p.Cys104Ter)",
"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": "RAD51C",
"source_db": "UniProt",
"payload": {
"accession": "O43502",
"sequence": "MRGKTFRFEMQRDLVSFPLSPAVRVKLVSAGFQTAEELLEVKPSELSKEVGISKAEALETLQIIRRECLTNKPRYAGTSESHKKCTALELLEQEHTQGFIITFCSALDDILGGGVPLMKTTEICGAPGVGKT... | [
{
"source_db": "ClinVar",
"source_id": "RAD51C",
"text": "NM_058216.3(RAD51C):c.312T>A (p.Cys104Ter) VARIANT_IN_GENE RAD51C",
"confidence": 1
}
] | {
"variant": "NM_058216.3(RAD51C):c.312T>A (p.Cys104Ter)",
"gene": "RAD51C",
"truncation_residue": 104,
"protein_length": 376,
"fraction_lost": 0.723
} | 1 |
co_stru_00060 | structural_effect | coding_variant | easy | 1 | NM_000251.3(MSH2):c.1989_1994delinsAAAC (p.Met663fs) introduces a premature truncation at residue 663 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.1989_1994delinsAAAC (p.Met663fs) VARIANT_IN_GENE MSH2 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000251.3(MSH2):c.1989_1994delinsAAAC (p.Met663fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000251.3(MSH2):c.1989_1994delinsAAAC (p.Met663fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
... | 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": "MSH2",
"source_db": "UniProt",
"payload": {
"accession": "P43246",
"sequence": "MAVQPKETLQLESAAEVGFVRFFQGMPEKPTTTVRLFDRGDFYTAHGEDALLAAREVFKTQGVIKYMGPAGAKNLQSVVLSKMNFESFVKDLLLVRQYRVEVYKNRAGNKASKENDWYLAYKASPGNLSQFEDI... | [
{
"source_db": "ClinVar",
"source_id": "MSH2",
"text": "NM_000251.3(MSH2):c.1989_1994delinsAAAC (p.Met663fs) VARIANT_IN_GENE MSH2",
"confidence": 1
}
] | {
"variant": "NM_000251.3(MSH2):c.1989_1994delinsAAAC (p.Met663fs)",
"gene": "MSH2",
"truncation_residue": 663,
"protein_length": 934,
"fraction_lost": 0.29
} | 1 |
co_stru_00061 | structural_effect | coding_variant | easy | 1 | NM_007194.4(CHEK2):c.188T>A (p.Leu63Ter) introduces a premature truncation at residue 63 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.188T>A (p.Leu63Ter) VARIANT_IN_GENE CHEK2 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_007194.4(CHEK2):c.188T>A (p.Leu63Ter)",
"source_node_type": "VARIANT",
"source_node_label": "NM_007194.4(CHEK2):c.188T>A (p.Leu63Ter)",
"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": "CHEK2",
"source_db": "UniProt",
"payload": {
"accession": "O96017",
"sequence": "MSRESDVEAQQSHGSSACSQPHGSVTQSQGSSSQSQGISSSSTSTMPNSSQSSHSSSGTLSSLETVSTQELYSIPEDQEPEDQEPEEPTPAPWARLWALQDGFANLECVNDNYWFGRDKSCEYCFDEPLLKRT... | [
{
"source_db": "ClinVar",
"source_id": "CHEK2",
"text": "NM_007194.4(CHEK2):c.188T>A (p.Leu63Ter) VARIANT_IN_GENE CHEK2",
"confidence": 1
}
] | {
"variant": "NM_007194.4(CHEK2):c.188T>A (p.Leu63Ter)",
"gene": "CHEK2",
"truncation_residue": 63,
"protein_length": 543,
"fraction_lost": 0.884
} | 1 |
co_stru_00062 | structural_effect | coding_variant | easy | 1 | NM_000465.4(BARD1):c.2301_2303delinsACATC (p.Met768fs) introduces a premature truncation at residue 768 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.2301_2303delinsACATC (p.Met768fs) VARIANT_IN_GENE BARD1 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000465.4(BARD1):c.2301_2303delinsACATC (p.Met768fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000465.4(BARD1):c.2301_2303delinsACATC (p.Met768fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated"... | 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": "BARD1",
"source_db": "UniProt",
"payload": {
"accession": "Q99728",
"sequence": "MPDNRQPRNRQPRIRSGNEPRSAPAMEPDGRGAWAHSRAALDRLEKLLRCSRCTNILREPVCLGGCEHIFCSNCVSDCIGTGCPVCYTPAWIQDLKINRQLDSMIQLCSKLRNLLHDNELSDLKEDKPRKSLF... | [
{
"source_db": "ClinVar",
"source_id": "BARD1",
"text": "NM_000465.4(BARD1):c.2301_2303delinsACATC (p.Met768fs) VARIANT_IN_GENE BARD1",
"confidence": 1
}
] | {
"variant": "NM_000465.4(BARD1):c.2301_2303delinsACATC (p.Met768fs)",
"gene": "BARD1",
"truncation_residue": 768,
"protein_length": 777,
"fraction_lost": 0.012
} | 1 |
co_stru_00063 | structural_effect | coding_variant | easy | 1 | NM_000465.4(BARD1):c.1944del (p.Glu649fs) introduces a premature truncation at residue 649 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.1944del (p.Glu649fs) VARIANT_IN_GENE BARD1 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000465.4(BARD1):c.1944del (p.Glu649fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000465.4(BARD1):c.1944del (p.Glu649fs)",
"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.1944del (p.Glu649fs) VARIANT_IN_GENE BARD1",
"confidence": 1
}
] | {
"variant": "NM_000465.4(BARD1):c.1944del (p.Glu649fs)",
"gene": "BARD1",
"truncation_residue": 649,
"protein_length": 777,
"fraction_lost": 0.165
} | 1 |
co_stru_00064 | structural_effect | coding_variant | easy | 1 | NM_001903.5(CTNNA1):c.1999C>T (p.Gln667Ter) introduces a premature truncation at residue 667 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.1999C>T (p.Gln667Ter) VARIANT_IN_GENE CTNNA1 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_001903.5(CTNNA1):c.1999C>T (p.Gln667Ter)",
"source_node_type": "VARIANT",
"source_node_label": "NM_001903.5(CTNNA1):c.1999C>T (p.Gln667Ter)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confiden... | 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": "CTNNA1",
"source_db": "UniProt",
"payload": {
"accession": "P35221",
"sequence": "MTAVHAGNINFKWDPKSLEIRTLAVERLLEPLVTQVTTLVNTNSKGPSNKKRGRSKKAHVLAASVEQATENFLEKGDKIAKESQFLKEELVAAVEDVRKQGDLMKAAAGEFADDPCSSVKRGNMVRAARALL... | [
{
"source_db": "ClinVar",
"source_id": "CTNNA1",
"text": "NM_001903.5(CTNNA1):c.1999C>T (p.Gln667Ter) VARIANT_IN_GENE CTNNA1",
"confidence": 1
}
] | {
"variant": "NM_001903.5(CTNNA1):c.1999C>T (p.Gln667Ter)",
"gene": "CTNNA1",
"truncation_residue": 667,
"protein_length": 906,
"fraction_lost": 0.264
} | 1 |
co_stru_00065 | structural_effect | coding_variant | easy | 1 | NM_000535.7(PMS2):c.1010del (p.Thr337fs) introduces a premature truncation at residue 337 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.1010del (p.Thr337fs) VARIANT_IN_GENE PMS2 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000535.7(PMS2):c.1010del (p.Thr337fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000535.7(PMS2):c.1010del (p.Thr337fs)",
"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": "PMS2",
"source_db": "UniProt",
"payload": {
"accession": "P54278",
"sequence": "MERAESSSTEPAKAIKPIDRKSVHQICSGQVVLSLSTAVKELVENSLDAGATNIDLKLKDYGVDLIEVSDNGCGVEEENFEGLTLKHHTSKIQEFADLTQVETFGFRGEALSSLCALSDVTISTCHASAKVGTR... | [
{
"source_db": "ClinVar",
"source_id": "PMS2",
"text": "NM_000535.7(PMS2):c.1010del (p.Thr337fs) VARIANT_IN_GENE PMS2",
"confidence": 1
}
] | {
"variant": "NM_000535.7(PMS2):c.1010del (p.Thr337fs)",
"gene": "PMS2",
"truncation_residue": 337,
"protein_length": 862,
"fraction_lost": 0.609
} | 1 |
co_stru_00066 | structural_effect | coding_variant | easy | 1 | NM_007194.4(CHEK2):c.94del (p.Ser32fs) introduces a premature truncation at residue 32 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.94del (p.Ser32fs) VARIANT_IN_GENE CHEK2 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_007194.4(CHEK2):c.94del (p.Ser32fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_007194.4(CHEK2):c.94del (p.Ser32fs)",
"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": "CHEK2",
"source_db": "UniProt",
"payload": {
"accession": "O96017",
"sequence": "MSRESDVEAQQSHGSSACSQPHGSVTQSQGSSSQSQGISSSSTSTMPNSSQSSHSSSGTLSSLETVSTQELYSIPEDQEPEDQEPEEPTPAPWARLWALQDGFANLECVNDNYWFGRDKSCEYCFDEPLLKRT... | [
{
"source_db": "ClinVar",
"source_id": "CHEK2",
"text": "NM_007194.4(CHEK2):c.94del (p.Ser32fs) VARIANT_IN_GENE CHEK2",
"confidence": 1
}
] | {
"variant": "NM_007194.4(CHEK2):c.94del (p.Ser32fs)",
"gene": "CHEK2",
"truncation_residue": 32,
"protein_length": 543,
"fraction_lost": 0.9410000000000001
} | 1 |
co_stru_00067 | structural_effect | coding_variant | easy | 1 | NM_004360.5(CDH1):c.1450_1463del (p.Pro484fs) introduces a premature truncation at residue 484 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.1450_1463del (p.Pro484fs) VARIANT_IN_GENE CDH1 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_004360.5(CDH1):c.1450_1463del (p.Pro484fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_004360.5(CDH1):c.1450_1463del (p.Pro484fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_conf... | 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": "CDH1",
"source_db": "UniProt",
"payload": {
"accession": "P12830",
"sequence": "MGPWSRSLSALLLLLQVSSWLCQEPEPCHPGFDAESYTFTVPRRHLERGRVLGRVNFEDCTGRQRTAYFSLDTRFKVGTDGVITVKRPLRFHNPQIHFLVYAWDSTYRKFSTKVTLNTVGHHHRPPPHQASVSG... | [
{
"source_db": "ClinVar",
"source_id": "CDH1",
"text": "NM_004360.5(CDH1):c.1450_1463del (p.Pro484fs) VARIANT_IN_GENE CDH1",
"confidence": 1
}
] | {
"variant": "NM_004360.5(CDH1):c.1450_1463del (p.Pro484fs)",
"gene": "CDH1",
"truncation_residue": 484,
"protein_length": 882,
"fraction_lost": 0.451
} | 1 |
co_stru_00068 | structural_effect | coding_variant | easy | 1 | NM_007294.4(BRCA1):c.2905_2912del (p.Asn969fs) introduces a premature truncation at residue 969 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.2905_2912del (p.Asn969fs) VARIANT_IN_GENE BRCA1 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_007294.4(BRCA1):c.2905_2912del (p.Asn969fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_007294.4(BRCA1):c.2905_2912del (p.Asn969fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_co... | 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.2905_2912del (p.Asn969fs) VARIANT_IN_GENE BRCA1",
"confidence": 1
}
] | {
"variant": "NM_007294.4(BRCA1):c.2905_2912del (p.Asn969fs)",
"gene": "BRCA1",
"truncation_residue": 969,
"protein_length": 1863,
"fraction_lost": 0.48
} | 1 |
co_stru_00069 | structural_effect | coding_variant | easy | 1 | NM_004360.5(CDH1):c.4_7dup (p.Pro3fs) introduces a premature truncation at residue 3 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.4_7dup (p.Pro3fs) VARIANT_IN_GENE CDH1 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_004360.5(CDH1):c.4_7dup (p.Pro3fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_004360.5(CDH1):c.4_7dup (p.Pro3fs)",
"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": "CDH1",
"source_db": "UniProt",
"payload": {
"accession": "P12830",
"sequence": "MGPWSRSLSALLLLLQVSSWLCQEPEPCHPGFDAESYTFTVPRRHLERGRVLGRVNFEDCTGRQRTAYFSLDTRFKVGTDGVITVKRPLRFHNPQIHFLVYAWDSTYRKFSTKVTLNTVGHHHRPPPHQASVSG... | [
{
"source_db": "ClinVar",
"source_id": "CDH1",
"text": "NM_004360.5(CDH1):c.4_7dup (p.Pro3fs) VARIANT_IN_GENE CDH1",
"confidence": 1
}
] | {
"variant": "NM_004360.5(CDH1):c.4_7dup (p.Pro3fs)",
"gene": "CDH1",
"truncation_residue": 3,
"protein_length": 882,
"fraction_lost": 0.997
} | 1 |
co_stru_00070 | structural_effect | coding_variant | easy | 1 | NM_004360.5(CDH1):c.52_53dup (p.Ser19fs) introduces a premature truncation at residue 19 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.52_53dup (p.Ser19fs) VARIANT_IN_GENE CDH1 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_004360.5(CDH1):c.52_53dup (p.Ser19fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_004360.5(CDH1):c.52_53dup (p.Ser19fs)",
"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": "CDH1",
"source_db": "UniProt",
"payload": {
"accession": "P12830",
"sequence": "MGPWSRSLSALLLLLQVSSWLCQEPEPCHPGFDAESYTFTVPRRHLERGRVLGRVNFEDCTGRQRTAYFSLDTRFKVGTDGVITVKRPLRFHNPQIHFLVYAWDSTYRKFSTKVTLNTVGHHHRPPPHQASVSG... | [
{
"source_db": "ClinVar",
"source_id": "CDH1",
"text": "NM_004360.5(CDH1):c.52_53dup (p.Ser19fs) VARIANT_IN_GENE CDH1",
"confidence": 1
}
] | {
"variant": "NM_004360.5(CDH1):c.52_53dup (p.Ser19fs)",
"gene": "CDH1",
"truncation_residue": 19,
"protein_length": 882,
"fraction_lost": 0.978
} | 1 |
co_stru_00071 | structural_effect | coding_variant | easy | 1 | NM_007294.4(BRCA1):c.3112del (p.Glu1038fs) introduces a premature truncation at residue 1038 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.3112del (p.Glu1038fs) VARIANT_IN_GENE BRCA1 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_007294.4(BRCA1):c.3112del (p.Glu1038fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_007294.4(BRCA1):c.3112del (p.Glu1038fs)",
"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",
"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.3112del (p.Glu1038fs) VARIANT_IN_GENE BRCA1",
"confidence": 1
}
] | {
"variant": "NM_007294.4(BRCA1):c.3112del (p.Glu1038fs)",
"gene": "BRCA1",
"truncation_residue": 1038,
"protein_length": 1863,
"fraction_lost": 0.443
} | 1 |
co_stru_00072 | structural_effect | coding_variant | easy | 1 | NM_000465.4(BARD1):c.2276dup (p.Ser760fs) introduces a premature truncation at residue 760 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.2276dup (p.Ser760fs) VARIANT_IN_GENE BARD1 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000465.4(BARD1):c.2276dup (p.Ser760fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000465.4(BARD1):c.2276dup (p.Ser760fs)",
"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",
"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.2276dup (p.Ser760fs) VARIANT_IN_GENE BARD1",
"confidence": 1
}
] | {
"variant": "NM_000465.4(BARD1):c.2276dup (p.Ser760fs)",
"gene": "BARD1",
"truncation_residue": 760,
"protein_length": 777,
"fraction_lost": 0.022
} | 1 |
co_stru_00073 | structural_effect | coding_variant | easy | 1 | NM_000249.4(MLH1):c.133del (p.Thr45fs) introduces a premature truncation at residue 45 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.133del (p.Thr45fs) VARIANT_IN_GENE MLH1 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000249.4(MLH1):c.133del (p.Thr45fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000249.4(MLH1):c.133del (p.Thr45fs)",
"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": "MLH1",
"source_db": "UniProt",
"payload": {
"accession": "P40692",
"sequence": "MSFVAGVIRRLDETVVNRIAAGEVIQRPANAIKEMIENCLDAKSTSIQVIVKEGGLKLIQIQDNGTGIRKEDLDIVCERFTTSKLQSFEDLASISTYGFRGEALASISHVAHVTITTKTADGKCAYRASYSDGK... | [
{
"source_db": "ClinVar",
"source_id": "MLH1",
"text": "NM_000249.4(MLH1):c.133del (p.Thr45fs) VARIANT_IN_GENE MLH1",
"confidence": 1
}
] | {
"variant": "NM_000249.4(MLH1):c.133del (p.Thr45fs)",
"gene": "MLH1",
"truncation_residue": 45,
"protein_length": 756,
"fraction_lost": 0.9400000000000001
} | 1 |
co_stru_00074 | structural_effect | coding_variant | easy | 1 | NM_000465.4(BARD1):c.1696_1697del (p.Arg566fs) introduces a premature truncation at residue 566 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.1696_1697del (p.Arg566fs) VARIANT_IN_GENE BARD1 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000465.4(BARD1):c.1696_1697del (p.Arg566fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000465.4(BARD1):c.1696_1697del (p.Arg566fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_co... | 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": "BARD1",
"source_db": "UniProt",
"payload": {
"accession": "Q99728",
"sequence": "MPDNRQPRNRQPRIRSGNEPRSAPAMEPDGRGAWAHSRAALDRLEKLLRCSRCTNILREPVCLGGCEHIFCSNCVSDCIGTGCPVCYTPAWIQDLKINRQLDSMIQLCSKLRNLLHDNELSDLKEDKPRKSLF... | [
{
"source_db": "ClinVar",
"source_id": "BARD1",
"text": "NM_000465.4(BARD1):c.1696_1697del (p.Arg566fs) VARIANT_IN_GENE BARD1",
"confidence": 1
}
] | {
"variant": "NM_000465.4(BARD1):c.1696_1697del (p.Arg566fs)",
"gene": "BARD1",
"truncation_residue": 566,
"protein_length": 777,
"fraction_lost": 0.272
} | 1 |
co_stru_00075 | structural_effect | coding_variant | easy | 1 | NM_000136.3(FANCC):c.1238dup (p.Met413fs) introduces a premature truncation at residue 413 of AOPEP's 819-residue protein product (AlphaFold model, mean pLDDT 82.95). Approximately how much of the protein is lost downstream of the truncation? | NM_000136.3(FANCC):c.1238dup (p.Met413fs) VARIANT_IN_GENE AOPEP | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000136.3(FANCC):c.1238dup (p.Met413fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000136.3(FANCC):c.1238dup (p.Met413fs)",
"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%)"
] | [
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "AOPEP",
"source_db": "UniProt",
"payload": {
"accession": "Q8N6M6",
"sequence": "MDIQLDPARDDLPLMANTSHILVKHYVLDLDVDFESQVIEGTIVLFLEDGNRFKKQNSSIEEACQSESNKACKFGMPEPCHIPVTNARTFSSEMEYNDFAICSKGEKDTSDKDGNHDNQEHASGISSSKYCCD... | [
{
"source_db": "ClinVar",
"source_id": "AOPEP",
"text": "NM_000136.3(FANCC):c.1238dup (p.Met413fs) VARIANT_IN_GENE AOPEP",
"confidence": 1
}
] | {
"variant": "NM_000136.3(FANCC):c.1238dup (p.Met413fs)",
"gene": "AOPEP",
"truncation_residue": 413,
"protein_length": 819,
"fraction_lost": 0.496
} | 1 |
co_stru_00076 | structural_effect | coding_variant | easy | 1 | NM_000465.4(BARD1):c.2267G>A (p.Trp756Ter) introduces a premature truncation at residue 756 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.2267G>A (p.Trp756Ter) VARIANT_IN_GENE BARD1 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000465.4(BARD1):c.2267G>A (p.Trp756Ter)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000465.4(BARD1):c.2267G>A (p.Trp756Ter)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence... | 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": "BARD1",
"source_db": "UniProt",
"payload": {
"accession": "Q99728",
"sequence": "MPDNRQPRNRQPRIRSGNEPRSAPAMEPDGRGAWAHSRAALDRLEKLLRCSRCTNILREPVCLGGCEHIFCSNCVSDCIGTGCPVCYTPAWIQDLKINRQLDSMIQLCSKLRNLLHDNELSDLKEDKPRKSLF... | [
{
"source_db": "ClinVar",
"source_id": "BARD1",
"text": "NM_000465.4(BARD1):c.2267G>A (p.Trp756Ter) VARIANT_IN_GENE BARD1",
"confidence": 1
}
] | {
"variant": "NM_000465.4(BARD1):c.2267G>A (p.Trp756Ter)",
"gene": "BARD1",
"truncation_residue": 756,
"protein_length": 777,
"fraction_lost": 0.027
} | 1 |
co_stru_00077 | structural_effect | coding_variant | easy | 1 | NM_024675.4(PALB2):c.801_802dup (p.Lys268fs) introduces a premature truncation at residue 268 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.801_802dup (p.Lys268fs) VARIANT_IN_GENE PALB2 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_024675.4(PALB2):c.801_802dup (p.Lys268fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_024675.4(PALB2):c.801_802dup (p.Lys268fs)",
"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",
"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.801_802dup (p.Lys268fs) VARIANT_IN_GENE PALB2",
"confidence": 1
}
] | {
"variant": "NM_024675.4(PALB2):c.801_802dup (p.Lys268fs)",
"gene": "PALB2",
"truncation_residue": 268,
"protein_length": 1186,
"fraction_lost": 0.774
} | 1 |
co_stru_00078 | structural_effect | coding_variant | easy | 1 | NM_000546.6(TP53):c.642del (p.His214fs) introduces a premature truncation at residue 214 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.642del (p.His214fs) VARIANT_IN_GENE TP53 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000546.6(TP53):c.642del (p.His214fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000546.6(TP53):c.642del (p.His214fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
... | B | [
"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": "TP53",
"source_db": "UniProt",
"payload": {
"accession": "P04637",
"sequence": "MEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPGPDEAPRMPEAAPPVAPAPAAPTPAAPAPAPSWPLSSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMF... | [
{
"source_db": "ClinVar",
"source_id": "TP53",
"text": "NM_000546.6(TP53):c.642del (p.His214fs) VARIANT_IN_GENE TP53",
"confidence": 1
}
] | {
"variant": "NM_000546.6(TP53):c.642del (p.His214fs)",
"gene": "TP53",
"truncation_residue": 214,
"protein_length": 393,
"fraction_lost": 0.455
} | 1 |
co_stru_00079 | structural_effect | coding_variant | easy | 1 | NM_000057.4(BLM):c.1720_1735del (p.Ala575fs) introduces a premature truncation at residue 575 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.1720_1735del (p.Ala575fs) VARIANT_IN_GENE BLM | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000057.4(BLM):c.1720_1735del (p.Ala575fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000057.4(BLM):c.1720_1735del (p.Ala575fs)",
"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": "BLM",
"source_db": "UniProt",
"payload": {
"accession": "P54132",
"sequence": "MAAVPQNNLQEQLERHSARTLNNKLSLSKPKFSGFTFKKKTSSDNNVSVTNVSVAKTPVLRNKDVNVTEDFSFSEPLPNTTNQQRVKDFFKNAPAGQETQRGGSKSLLPDFLQTPKEVVCTTQNTPTVKKSRDTA... | [
{
"source_db": "ClinVar",
"source_id": "BLM",
"text": "NM_000057.4(BLM):c.1720_1735del (p.Ala575fs) VARIANT_IN_GENE BLM",
"confidence": 1
}
] | {
"variant": "NM_000057.4(BLM):c.1720_1735del (p.Ala575fs)",
"gene": "BLM",
"truncation_residue": 575,
"protein_length": 1417,
"fraction_lost": 0.594
} | 1 |
co_stru_00080 | structural_effect | coding_variant | easy | 1 | NM_000314.8(PTEN):c.878del (p.Gly293fs) introduces a premature truncation at residue 293 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.878del (p.Gly293fs) VARIANT_IN_GENE PTEN | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000314.8(PTEN):c.878del (p.Gly293fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000314.8(PTEN):c.878del (p.Gly293fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
... | 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": "PTEN",
"source_db": "UniProt",
"payload": {
"accession": "P60484",
"sequence": "MTAIIKEIVSRNKRRYQEDGFDLDLTYIYPNIIAMGFPAERLEGVYRNNIDDVVRFLDSKHKNHYKIYNLCAERHYDTAKFNCRVAQYPFEDHNPPQLELIKPFCEDLDQWLSEDDNHVAAIHCKAGKGRTGVM... | [
{
"source_db": "ClinVar",
"source_id": "PTEN",
"text": "NM_000314.8(PTEN):c.878del (p.Gly293fs) VARIANT_IN_GENE PTEN",
"confidence": 1
}
] | {
"variant": "NM_000314.8(PTEN):c.878del (p.Gly293fs)",
"gene": "PTEN",
"truncation_residue": 293,
"protein_length": 403,
"fraction_lost": 0.273
} | 1 |
co_stru_00081 | structural_effect | coding_variant | easy | 1 | NM_000057.4(BLM):c.1076_1077del (p.Thr359fs) introduces a premature truncation at residue 359 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.1076_1077del (p.Thr359fs) VARIANT_IN_GENE BLM | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000057.4(BLM):c.1076_1077del (p.Thr359fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000057.4(BLM):c.1076_1077del (p.Thr359fs)",
"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": "BLM",
"source_db": "UniProt",
"payload": {
"accession": "P54132",
"sequence": "MAAVPQNNLQEQLERHSARTLNNKLSLSKPKFSGFTFKKKTSSDNNVSVTNVSVAKTPVLRNKDVNVTEDFSFSEPLPNTTNQQRVKDFFKNAPAGQETQRGGSKSLLPDFLQTPKEVVCTTQNTPTVKKSRDTA... | [
{
"source_db": "ClinVar",
"source_id": "BLM",
"text": "NM_000057.4(BLM):c.1076_1077del (p.Thr359fs) VARIANT_IN_GENE BLM",
"confidence": 1
}
] | {
"variant": "NM_000057.4(BLM):c.1076_1077del (p.Thr359fs)",
"gene": "BLM",
"truncation_residue": 359,
"protein_length": 1417,
"fraction_lost": 0.747
} | 1 |
co_stru_00082 | structural_effect | coding_variant | easy | 1 | NM_007294.4(BRCA1):c.4623_4632del (p.Glu1541fs) introduces a premature truncation at residue 1541 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.4623_4632del (p.Glu1541fs) VARIANT_IN_GENE BRCA1 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_007294.4(BRCA1):c.4623_4632del (p.Glu1541fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_007294.4(BRCA1):c.4623_4632del (p.Glu1541fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_... | 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.4623_4632del (p.Glu1541fs) VARIANT_IN_GENE BRCA1",
"confidence": 1
}
] | {
"variant": "NM_007294.4(BRCA1):c.4623_4632del (p.Glu1541fs)",
"gene": "BRCA1",
"truncation_residue": 1541,
"protein_length": 1863,
"fraction_lost": 0.17300000000000001
} | 1 |
co_stru_00083 | structural_effect | coding_variant | easy | 1 | NM_006231.4(POLE):c.2090_2091del (p.Pro697fs) introduces a premature truncation at residue 697 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.2090_2091del (p.Pro697fs) VARIANT_IN_GENE POLE | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_006231.4(POLE):c.2090_2091del (p.Pro697fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_006231.4(POLE):c.2090_2091del (p.Pro697fs)",
"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": "POLE",
"source_db": "UniProt",
"payload": {
"accession": "Q07864",
"sequence": "MSLRSGGRRRADPGADGEASRDDGATSSVSALKRLERSQWTDKMDLRFGFERLKEPGEKTGWLINMHPTEILDEDKRLGSAVDYYFIQDDGSRFKVALPYKPYFYIATRKGCEREVSSFLSKKFQGKIAKVETV... | [
{
"source_db": "ClinVar",
"source_id": "POLE",
"text": "NM_006231.4(POLE):c.2090_2091del (p.Pro697fs) VARIANT_IN_GENE POLE",
"confidence": 1
}
] | {
"variant": "NM_006231.4(POLE):c.2090_2091del (p.Pro697fs)",
"gene": "POLE",
"truncation_residue": 697,
"protein_length": 2286,
"fraction_lost": 0.6950000000000001
} | 1 |
co_stru_00084 | structural_effect | coding_variant | easy | 1 | NM_006231.4(POLE):c.3396C>A (p.Tyr1132Ter) introduces a premature truncation at residue 1132 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.3396C>A (p.Tyr1132Ter) VARIANT_IN_GENE POLE | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_006231.4(POLE):c.3396C>A (p.Tyr1132Ter)",
"source_node_type": "VARIANT",
"source_node_label": "NM_006231.4(POLE):c.3396C>A (p.Tyr1132Ter)",
"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": "POLE",
"source_db": "UniProt",
"payload": {
"accession": "Q07864",
"sequence": "MSLRSGGRRRADPGADGEASRDDGATSSVSALKRLERSQWTDKMDLRFGFERLKEPGEKTGWLINMHPTEILDEDKRLGSAVDYYFIQDDGSRFKVALPYKPYFYIATRKGCEREVSSFLSKKFQGKIAKVETV... | [
{
"source_db": "ClinVar",
"source_id": "POLE",
"text": "NM_006231.4(POLE):c.3396C>A (p.Tyr1132Ter) VARIANT_IN_GENE POLE",
"confidence": 1
}
] | {
"variant": "NM_006231.4(POLE):c.3396C>A (p.Tyr1132Ter)",
"gene": "POLE",
"truncation_residue": 1132,
"protein_length": 2286,
"fraction_lost": 0.505
} | 1 |
co_stru_00085 | structural_effect | coding_variant | easy | 1 | NM_004364.5(CEBPA):c.175G>T (p.Glu59Ter) introduces a premature truncation at residue 59 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.175G>T (p.Glu59Ter) VARIANT_IN_GENE CEBPA | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_004364.5(CEBPA):c.175G>T (p.Glu59Ter)",
"source_node_type": "VARIANT",
"source_node_label": "NM_004364.5(CEBPA):c.175G>T (p.Glu59Ter)",
"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": "CEBPA",
"source_db": "UniProt",
"payload": {
"accession": "P49715",
"sequence": "MESADFYEAEPRPPMSSHLQSPPHAPSSAAFGFPRGAGPAQPPAPPAAPEPLGGICEHETSIDISAYIDPAAFNDEFLADLFQHSRQQEKAKAAVGPTGGGGGGDFDYPGAPAGPGGAVMPGGAHGPPPGYGC... | [
{
"source_db": "ClinVar",
"source_id": "CEBPA",
"text": "NM_004364.5(CEBPA):c.175G>T (p.Glu59Ter) VARIANT_IN_GENE CEBPA",
"confidence": 1
}
] | {
"variant": "NM_004364.5(CEBPA):c.175G>T (p.Glu59Ter)",
"gene": "CEBPA",
"truncation_residue": 59,
"protein_length": 358,
"fraction_lost": 0.835
} | 1 |
co_stru_00086 | structural_effect | coding_variant | easy | 1 | NM_013254.4(TBK1):c.935dup (p.His312fs) introduces a premature truncation at residue 312 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.935dup (p.His312fs) VARIANT_IN_GENE TBK1 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_013254.4(TBK1):c.935dup (p.His312fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_013254.4(TBK1):c.935dup (p.His312fs)",
"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": "TBK1",
"source_db": "UniProt",
"payload": {
"accession": "Q9UHD2",
"sequence": "MQSTSNHLWLLSDILGQGATANVFRGRHKKTGDLFAIKVFNNISFLRPVDVQMREFEVLKKLNHKNIVKLFAIEEETTTRHKVLIMEFCPCGSLYTVLEEPSNAYGLPESEFLIVLRDVVGGMNHLRENGIVHR... | [
{
"source_db": "ClinVar",
"source_id": "TBK1",
"text": "NM_013254.4(TBK1):c.935dup (p.His312fs) VARIANT_IN_GENE TBK1",
"confidence": 1
}
] | {
"variant": "NM_013254.4(TBK1):c.935dup (p.His312fs)",
"gene": "TBK1",
"truncation_residue": 312,
"protein_length": 729,
"fraction_lost": 0.5720000000000001
} | 1 |
co_stru_00087 | structural_effect | coding_variant | easy | 1 | NM_007294.4(BRCA1):c.788del (p.Gly263fs) introduces a premature truncation at residue 263 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.788del (p.Gly263fs) VARIANT_IN_GENE BRCA1 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_007294.4(BRCA1):c.788del (p.Gly263fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_007294.4(BRCA1):c.788del (p.Gly263fs)",
"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",
"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.788del (p.Gly263fs) VARIANT_IN_GENE BRCA1",
"confidence": 1
}
] | {
"variant": "NM_007294.4(BRCA1):c.788del (p.Gly263fs)",
"gene": "BRCA1",
"truncation_residue": 263,
"protein_length": 1863,
"fraction_lost": 0.859
} | 1 |
co_stru_00088 | structural_effect | coding_variant | easy | 1 | NM_007294.4(BRCA1):c.532_533dup (p.Tyr179fs) introduces a premature truncation at residue 179 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.532_533dup (p.Tyr179fs) VARIANT_IN_GENE BRCA1 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_007294.4(BRCA1):c.532_533dup (p.Tyr179fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_007294.4(BRCA1):c.532_533dup (p.Tyr179fs)",
"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",
"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.532_533dup (p.Tyr179fs) VARIANT_IN_GENE BRCA1",
"confidence": 1
}
] | {
"variant": "NM_007294.4(BRCA1):c.532_533dup (p.Tyr179fs)",
"gene": "BRCA1",
"truncation_residue": 179,
"protein_length": 1863,
"fraction_lost": 0.904
} | 1 |
co_stru_00089 | structural_effect | coding_variant | easy | 1 | NM_000546.6(TP53):c.279_286del (p.Ser94fs) introduces a premature truncation at residue 94 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.279_286del (p.Ser94fs) VARIANT_IN_GENE TP53 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000546.6(TP53):c.279_286del (p.Ser94fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000546.6(TP53):c.279_286del (p.Ser94fs)",
"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": "TP53",
"source_db": "UniProt",
"payload": {
"accession": "P04637",
"sequence": "MEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPGPDEAPRMPEAAPPVAPAPAAPTPAAPAPAPSWPLSSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMF... | [
{
"source_db": "ClinVar",
"source_id": "TP53",
"text": "NM_000546.6(TP53):c.279_286del (p.Ser94fs) VARIANT_IN_GENE TP53",
"confidence": 1
}
] | {
"variant": "NM_000546.6(TP53):c.279_286del (p.Ser94fs)",
"gene": "TP53",
"truncation_residue": 94,
"protein_length": 393,
"fraction_lost": 0.761
} | 1 |
co_stru_00090 | structural_effect | coding_variant | easy | 1 | NM_000455.5(STK11):c.418del (p.Leu140fs) introduces a premature truncation at residue 140 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.418del (p.Leu140fs) VARIANT_IN_GENE STK11 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000455.5(STK11):c.418del (p.Leu140fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000455.5(STK11):c.418del (p.Leu140fs)",
"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": "STK11",
"source_db": "UniProt",
"payload": {
"accession": "Q15831",
"sequence": "MEVVDPQQLGMFTEGELMSVGMDTFIHRIDSTEVIYQPRRKRAKLIGKYLMGDLLGEGSYGKVKEVLDSETLCRRAVKILKKKKLRRIPNGEANVKKEIQLLRRLRHKNVIQLVDVLYNEEKQKMYMVMEYCV... | [
{
"source_db": "ClinVar",
"source_id": "STK11",
"text": "NM_000455.5(STK11):c.418del (p.Leu140fs) VARIANT_IN_GENE STK11",
"confidence": 1
}
] | {
"variant": "NM_000455.5(STK11):c.418del (p.Leu140fs)",
"gene": "STK11",
"truncation_residue": 140,
"protein_length": 433,
"fraction_lost": 0.677
} | 1 |
co_stru_00091 | structural_effect | coding_variant | easy | 1 | NM_007194.4(CHEK2):c.1065del (p.Ser356fs) introduces a premature truncation at residue 356 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.1065del (p.Ser356fs) VARIANT_IN_GENE CHEK2 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_007194.4(CHEK2):c.1065del (p.Ser356fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_007194.4(CHEK2):c.1065del (p.Ser356fs)",
"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%)"
] | [
"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.1065del (p.Ser356fs) VARIANT_IN_GENE CHEK2",
"confidence": 1
}
] | {
"variant": "NM_007194.4(CHEK2):c.1065del (p.Ser356fs)",
"gene": "CHEK2",
"truncation_residue": 356,
"protein_length": 543,
"fraction_lost": 0.34400000000000003
} | 1 |
co_stru_00092 | structural_effect | coding_variant | easy | 1 | NM_002087.4(GRN):c.910_911dup (p.Trp304fs) introduces a premature truncation at residue 304 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.910_911dup (p.Trp304fs) VARIANT_IN_GENE GRN | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_002087.4(GRN):c.910_911dup (p.Trp304fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_002087.4(GRN):c.910_911dup (p.Trp304fs)",
"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": "GRN",
"source_db": "UniProt",
"payload": {
"accession": "P28799",
"sequence": "MWTLVSWVALTAGLVAGTRCPDGQFCPVACCLDPGGASYSCCRPLLDKWPTTLSRHLGGPCQVDAHCSAGHSCIFTVSGTSSCCPFPEAVACGDGHHCCPRGFHCSADGRSCFQRSGNNSVGAIQCPDSQFECPD... | [
{
"source_db": "ClinVar",
"source_id": "GRN",
"text": "NM_002087.4(GRN):c.910_911dup (p.Trp304fs) VARIANT_IN_GENE GRN",
"confidence": 1
}
] | {
"variant": "NM_002087.4(GRN):c.910_911dup (p.Trp304fs)",
"gene": "GRN",
"truncation_residue": 304,
"protein_length": 593,
"fraction_lost": 0.487
} | 1 |
co_stru_00093 | structural_effect | coding_variant | easy | 1 | NM_000546.6(TP53):c.539_545del (p.Glu180fs) introduces a premature truncation at residue 180 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.539_545del (p.Glu180fs) VARIANT_IN_GENE TP53 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000546.6(TP53):c.539_545del (p.Glu180fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000546.6(TP53):c.539_545del (p.Glu180fs)",
"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": "TP53",
"source_db": "UniProt",
"payload": {
"accession": "P04637",
"sequence": "MEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPGPDEAPRMPEAAPPVAPAPAAPTPAAPAPAPSWPLSSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMF... | [
{
"source_db": "ClinVar",
"source_id": "TP53",
"text": "NM_000546.6(TP53):c.539_545del (p.Glu180fs) VARIANT_IN_GENE TP53",
"confidence": 1
}
] | {
"variant": "NM_000546.6(TP53):c.539_545del (p.Glu180fs)",
"gene": "TP53",
"truncation_residue": 180,
"protein_length": 393,
"fraction_lost": 0.542
} | 1 |
co_stru_00094 | structural_effect | coding_variant | easy | 1 | NM_007294.4(BRCA1):c.4222del (p.Gln1408fs) introduces a premature truncation at residue 1408 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.4222del (p.Gln1408fs) VARIANT_IN_GENE BRCA1 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_007294.4(BRCA1):c.4222del (p.Gln1408fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_007294.4(BRCA1):c.4222del (p.Gln1408fs)",
"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.4222del (p.Gln1408fs) VARIANT_IN_GENE BRCA1",
"confidence": 1
}
] | {
"variant": "NM_007294.4(BRCA1):c.4222del (p.Gln1408fs)",
"gene": "BRCA1",
"truncation_residue": 1408,
"protein_length": 1863,
"fraction_lost": 0.244
} | 1 |
co_stru_00095 | structural_effect | coding_variant | easy | 1 | NM_006231.4(POLE):c.3476del (p.Pro1159fs) introduces a premature truncation at residue 1159 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.3476del (p.Pro1159fs) VARIANT_IN_GENE POLE | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_006231.4(POLE):c.3476del (p.Pro1159fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_006231.4(POLE):c.3476del (p.Pro1159fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence":... | B | [
"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_006231.4(POLE):c.3476del (p.Pro1159fs)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr12",
"pos": 132657242,
"track": "phyloP100way",
"window": 20,
"scores": [
9.06343,
... | [
{
"source_db": "ClinVar",
"source_id": "POLE",
"text": "NM_006231.4(POLE):c.3476del (p.Pro1159fs) VARIANT_IN_GENE POLE",
"confidence": 1
}
] | {
"variant": "NM_006231.4(POLE):c.3476del (p.Pro1159fs)",
"gene": "POLE",
"truncation_residue": 1159,
"protein_length": 2286,
"fraction_lost": 0.493
} | 1 |
co_stru_00096 | structural_effect | coding_variant | easy | 1 | NM_002878.4(RAD51D):c.210_229del (p.Tyr72fs) introduces a premature truncation at residue 72 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.210_229del (p.Tyr72fs) VARIANT_IN_GENE RAD51D | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_002878.4(RAD51D):c.210_229del (p.Tyr72fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_002878.4(RAD51D):c.210_229del (p.Tyr72fs)",
"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": "RAD51D",
"source_db": "UniProt",
"payload": {
"accession": "O75771",
"sequence": "MGVLRVGLCPGLTEEMIQLLRSHRIKTVVDLVSADLEEVAQKCGLSYKALVALRRVLLAQFSAFPVNGADLYEELKTSTAILSTGIGSLDKLLDAGLYTGEVTEIVGGPGSGKTQVCLCMAANVAHGLQQNV... | [
{
"source_db": "ClinVar",
"source_id": "RAD51D",
"text": "NM_002878.4(RAD51D):c.210_229del (p.Tyr72fs) VARIANT_IN_GENE RAD51D",
"confidence": 1
}
] | {
"variant": "NM_002878.4(RAD51D):c.210_229del (p.Tyr72fs)",
"gene": "RAD51D",
"truncation_residue": 72,
"protein_length": 328,
"fraction_lost": 0.78
} | 1 |
co_stru_00097 | structural_effect | coding_variant | easy | 1 | NM_007194.4(CHEK2):c.1558_1559insC (p.Lys520fs) introduces a premature truncation at residue 520 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.1558_1559insC (p.Lys520fs) VARIANT_IN_GENE CHEK2 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_007194.4(CHEK2):c.1558_1559insC (p.Lys520fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_007194.4(CHEK2):c.1558_1559insC (p.Lys520fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_... | 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": "CHEK2",
"source_db": "UniProt",
"payload": {
"accession": "O96017",
"sequence": "MSRESDVEAQQSHGSSACSQPHGSVTQSQGSSSQSQGISSSSTSTMPNSSQSSHSSSGTLSSLETVSTQELYSIPEDQEPEDQEPEEPTPAPWARLWALQDGFANLECVNDNYWFGRDKSCEYCFDEPLLKRT... | [
{
"source_db": "ClinVar",
"source_id": "CHEK2",
"text": "NM_007194.4(CHEK2):c.1558_1559insC (p.Lys520fs) VARIANT_IN_GENE CHEK2",
"confidence": 1
}
] | {
"variant": "NM_007194.4(CHEK2):c.1558_1559insC (p.Lys520fs)",
"gene": "CHEK2",
"truncation_residue": 520,
"protein_length": 543,
"fraction_lost": 0.042
} | 1 |
co_stru_00098 | structural_effect | coding_variant | easy | 1 | NM_000251.3(MSH2):c.296_308del (p.Arg99fs) introduces a premature truncation at residue 99 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.296_308del (p.Arg99fs) VARIANT_IN_GENE MSH2 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000251.3(MSH2):c.296_308del (p.Arg99fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000251.3(MSH2):c.296_308del (p.Arg99fs)",
"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": "MSH2",
"source_db": "UniProt",
"payload": {
"accession": "P43246",
"sequence": "MAVQPKETLQLESAAEVGFVRFFQGMPEKPTTTVRLFDRGDFYTAHGEDALLAAREVFKTQGVIKYMGPAGAKNLQSVVLSKMNFESFVKDLLLVRQYRVEVYKNRAGNKASKENDWYLAYKASPGNLSQFEDI... | [
{
"source_db": "ClinVar",
"source_id": "MSH2",
"text": "NM_000251.3(MSH2):c.296_308del (p.Arg99fs) VARIANT_IN_GENE MSH2",
"confidence": 1
}
] | {
"variant": "NM_000251.3(MSH2):c.296_308del (p.Arg99fs)",
"gene": "MSH2",
"truncation_residue": 99,
"protein_length": 934,
"fraction_lost": 0.894
} | 1 |
co_stru_00099 | structural_effect | coding_variant | easy | 1 | NM_000249.4(MLH1):c.864del (p.His289fs) introduces a premature truncation at residue 289 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.864del (p.His289fs) VARIANT_IN_GENE MLH1 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000249.4(MLH1):c.864del (p.His289fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000249.4(MLH1):c.864del (p.His289fs)",
"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": "MLH1",
"source_db": "UniProt",
"payload": {
"accession": "P40692",
"sequence": "MSFVAGVIRRLDETVVNRIAAGEVIQRPANAIKEMIENCLDAKSTSIQVIVKEGGLKLIQIQDNGTGIRKEDLDIVCERFTTSKLQSFEDLASISTYGFRGEALASISHVAHVTITTKTADGKCAYRASYSDGK... | [
{
"source_db": "ClinVar",
"source_id": "MLH1",
"text": "NM_000249.4(MLH1):c.864del (p.His289fs) VARIANT_IN_GENE MLH1",
"confidence": 1
}
] | {
"variant": "NM_000249.4(MLH1):c.864del (p.His289fs)",
"gene": "MLH1",
"truncation_residue": 289,
"protein_length": 756,
"fraction_lost": 0.618
} | 1 |
co_stru_00100 | structural_effect | coding_variant | easy | 1 | NM_007294.4(BRCA1):c.4211del (p.Leu1404fs) introduces a premature truncation at residue 1404 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.4211del (p.Leu1404fs) VARIANT_IN_GENE BRCA1 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_007294.4(BRCA1):c.4211del (p.Leu1404fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_007294.4(BRCA1):c.4211del (p.Leu1404fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence... | A | [
"A. a small C-terminal portion (<25%)",
"B. more than half the protein (>50%)",
"C. a substantial portion (25-50%)"
] | [
"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.4211del (p.Leu1404fs) VARIANT_IN_GENE BRCA1",
"confidence": 1
}
] | {
"variant": "NM_007294.4(BRCA1):c.4211del (p.Leu1404fs)",
"gene": "BRCA1",
"truncation_residue": 1404,
"protein_length": 1863,
"fraction_lost": 0.246
} | 1 |
co_stru_00101 | structural_effect | coding_variant | easy | 1 | NM_006231.4(POLE):c.2811C>A (p.Tyr937Ter) introduces a premature truncation at residue 937 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.2811C>A (p.Tyr937Ter) VARIANT_IN_GENE POLE | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_006231.4(POLE):c.2811C>A (p.Tyr937Ter)",
"source_node_type": "VARIANT",
"source_node_label": "NM_006231.4(POLE):c.2811C>A (p.Tyr937Ter)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence":... | 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.2811C>A (p.Tyr937Ter) VARIANT_IN_GENE POLE",
"confidence": 1
}
] | {
"variant": "NM_006231.4(POLE):c.2811C>A (p.Tyr937Ter)",
"gene": "POLE",
"truncation_residue": 937,
"protein_length": 2286,
"fraction_lost": 0.59
} | 1 |
co_stru_00102 | structural_effect | coding_variant | easy | 1 | NM_001904.4(CTNNB1):c.1154_1155del (p.Leu385fs) introduces a premature truncation at residue 385 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.1154_1155del (p.Leu385fs) VARIANT_IN_GENE CTNNB1 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_001904.4(CTNNB1):c.1154_1155del (p.Leu385fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_001904.4(CTNNB1):c.1154_1155del (p.Leu385fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_... | 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": "CTNNB1",
"source_db": "UniProt",
"payload": {
"accession": "P35222",
"sequence": "MATQADLMELDMAMEPDRKAAVSHWQQQSYLDSGIHSGATTTAPSLSGKGNPEEEDVDTSQVLYEWEQGFSQSFTQEQVADIDGQYAMTRAQRVRAAMFPETLDEGMQIPSTQFDAAHPTNVQRLAEPSQML... | [
{
"source_db": "ClinVar",
"source_id": "CTNNB1",
"text": "NM_001904.4(CTNNB1):c.1154_1155del (p.Leu385fs) VARIANT_IN_GENE CTNNB1",
"confidence": 1
}
] | {
"variant": "NM_001904.4(CTNNB1):c.1154_1155del (p.Leu385fs)",
"gene": "CTNNB1",
"truncation_residue": 385,
"protein_length": 781,
"fraction_lost": 0.507
} | 1 |
co_stru_00103 | structural_effect | coding_variant | easy | 1 | NM_000044.6(AR):c.35del (p.Pro12fs) introduces a premature truncation at residue 12 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.35del (p.Pro12fs) VARIANT_IN_GENE AR | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000044.6(AR):c.35del (p.Pro12fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000044.6(AR):c.35del (p.Pro12fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"e... | 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": "AR",
"source_db": "UniProt",
"payload": {
"accession": "P10275",
"sequence": "MEVQLGLGRVYPRPPSKTYRGAFQNLFQSVREVIQNPGPRHPEAASAAPPGASLLLLQQQQQQQQQQQQQQQQQQQQQQQETSPRQQQQQQGEDGSPQAHRRGPTGYLVLDEEQQPSQPQSALECHPERGCVPEPG... | [
{
"source_db": "ClinVar",
"source_id": "AR",
"text": "NM_000044.6(AR):c.35del (p.Pro12fs) VARIANT_IN_GENE AR",
"confidence": 1
}
] | {
"variant": "NM_000044.6(AR):c.35del (p.Pro12fs)",
"gene": "AR",
"truncation_residue": 12,
"protein_length": 920,
"fraction_lost": 0.987
} | 1 |
co_stru_00104 | structural_effect | coding_variant | easy | 1 | NM_000465.4(BARD1):c.1735dup (p.Ser579fs) introduces a premature truncation at residue 579 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.1735dup (p.Ser579fs) VARIANT_IN_GENE BARD1 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000465.4(BARD1):c.1735dup (p.Ser579fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000465.4(BARD1):c.1735dup (p.Ser579fs)",
"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": "BARD1",
"source_db": "UniProt",
"payload": {
"accession": "Q99728",
"sequence": "MPDNRQPRNRQPRIRSGNEPRSAPAMEPDGRGAWAHSRAALDRLEKLLRCSRCTNILREPVCLGGCEHIFCSNCVSDCIGTGCPVCYTPAWIQDLKINRQLDSMIQLCSKLRNLLHDNELSDLKEDKPRKSLF... | [
{
"source_db": "ClinVar",
"source_id": "BARD1",
"text": "NM_000465.4(BARD1):c.1735dup (p.Ser579fs) VARIANT_IN_GENE BARD1",
"confidence": 1
}
] | {
"variant": "NM_000465.4(BARD1):c.1735dup (p.Ser579fs)",
"gene": "BARD1",
"truncation_residue": 579,
"protein_length": 777,
"fraction_lost": 0.255
} | 1 |
co_stru_00105 | structural_effect | coding_variant | easy | 1 | NM_007294.4(BRCA1):c.4258del (p.Gln1420fs) introduces a premature truncation at residue 1420 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.4258del (p.Gln1420fs) VARIANT_IN_GENE BRCA1 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_007294.4(BRCA1):c.4258del (p.Gln1420fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_007294.4(BRCA1):c.4258del (p.Gln1420fs)",
"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.4258del (p.Gln1420fs) VARIANT_IN_GENE BRCA1",
"confidence": 1
}
] | {
"variant": "NM_007294.4(BRCA1):c.4258del (p.Gln1420fs)",
"gene": "BRCA1",
"truncation_residue": 1420,
"protein_length": 1863,
"fraction_lost": 0.23800000000000002
} | 1 |
co_stru_00106 | structural_effect | coding_variant | easy | 1 | NM_000179.3(MSH6):c.171del (p.Arg58fs) introduces a premature truncation at residue 58 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.171del (p.Arg58fs) VARIANT_IN_GENE MSH6 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000179.3(MSH6):c.171del (p.Arg58fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000179.3(MSH6):c.171del (p.Arg58fs)",
"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": "MSH6",
"source_db": "UniProt",
"payload": {
"accession": "P52701",
"sequence": "MSRQSTLYSFFPKSPALSDANKASARASREGGRAAAAPGASPSPGGDAAWSEAGPGPRPLARSASPPKAKNLNGGLRRSVAPAAPTSCDFSPGDLVWAKMEGYPWWPCLVYNHPFDGTFIREKGKSVRVHVQFF... | [
{
"source_db": "ClinVar",
"source_id": "MSH6",
"text": "NM_000179.3(MSH6):c.171del (p.Arg58fs) VARIANT_IN_GENE MSH6",
"confidence": 1
}
] | {
"variant": "NM_000179.3(MSH6):c.171del (p.Arg58fs)",
"gene": "MSH6",
"truncation_residue": 58,
"protein_length": 1360,
"fraction_lost": 0.9570000000000001
} | 1 |
co_stru_00107 | structural_effect | coding_variant | easy | 1 | NM_000314.8(PTEN):c.170del (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.170del (p.Leu57fs) VARIANT_IN_GENE PTEN | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000314.8(PTEN):c.170del (p.Leu57fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000314.8(PTEN):c.170del (p.Leu57fs)",
"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": "PTEN",
"source_db": "UniProt",
"payload": {
"accession": "P60484",
"sequence": "MTAIIKEIVSRNKRRYQEDGFDLDLTYIYPNIIAMGFPAERLEGVYRNNIDDVVRFLDSKHKNHYKIYNLCAERHYDTAKFNCRVAQYPFEDHNPPQLELIKPFCEDLDQWLSEDDNHVAAIHCKAGKGRTGVM... | [
{
"source_db": "ClinVar",
"source_id": "PTEN",
"text": "NM_000314.8(PTEN):c.170del (p.Leu57fs) VARIANT_IN_GENE PTEN",
"confidence": 1
}
] | {
"variant": "NM_000314.8(PTEN):c.170del (p.Leu57fs)",
"gene": "PTEN",
"truncation_residue": 57,
"protein_length": 403,
"fraction_lost": 0.859
} | 1 |
co_stru_00108 | structural_effect | coding_variant | easy | 1 | NM_000044.6(AR):c.2562_2563del (p.Arg855fs) introduces a premature truncation at residue 855 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.2562_2563del (p.Arg855fs) VARIANT_IN_GENE AR | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000044.6(AR):c.2562_2563del (p.Arg855fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000044.6(AR):c.2562_2563del (p.Arg855fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confiden... | 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_000044.6(AR):c.2562_2563del (p.Arg855fs)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chrX",
"pos": 67722939,
"track": "phyloP100way",
"window": 20,
"scores": [
4.34428,
... | [
{
"source_db": "ClinVar",
"source_id": "AR",
"text": "NM_000044.6(AR):c.2562_2563del (p.Arg855fs) VARIANT_IN_GENE AR",
"confidence": 1
}
] | {
"variant": "NM_000044.6(AR):c.2562_2563del (p.Arg855fs)",
"gene": "AR",
"truncation_residue": 855,
"protein_length": 920,
"fraction_lost": 0.07100000000000001
} | 1 |
co_stru_00109 | structural_effect | coding_variant | easy | 1 | NM_000314.8(PTEN):c.1039_1043del (p.Phe347fs) introduces a premature truncation at residue 347 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.1039_1043del (p.Phe347fs) VARIANT_IN_GENE PTEN | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000314.8(PTEN):c.1039_1043del (p.Phe347fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000314.8(PTEN):c.1039_1043del (p.Phe347fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_conf... | 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": "PTEN",
"source_db": "UniProt",
"payload": {
"accession": "P60484",
"sequence": "MTAIIKEIVSRNKRRYQEDGFDLDLTYIYPNIIAMGFPAERLEGVYRNNIDDVVRFLDSKHKNHYKIYNLCAERHYDTAKFNCRVAQYPFEDHNPPQLELIKPFCEDLDQWLSEDDNHVAAIHCKAGKGRTGVM... | [
{
"source_db": "ClinVar",
"source_id": "PTEN",
"text": "NM_000314.8(PTEN):c.1039_1043del (p.Phe347fs) VARIANT_IN_GENE PTEN",
"confidence": 1
}
] | {
"variant": "NM_000314.8(PTEN):c.1039_1043del (p.Phe347fs)",
"gene": "PTEN",
"truncation_residue": 347,
"protein_length": 403,
"fraction_lost": 0.139
} | 1 |
co_stru_00110 | structural_effect | coding_variant | easy | 1 | NM_001211.6(BUB1B):c.925C>T (p.Gln309Ter) introduces a premature truncation at residue 309 of BUB1B's 1050-residue protein product (AlphaFold model, mean pLDDT 63.61). Approximately how much of the protein is lost downstream of the truncation? | NM_001211.6(BUB1B):c.925C>T (p.Gln309Ter) VARIANT_IN_GENE BUB1B | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_001211.6(BUB1B):c.925C>T (p.Gln309Ter)",
"source_node_type": "VARIANT",
"source_node_label": "NM_001211.6(BUB1B):c.925C>T (p.Gln309Ter)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence":... | 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_001211.6(BUB1B):c.925C>T (p.Gln309Ter)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr15",
"pos": 40185338,
"track": "phyloP100way",
"window": 20,
"scores": [
3.36161,
... | [
{
"source_db": "ClinVar",
"source_id": "BUB1B",
"text": "NM_001211.6(BUB1B):c.925C>T (p.Gln309Ter) VARIANT_IN_GENE BUB1B",
"confidence": 1
}
] | {
"variant": "NM_001211.6(BUB1B):c.925C>T (p.Gln309Ter)",
"gene": "BUB1B",
"truncation_residue": 309,
"protein_length": 1050,
"fraction_lost": 0.706
} | 1 |
co_stru_00111 | structural_effect | coding_variant | easy | 1 | NM_001904.4(CTNNB1):c.808A>T (p.Lys270Ter) introduces a premature truncation at residue 270 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.808A>T (p.Lys270Ter) VARIANT_IN_GENE CTNNB1 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_001904.4(CTNNB1):c.808A>T (p.Lys270Ter)",
"source_node_type": "VARIANT",
"source_node_label": "NM_001904.4(CTNNB1):c.808A>T (p.Lys270Ter)",
"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": "CTNNB1",
"source_db": "UniProt",
"payload": {
"accession": "P35222",
"sequence": "MATQADLMELDMAMEPDRKAAVSHWQQQSYLDSGIHSGATTTAPSLSGKGNPEEEDVDTSQVLYEWEQGFSQSFTQEQVADIDGQYAMTRAQRVRAAMFPETLDEGMQIPSTQFDAAHPTNVQRLAEPSQML... | [
{
"source_db": "ClinVar",
"source_id": "CTNNB1",
"text": "NM_001904.4(CTNNB1):c.808A>T (p.Lys270Ter) VARIANT_IN_GENE CTNNB1",
"confidence": 1
}
] | {
"variant": "NM_001904.4(CTNNB1):c.808A>T (p.Lys270Ter)",
"gene": "CTNNB1",
"truncation_residue": 270,
"protein_length": 781,
"fraction_lost": 0.654
} | 1 |
co_stru_00112 | structural_effect | coding_variant | easy | 1 | NM_032043.3(BRIP1):c.443del (p.Arg148fs) introduces a premature truncation at residue 148 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.443del (p.Arg148fs) VARIANT_IN_GENE BRIP1 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_032043.3(BRIP1):c.443del (p.Arg148fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_032043.3(BRIP1):c.443del (p.Arg148fs)",
"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": "BRIP1",
"source_db": "UniProt",
"payload": {
"accession": "Q9BX63",
"sequence": "MSSMWSEYTIGGVKIYFPYKAYPSQLAMMNSILRGLNSKQHCLLESPTGSGKSLALLCSALAWQQSLSGKPADEGVSEKAEVQLSCCCACHSKDFTNNDMNQGTSRHFNYPSTPPSERNGTSSTCQDSPEKTT... | [
{
"source_db": "ClinVar",
"source_id": "BRIP1",
"text": "NM_032043.3(BRIP1):c.443del (p.Arg148fs) VARIANT_IN_GENE BRIP1",
"confidence": 1
}
] | {
"variant": "NM_032043.3(BRIP1):c.443del (p.Arg148fs)",
"gene": "BRIP1",
"truncation_residue": 148,
"protein_length": 1249,
"fraction_lost": 0.882
} | 1 |
co_stru_00113 | structural_effect | coding_variant | easy | 1 | NM_000057.4(BLM):c.1429_1432del (p.Thr477fs) introduces a premature truncation at residue 477 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.1429_1432del (p.Thr477fs) VARIANT_IN_GENE BLM | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000057.4(BLM):c.1429_1432del (p.Thr477fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000057.4(BLM):c.1429_1432del (p.Thr477fs)",
"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": "BLM",
"source_db": "UniProt",
"payload": {
"accession": "P54132",
"sequence": "MAAVPQNNLQEQLERHSARTLNNKLSLSKPKFSGFTFKKKTSSDNNVSVTNVSVAKTPVLRNKDVNVTEDFSFSEPLPNTTNQQRVKDFFKNAPAGQETQRGGSKSLLPDFLQTPKEVVCTTQNTPTVKKSRDTA... | [
{
"source_db": "ClinVar",
"source_id": "BLM",
"text": "NM_000057.4(BLM):c.1429_1432del (p.Thr477fs) VARIANT_IN_GENE BLM",
"confidence": 1
}
] | {
"variant": "NM_000057.4(BLM):c.1429_1432del (p.Thr477fs)",
"gene": "BLM",
"truncation_residue": 477,
"protein_length": 1417,
"fraction_lost": 0.663
} | 1 |
co_stru_00114 | structural_effect | coding_variant | easy | 1 | NM_020919.4(ALS2):c.4528C>T (p.Arg1510Ter) introduces a premature truncation at residue 1510 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.4528C>T (p.Arg1510Ter) VARIANT_IN_GENE ALS2 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_020919.4(ALS2):c.4528C>T (p.Arg1510Ter)",
"source_node_type": "VARIANT",
"source_node_label": "NM_020919.4(ALS2):c.4528C>T (p.Arg1510Ter)",
"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_020919.4(ALS2):c.4528C>T (p.Arg1510Ter)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr2",
"pos": 201706898,
"track": "phyloP100way",
"window": 20,
"scores": [
0.0215984,
... | [
{
"source_db": "ClinVar",
"source_id": "ALS2",
"text": "NM_020919.4(ALS2):c.4528C>T (p.Arg1510Ter) VARIANT_IN_GENE ALS2",
"confidence": 1
}
] | {
"variant": "NM_020919.4(ALS2):c.4528C>T (p.Arg1510Ter)",
"gene": "ALS2",
"truncation_residue": 1510,
"protein_length": 1657,
"fraction_lost": 0.089
} | 1 |
co_stru_00115 | structural_effect | coding_variant | easy | 1 | NM_032043.3(BRIP1):c.251T>A (p.Leu84Ter) introduces a premature truncation at residue 84 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.251T>A (p.Leu84Ter) VARIANT_IN_GENE BRIP1 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_032043.3(BRIP1):c.251T>A (p.Leu84Ter)",
"source_node_type": "VARIANT",
"source_node_label": "NM_032043.3(BRIP1):c.251T>A (p.Leu84Ter)",
"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": "BRIP1",
"source_db": "UniProt",
"payload": {
"accession": "Q9BX63",
"sequence": "MSSMWSEYTIGGVKIYFPYKAYPSQLAMMNSILRGLNSKQHCLLESPTGSGKSLALLCSALAWQQSLSGKPADEGVSEKAEVQLSCCCACHSKDFTNNDMNQGTSRHFNYPSTPPSERNGTSSTCQDSPEKTT... | [
{
"source_db": "ClinVar",
"source_id": "BRIP1",
"text": "NM_032043.3(BRIP1):c.251T>A (p.Leu84Ter) VARIANT_IN_GENE BRIP1",
"confidence": 1
}
] | {
"variant": "NM_032043.3(BRIP1):c.251T>A (p.Leu84Ter)",
"gene": "BRIP1",
"truncation_residue": 84,
"protein_length": 1249,
"fraction_lost": 0.933
} | 1 |
co_stru_00116 | structural_effect | coding_variant | easy | 1 | NM_000465.4(BARD1):c.1604_1622delinsCA (p.Asp535fs) introduces a premature truncation at residue 535 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.1604_1622delinsCA (p.Asp535fs) VARIANT_IN_GENE BARD1 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000465.4(BARD1):c.1604_1622delinsCA (p.Asp535fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000465.4(BARD1):c.1604_1622delinsCA (p.Asp535fs)",
"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%)"
] | [
"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.1604_1622delinsCA (p.Asp535fs) VARIANT_IN_GENE BARD1",
"confidence": 1
}
] | {
"variant": "NM_000465.4(BARD1):c.1604_1622delinsCA (p.Asp535fs)",
"gene": "BARD1",
"truncation_residue": 535,
"protein_length": 777,
"fraction_lost": 0.311
} | 1 |
co_stru_00117 | structural_effect | coding_variant | easy | 1 | NM_006231.4(POLE):c.5012del (p.Leu1671fs) introduces a premature truncation at residue 1671 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.5012del (p.Leu1671fs) VARIANT_IN_GENE POLE | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_006231.4(POLE):c.5012del (p.Leu1671fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_006231.4(POLE):c.5012del (p.Leu1671fs)",
"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",
"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.5012del (p.Leu1671fs) VARIANT_IN_GENE POLE",
"confidence": 1
}
] | {
"variant": "NM_006231.4(POLE):c.5012del (p.Leu1671fs)",
"gene": "POLE",
"truncation_residue": 1671,
"protein_length": 2286,
"fraction_lost": 0.269
} | 1 |
co_stru_00118 | structural_effect | coding_variant | easy | 1 | NM_032043.3(BRIP1):c.1378_1379del (p.Asp460fs) introduces a premature truncation at residue 460 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.1378_1379del (p.Asp460fs) VARIANT_IN_GENE BRIP1 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_032043.3(BRIP1):c.1378_1379del (p.Asp460fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_032043.3(BRIP1):c.1378_1379del (p.Asp460fs)",
"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.1378_1379del (p.Asp460fs) VARIANT_IN_GENE BRIP1",
"confidence": 1
}
] | {
"variant": "NM_032043.3(BRIP1):c.1378_1379del (p.Asp460fs)",
"gene": "BRIP1",
"truncation_residue": 460,
"protein_length": 1249,
"fraction_lost": 0.632
} | 1 |
co_stru_00119 | structural_effect | coding_variant | easy | 1 | NM_000465.4(BARD1):c.2217T>G (p.Tyr739Ter) introduces a premature truncation at residue 739 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.2217T>G (p.Tyr739Ter) VARIANT_IN_GENE BARD1 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000465.4(BARD1):c.2217T>G (p.Tyr739Ter)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000465.4(BARD1):c.2217T>G (p.Tyr739Ter)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence... | 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": "BARD1",
"source_db": "UniProt",
"payload": {
"accession": "Q99728",
"sequence": "MPDNRQPRNRQPRIRSGNEPRSAPAMEPDGRGAWAHSRAALDRLEKLLRCSRCTNILREPVCLGGCEHIFCSNCVSDCIGTGCPVCYTPAWIQDLKINRQLDSMIQLCSKLRNLLHDNELSDLKEDKPRKSLF... | [
{
"source_db": "ClinVar",
"source_id": "BARD1",
"text": "NM_000465.4(BARD1):c.2217T>G (p.Tyr739Ter) VARIANT_IN_GENE BARD1",
"confidence": 1
}
] | {
"variant": "NM_000465.4(BARD1):c.2217T>G (p.Tyr739Ter)",
"gene": "BARD1",
"truncation_residue": 739,
"protein_length": 777,
"fraction_lost": 0.049
} | 1 |
co_stru_00120 | structural_effect | coding_variant | easy | 1 | NM_007294.4(BRCA1):c.5558_5561del (p.Thr1852_Tyr1853insTer) introduces a premature truncation at residue 1852 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.5558_5561del (p.Thr1852_Tyr1853insTer) VARIANT_IN_GENE BRCA1 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_007294.4(BRCA1):c.5558_5561del (p.Thr1852_Tyr1853insTer)",
"source_node_type": "VARIANT",
"source_node_label": "NM_007294.4(BRCA1):c.5558_5561del (p.Thr1852_Tyr1853insTer)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type":... | C | [
"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.5558_5561del (p.Thr1852_Tyr1853insTer) VARIANT_IN_GENE BRCA1",
"confidence": 1
}
] | {
"variant": "NM_007294.4(BRCA1):c.5558_5561del (p.Thr1852_Tyr1853insTer)",
"gene": "BRCA1",
"truncation_residue": 1852,
"protein_length": 1863,
"fraction_lost": 0.006
} | 1 |
co_stru_00121 | structural_effect | coding_variant | easy | 1 | NM_000251.3(MSH2):c.2374_2375del (p.Asn792fs) introduces a premature truncation at residue 792 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.2374_2375del (p.Asn792fs) VARIANT_IN_GENE MSH2 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000251.3(MSH2):c.2374_2375del (p.Asn792fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000251.3(MSH2):c.2374_2375del (p.Asn792fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_conf... | 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": "MSH2",
"source_db": "UniProt",
"payload": {
"accession": "P43246",
"sequence": "MAVQPKETLQLESAAEVGFVRFFQGMPEKPTTTVRLFDRGDFYTAHGEDALLAAREVFKTQGVIKYMGPAGAKNLQSVVLSKMNFESFVKDLLLVRQYRVEVYKNRAGNKASKENDWYLAYKASPGNLSQFEDI... | [
{
"source_db": "ClinVar",
"source_id": "MSH2",
"text": "NM_000251.3(MSH2):c.2374_2375del (p.Asn792fs) VARIANT_IN_GENE MSH2",
"confidence": 1
}
] | {
"variant": "NM_000251.3(MSH2):c.2374_2375del (p.Asn792fs)",
"gene": "MSH2",
"truncation_residue": 792,
"protein_length": 934,
"fraction_lost": 0.152
} | 1 |
co_stru_00122 | structural_effect | coding_variant | easy | 1 | NM_000249.4(MLH1):c.1837del (p.Glu613fs) introduces a premature truncation at residue 613 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.1837del (p.Glu613fs) VARIANT_IN_GENE MLH1 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000249.4(MLH1):c.1837del (p.Glu613fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000249.4(MLH1):c.1837del (p.Glu613fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1... | 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": "MLH1",
"source_db": "UniProt",
"payload": {
"accession": "P40692",
"sequence": "MSFVAGVIRRLDETVVNRIAAGEVIQRPANAIKEMIENCLDAKSTSIQVIVKEGGLKLIQIQDNGTGIRKEDLDIVCERFTTSKLQSFEDLASISTYGFRGEALASISHVAHVTITTKTADGKCAYRASYSDGK... | [
{
"source_db": "ClinVar",
"source_id": "MLH1",
"text": "NM_000249.4(MLH1):c.1837del (p.Glu613fs) VARIANT_IN_GENE MLH1",
"confidence": 1
}
] | {
"variant": "NM_000249.4(MLH1):c.1837del (p.Glu613fs)",
"gene": "MLH1",
"truncation_residue": 613,
"protein_length": 756,
"fraction_lost": 0.189
} | 1 |
co_stru_00123 | structural_effect | coding_variant | easy | 1 | NM_007294.4(BRCA1):c.4346del (p.Thr1449fs) introduces a premature truncation at residue 1449 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.4346del (p.Thr1449fs) VARIANT_IN_GENE BRCA1 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_007294.4(BRCA1):c.4346del (p.Thr1449fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_007294.4(BRCA1):c.4346del (p.Thr1449fs)",
"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.4346del (p.Thr1449fs) VARIANT_IN_GENE BRCA1",
"confidence": 1
}
] | {
"variant": "NM_007294.4(BRCA1):c.4346del (p.Thr1449fs)",
"gene": "BRCA1",
"truncation_residue": 1449,
"protein_length": 1863,
"fraction_lost": 0.222
} | 1 |
co_stru_00124 | structural_effect | coding_variant | easy | 1 | NM_000179.3(MSH6):c.3849_3850del (p.Thr1284fs) introduces a premature truncation at residue 1284 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.3849_3850del (p.Thr1284fs) VARIANT_IN_GENE MSH6 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000179.3(MSH6):c.3849_3850del (p.Thr1284fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000179.3(MSH6):c.3849_3850del (p.Thr1284fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_co... | 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": "MSH6",
"source_db": "UniProt",
"payload": {
"accession": "P52701",
"sequence": "MSRQSTLYSFFPKSPALSDANKASARASREGGRAAAAPGASPSPGGDAAWSEAGPGPRPLARSASPPKAKNLNGGLRRSVAPAAPTSCDFSPGDLVWAKMEGYPWWPCLVYNHPFDGTFIREKGKSVRVHVQFF... | [
{
"source_db": "ClinVar",
"source_id": "MSH6",
"text": "NM_000179.3(MSH6):c.3849_3850del (p.Thr1284fs) VARIANT_IN_GENE MSH6",
"confidence": 1
}
] | {
"variant": "NM_000179.3(MSH6):c.3849_3850del (p.Thr1284fs)",
"gene": "MSH6",
"truncation_residue": 1284,
"protein_length": 1360,
"fraction_lost": 0.056
} | 1 |
co_stru_00125 | structural_effect | coding_variant | easy | 1 | NM_000455.5(STK11):c.347_350dup (p.Leu117fs) introduces a premature truncation at residue 117 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.347_350dup (p.Leu117fs) VARIANT_IN_GENE STK11 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000455.5(STK11):c.347_350dup (p.Leu117fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000455.5(STK11):c.347_350dup (p.Leu117fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confid... | 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": "STK11",
"source_db": "UniProt",
"payload": {
"accession": "Q15831",
"sequence": "MEVVDPQQLGMFTEGELMSVGMDTFIHRIDSTEVIYQPRRKRAKLIGKYLMGDLLGEGSYGKVKEVLDSETLCRRAVKILKKKKLRRIPNGEANVKKEIQLLRRLRHKNVIQLVDVLYNEEKQKMYMVMEYCV... | [
{
"source_db": "ClinVar",
"source_id": "STK11",
"text": "NM_000455.5(STK11):c.347_350dup (p.Leu117fs) VARIANT_IN_GENE STK11",
"confidence": 1
}
] | {
"variant": "NM_000455.5(STK11):c.347_350dup (p.Leu117fs)",
"gene": "STK11",
"truncation_residue": 117,
"protein_length": 433,
"fraction_lost": 0.73
} | 1 |
co_stru_00126 | structural_effect | coding_variant | easy | 1 | NM_000535.7(PMS2):c.358_365dup (p.Ile122fs) introduces a premature truncation at residue 122 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.358_365dup (p.Ile122fs) VARIANT_IN_GENE PMS2 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000535.7(PMS2):c.358_365dup (p.Ile122fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000535.7(PMS2):c.358_365dup (p.Ile122fs)",
"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": "PMS2",
"source_db": "UniProt",
"payload": {
"accession": "P54278",
"sequence": "MERAESSSTEPAKAIKPIDRKSVHQICSGQVVLSLSTAVKELVENSLDAGATNIDLKLKDYGVDLIEVSDNGCGVEEENFEGLTLKHHTSKIQEFADLTQVETFGFRGEALSSLCALSDVTISTCHASAKVGTR... | [
{
"source_db": "ClinVar",
"source_id": "PMS2",
"text": "NM_000535.7(PMS2):c.358_365dup (p.Ile122fs) VARIANT_IN_GENE PMS2",
"confidence": 1
}
] | {
"variant": "NM_000535.7(PMS2):c.358_365dup (p.Ile122fs)",
"gene": "PMS2",
"truncation_residue": 122,
"protein_length": 862,
"fraction_lost": 0.858
} | 1 |
co_stru_00127 | structural_effect | coding_variant | easy | 1 | NM_000077.5(CDKN2A):c.122_123delinsT (p.Pro41fs) introduces a premature truncation at residue 41 of CDKN2A's 132-residue protein product (AlphaFold model, mean pLDDT 63.64). Approximately how much of the protein is lost downstream of the truncation? | NM_000077.5(CDKN2A):c.122_123delinsT (p.Pro41fs) VARIANT_IN_GENE CDKN2A | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000077.5(CDKN2A):c.122_123delinsT (p.Pro41fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000077.5(CDKN2A):c.122_123delinsT (p.Pro41fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edg... | 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": "CDKN2A",
"source_db": "UniProt",
"payload": {
"accession": "Q8N726",
"sequence": "MVRRFLVTLRIRRACGPPRVRVFVVHIPRLTGEWAAPGAPAAVALVLMLLRSQRLGQQPLPRRPGHDDGQRPSGGAAAAPRRGAQLRRPRHSHPTRARRCPGGLPGHAGGAAPGRGAAGRARCLGPSARGPG... | [
{
"source_db": "ClinVar",
"source_id": "CDKN2A",
"text": "NM_000077.5(CDKN2A):c.122_123delinsT (p.Pro41fs) VARIANT_IN_GENE CDKN2A",
"confidence": 1
}
] | {
"variant": "NM_000077.5(CDKN2A):c.122_123delinsT (p.Pro41fs)",
"gene": "CDKN2A",
"truncation_residue": 41,
"protein_length": 132,
"fraction_lost": 0.6890000000000001
} | 1 |
co_stru_00128 | structural_effect | coding_variant | easy | 1 | NM_005228.5(EGFR):c.2371C>T (p.Gln791Ter) introduces a premature truncation at residue 791 of EGFR's 1210-residue protein product (AlphaFold model, mean pLDDT 75.95). Approximately how much of the protein is lost downstream of the truncation? | NM_005228.5(EGFR):c.2371C>T (p.Gln791Ter) VARIANT_IN_GENE EGFR | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_005228.5(EGFR):c.2371C>T (p.Gln791Ter)",
"source_node_type": "VARIANT",
"source_node_label": "NM_005228.5(EGFR):c.2371C>T (p.Gln791Ter)",
"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": "EGFR",
"source_db": "UniProt",
"payload": {
"accession": "P00533",
"sequence": "MRPSGTAGAALLALLAALCPASRALEEKKVCQGTSNKLTQLGTFEDHFLSLQRMFNNCEVVLGNLEITYVQRNYDLSFLKTIQEVAGYVLIALNTVERIPLENLQIIRGNMYYENSYALAVLSNYDANKTGLKE... | [
{
"source_db": "ClinVar",
"source_id": "EGFR",
"text": "NM_005228.5(EGFR):c.2371C>T (p.Gln791Ter) VARIANT_IN_GENE EGFR",
"confidence": 1
}
] | {
"variant": "NM_005228.5(EGFR):c.2371C>T (p.Gln791Ter)",
"gene": "EGFR",
"truncation_residue": 791,
"protein_length": 1210,
"fraction_lost": 0.34600000000000003
} | 1 |
co_stru_00129 | structural_effect | coding_variant | easy | 1 | NM_004360.5(CDH1):c.1387G>T (p.Glu463Ter) introduces a premature truncation at residue 463 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.1387G>T (p.Glu463Ter) VARIANT_IN_GENE CDH1 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_004360.5(CDH1):c.1387G>T (p.Glu463Ter)",
"source_node_type": "VARIANT",
"source_node_label": "NM_004360.5(CDH1):c.1387G>T (p.Glu463Ter)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence":... | B | [
"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.1387G>T (p.Glu463Ter) VARIANT_IN_GENE CDH1",
"confidence": 1
}
] | {
"variant": "NM_004360.5(CDH1):c.1387G>T (p.Glu463Ter)",
"gene": "CDH1",
"truncation_residue": 463,
"protein_length": 882,
"fraction_lost": 0.47500000000000003
} | 1 |
co_stru_00130 | structural_effect | coding_variant | easy | 1 | NM_001288705.3(CSF1R):c.2491_2492del (p.Val831fs) introduces a premature truncation at residue 831 of CSF1R's 972-residue protein product (AlphaFold model, mean pLDDT 77.81). Approximately how much of the protein is lost downstream of the truncation? | NM_001288705.3(CSF1R):c.2491_2492del (p.Val831fs) VARIANT_IN_GENE CSF1R | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_001288705.3(CSF1R):c.2491_2492del (p.Val831fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_001288705.3(CSF1R):c.2491_2492del (p.Val831fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"e... | 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": "CSF1R",
"source_db": "UniProt",
"payload": {
"accession": "P07333",
"sequence": "MGPGVLLLLLVATAWHGQGIPVIEPSVPELVVKPGATVTLRCVGNGSVEWDGPPSPHWTLYSDGSSSILSTNNATFQNTGTYRCTEPGDPLGGSAAIHLYVKDPARPWNVLAQEVVVFEDQDALLPCLLTDPV... | [
{
"source_db": "ClinVar",
"source_id": "CSF1R",
"text": "NM_001288705.3(CSF1R):c.2491_2492del (p.Val831fs) VARIANT_IN_GENE CSF1R",
"confidence": 1
}
] | {
"variant": "NM_001288705.3(CSF1R):c.2491_2492del (p.Val831fs)",
"gene": "CSF1R",
"truncation_residue": 831,
"protein_length": 972,
"fraction_lost": 0.145
} | 1 |
co_stru_00131 | structural_effect | coding_variant | easy | 1 | NM_203446.3(SYNJ1):c.289C>T (p.Arg97Ter) introduces a premature truncation at residue 97 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.289C>T (p.Arg97Ter) VARIANT_IN_GENE SYNJ1 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_203446.3(SYNJ1):c.289C>T (p.Arg97Ter)",
"source_node_type": "VARIANT",
"source_node_label": "NM_203446.3(SYNJ1):c.289C>T (p.Arg97Ter)",
"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": "SYNJ1",
"source_db": "UniProt",
"payload": {
"accession": "O43426",
"sequence": "MAFSKGFRIYHKLDPPPFSLIVETRHKEECLMFESGAVAVLSSAEKEAIKGTYSKVLDAYGLLGVLRLNLGDTMLHYLVLVTGCMSVGKIQESEVFRVTSTEFISLRIDSSDEDRISEVRKVLNSGNFYFAWS... | [
{
"source_db": "ClinVar",
"source_id": "SYNJ1",
"text": "NM_203446.3(SYNJ1):c.289C>T (p.Arg97Ter) VARIANT_IN_GENE SYNJ1",
"confidence": 1
}
] | {
"variant": "NM_203446.3(SYNJ1):c.289C>T (p.Arg97Ter)",
"gene": "SYNJ1",
"truncation_residue": 97,
"protein_length": 1573,
"fraction_lost": 0.9380000000000001
} | 1 |
co_stru_00132 | structural_effect | coding_variant | easy | 1 | NM_003900.5(SQSTM1):c.1181_*644del (p.Leu394fs) introduces a premature truncation at residue 394 of SQSTM1's 440-residue protein product (AlphaFold model, mean pLDDT 67.25). Approximately how much of the protein is lost downstream of the truncation? | NM_003900.5(SQSTM1):c.1181_*644del (p.Leu394fs) VARIANT_IN_GENE SQSTM1 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_003900.5(SQSTM1):c.1181_*644del (p.Leu394fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_003900.5(SQSTM1):c.1181_*644del (p.Leu394fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_... | C | [
"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_003900.5(SQSTM1):c.1181_*644del (p.Leu394fs)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr5",
"pos": 179836448,
"track": "phyloP100way",
"window": 20,
"scores": [
-0.36793699... | [
{
"source_db": "ClinVar",
"source_id": "SQSTM1",
"text": "NM_003900.5(SQSTM1):c.1181_*644del (p.Leu394fs) VARIANT_IN_GENE SQSTM1",
"confidence": 1
}
] | {
"variant": "NM_003900.5(SQSTM1):c.1181_*644del (p.Leu394fs)",
"gene": "SQSTM1",
"truncation_residue": 394,
"protein_length": 440,
"fraction_lost": 0.105
} | 1 |
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