{ "@context": "http://reg.genome.network/schema/allele.jsonld", "@id": "http://reg.genome.network/allele/CA122775", "communityStandardTitle": [ "NM_001040142.2(SCN2A):c.3007C>A (p.Leu1003Ile)" ], "externalRecords": { "COSMIC": [ { "@id": "http://cancer.sanger.ac.uk/cosmic/mutation/overview?id=1008606", "active": true, "id": "COSM1008606" }, { "@id": "http://cancer.sanger.ac.uk/cosmic/mutation/overview?id=1008607", "active": true, "id": "COSM1008607" } ], "ClinVarAlleles": [ { "@id": "http://www.ncbi.nlm.nih.gov/clinvar/?term=27920[alleleid]", "alleleId": 27920, "preferredName": "NM_001040142.2(SCN2A):c.3007C>A (p.Leu1003Ile)" } ], "ClinVarVariations": [ { "@id": "http://www.ncbi.nlm.nih.gov/clinvar/variation/12881", "RCV": [ "RCV000013741", "RCV001217344" ], "variationId": 12881 } ], "MyVariantInfo_hg19": [ { "@id": "http://myvariant.info/v1/variant/chr2:g.166210789C>A?assembly=hg19", "id": "chr2:g.166210789C>A" } ], "MyVariantInfo_hg38": [ { "@id": "http://myvariant.info/v1/variant/chr2:g.165354279C>A?assembly=hg38", "id": "chr2:g.165354279C>A" } ], "dbSNP": [ { "@id": "http://www.ncbi.nlm.nih.gov/snp/121917754", "rs": 121917754 } ] }, "genomicAlleles": [ { "chromosome": "2", "coordinates": [ { "allele": "A", "end": 165354279, "referenceAllele": "C", "start": 165354278 } ], "hgvs": [ "NC_000002.12:g.165354279C>A", "CM000664.2:g.165354279C>A" ], "referenceGenome": "GRCh38", "referenceSequence": "http://reg.genome.network/refseq/RS000050" }, { "chromosome": "2", "coordinates": [ { "allele": "A", "end": 166210789, "referenceAllele": "C", "start": 166210788 } ], "hgvs": [ "NC_000002.11:g.166210789C>A", "CM000664.1:g.166210789C>A" ], "referenceGenome": "GRCh37", "referenceSequence": "http://reg.genome.network/refseq/RS000026" }, { "chromosome": "2", "coordinates": [ { "allele": "A", "end": 165919035, "referenceAllele": "C", "start": 165919034 } ], "hgvs": [ "NC_000002.10:g.165919035C>A" ], "referenceGenome": "NCBI36", "referenceSequence": "http://reg.genome.network/refseq/RS000002" }, { "coordinates": [ { "allele": "A", "end": 119878, "referenceAllele": "C", "start": 119877 } ], "hgvs": [ "NG_008143.1:g.119878C>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS000889" } ], "transcriptAlleles": [ { "coordinates": [ { "allele": "A", "end": 3285, "referenceAllele": "C", "start": 3284 } ], "gene": "http://reg.genome.network/gene/GN010588", "geneNCBI_id": 6326, "geneSymbol": "SCN2A", "hgvs": [ "ENST00000631182.3:c.3007C>A" ], "proteinEffect": { "hgvs": "ENSP00000486885.1:p.Leu1003Ile", "hgvsWellDefined": "ENSP00000486885.1:p.Leu1003Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS826623", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Plus Clinical", "nucleotide": { "Ensembl": { "hgvs": "ENST00000631182.3:c.3007C>A" }, "RefSeq": { "hgvs": "NM_001371246.1:c.3007C>A" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000486885.1:p.Leu1003Ile" }, "RefSeq": { "hgvs": "NP_001358175.1:p.Leu1003Ile" } } } }, { "coordinates": [ { "allele": "A", "end": 3285, "referenceAllele": "C", "start": 3284 } ], "gene": "http://reg.genome.network/gene/GN010588", "geneNCBI_id": 6326, "geneSymbol": "SCN2A", "hgvs": [ "ENST00000375437.7:c.3007C>A" ], "proteinEffect": { "hgvs": "ENSP00000364586.2:p.Leu1003Ile", "hgvsWellDefined": "ENSP00000364586.2:p.Leu1003Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS751612", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Select", "nucleotide": { "Ensembl": { "hgvs": "ENST00000375437.7:c.3007C>A" }, "RefSeq": { "hgvs": "NM_001040142.2:c.3007C>A" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000364586.2:p.Leu1003Ile" }, "RefSeq": { "hgvs": "NP_001035232.1:p.Leu1003Ile" } } } }, { "coordinates": [ { "allele": "A", "end": 3384, "referenceAllele": "C", "start": 3383 } ], "gene": "http://reg.genome.network/gene/GN010588", "geneNCBI_id": 6326, "geneSymbol": "SCN2A", "hgvs": [ "ENST00000636071.2:c.3007C>A" ], "proteinEffect": { "hgvs": "ENSP00000490107.1:p.Leu1003Ile", "hgvsWellDefined": "ENSP00000490107.1:p.Leu1003Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS762851" }, { "coordinates": [ { "allele": "A", "end": 3306, "referenceAllele": "C", "start": 3305 } ], "gene": "http://reg.genome.network/gene/GN010588", "geneNCBI_id": 6326, "geneSymbol": "SCN2A", "hgvs": [ "ENST00000636135.1:c.*1326C>A" ], "proteinEffect": { "hgvs": "ENSP00000489821.1:n.*1326C>A" }, "referenceSequence": "http://reg.genome.network/refseq/RS762897" }, { "coordinates": [ { "allele": "A", "end": 3510, "referenceAllele": "C", "start": 3509 } ], "gene": "http://reg.genome.network/gene/GN010588", "geneNCBI_id": 6326, "geneSymbol": "SCN2A", "hgvs": [ "ENST00000636384.2:c.*994C>A" ], "proteinEffect": { "hgvs": "ENSP00000490765.1:n.*994C>A" }, "referenceSequence": "http://reg.genome.network/refseq/RS763075" }, { "coordinates": [ { "allele": "A", "end": 3959, "referenceAllele": "C", "start": 3958 } ], "gene": "http://reg.genome.network/gene/GN010588", "geneNCBI_id": 6326, "geneSymbol": "SCN2A", "hgvs": [ "ENST00000636662.2:c.*3530C>A" ], "proteinEffect": { "hgvs": "ENSP00000489873.1:n.*3530C>A" }, "referenceSequence": "http://reg.genome.network/refseq/RS763290" }, { "coordinates": [ { "allele": "A", "end": 3240, "referenceAllele": "C", "start": 3239 } ], "gene": "http://reg.genome.network/gene/GN010588", "geneNCBI_id": 6326, "geneSymbol": "SCN2A", "hgvs": [ "ENST00000636769.1:c.*949C>A" ], "proteinEffect": { "hgvs": "ENSP00000490800.1:n.*949C>A" }, "referenceSequence": "http://reg.genome.network/refseq/RS763366" }, { "coordinates": [ { "allele": "A", "end": 3359, "referenceAllele": "C", "start": 3358 } ], "gene": "http://reg.genome.network/gene/GN010588", "geneNCBI_id": 6326, "geneSymbol": "SCN2A", "hgvs": [ "ENST00000636985.2:c.2611C>A" ], "proteinEffect": { "hgvs": "ENSP00000490849.1:p.Leu871Ile", "hgvsWellDefined": "ENSP00000490849.1:p.Leu871Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS763522" }, { "coordinates": [ { "allele": "A", "end": 3113, "referenceAllele": "C", "start": 3112 } ], "gene": "http://reg.genome.network/gene/GN010588", "geneNCBI_id": 6326, "geneSymbol": "SCN2A", "hgvs": [ "ENST00000637266.2:c.3007C>A" ], "proteinEffect": { "hgvs": "ENSP00000490866.1:p.Leu1003Ile", "hgvsWellDefined": "ENSP00000490866.1:p.Leu1003Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS763740" }, { "coordinates": [ { "allele": "A", "end": 753, "referenceAllele": "C", "start": 752 } ], "gene": "http://reg.genome.network/gene/GN010588", "geneNCBI_id": 6326, "geneSymbol": "SCN2A", "hgvs": [ "ENST00000673831.1:c.753C>A" ], "proteinEffect": { "hgvs": "ENSP00000501305.1:n.753C>A" }, "referenceSequence": "http://reg.genome.network/refseq/RS773902" }, { "coordinates": [ { "allele": "A", "end": 572, "referenceAllele": "C", "start": 571 } ], "gene": "http://reg.genome.network/gene/GN010588", "geneNCBI_id": 6326, "geneSymbol": "SCN2A", "hgvs": [ "ENST00000673883.1:c.572C>A" ], "proteinEffect": { "hgvs": "ENSP00000501309.1:n.572C>A" }, "referenceSequence": "http://reg.genome.network/refseq/RS773941" }, { "coordinates": [ { "allele": "A", "end": 858, "referenceAllele": "C", "start": 857 } ], "gene": "http://reg.genome.network/gene/GN010588", "geneNCBI_id": 6326, "geneSymbol": "SCN2A", "hgvs": [ "ENST00000674133.1:c.858C>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS774151" }, { "coordinates": [ { "allele": "A", "end": 3163, "referenceAllele": "C", "start": 3162 } ], "gene": "http://reg.genome.network/gene/GN010588", "geneNCBI_id": 6326, "geneSymbol": "SCN2A", "hgvs": [ "ENST00000283256.10:c.3007C>A" ], "proteinEffect": { "hgvs": "ENSP00000283256.6:p.Leu1003Ile", "hgvsWellDefined": "ENSP00000283256.6:p.Leu1003Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS253151" }, { "coordinates": [ { "allele": "A", "end": 3058, "referenceAllele": "C", "start": 3057 } ], "gene": "http://reg.genome.network/gene/GN010588", "geneNCBI_id": 6326, "geneSymbol": "SCN2A", "hgvs": [ "ENST00000375427.4:c.3007C>A" ], "proteinEffect": { "hgvs": "ENSP00000364576.2:p.Leu1003Ile", "hgvsWellDefined": "ENSP00000364576.2:p.Leu1003Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS270704" }, { "coordinates": [ { "allele": "A", "end": 3297, "referenceAllele": "C", "start": 3296 } ], "gene": "http://reg.genome.network/gene/GN010588", "geneNCBI_id": 6326, "geneSymbol": "SCN2A", "hgvs": [ "ENST00000375437.6:c.3007C>A" ], "proteinEffect": { "hgvs": "ENSP00000364586.2:p.Leu1003Ile", "hgvsWellDefined": "ENSP00000364586.2:p.Leu1003Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS270710" }, { "coordinates": [ { "allele": "A", "end": 3150, "referenceAllele": "C", "start": 3149 } ], "gene": "http://reg.genome.network/gene/GN010588", "geneNCBI_id": 6326, "geneSymbol": "SCN2A", "hgvs": [ "ENST00000480032.4:n.3150C>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS320280" }, { "coordinates": [ { "allele": "A", "end": 3211, "referenceAllele": "C", "start": 3210 } ], "gene": "http://reg.genome.network/gene/GN010588", "geneNCBI_id": 6326, "geneSymbol": "SCN2A", "hgvs": [ "ENST00000631182.2:c.3007C>A" ], "proteinEffect": { "hgvs": "ENSP00000486885.1:p.Leu1003Ile", "hgvsWellDefined": "ENSP00000486885.1:p.Leu1003Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS407485" }, { "@id": "http://reg.genome.network/allele/PA094473", "coordinates": [ { "allele": "A", "end": 3297, "referenceAllele": "C", "start": 3296 } ], "gene": "http://reg.genome.network/gene/GN010588", "geneNCBI_id": 6326, "geneSymbol": "SCN2A", "hgvs": [ "NM_001040142.1:c.3007C>A" ], "proteinEffect": { "hgvs": "NP_001035232.1:p.Leu1003Ile", "hgvsWellDefined": "NP_001035232.1:p.Leu1003Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS009521" }, { "@id": "http://reg.genome.network/allele/PA2825359192", "coordinates": [ { "allele": "A", "end": 3058, "referenceAllele": "C", "start": 3057 } ], "gene": "http://reg.genome.network/gene/GN010588", "geneNCBI_id": 6326, "geneSymbol": "SCN2A", "hgvs": [ "NM_001040143.1:c.3007C>A" ], "proteinEffect": { "hgvs": "NP_001035233.1:p.Leu1003Ile", "hgvsWellDefined": "NP_001035233.1:p.Leu1003Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS009522" }, { "@id": "http://reg.genome.network/allele/PA916055966", "coordinates": [ { "allele": "A", "end": 3363, "referenceAllele": "C", "start": 3362 } ], "gene": "http://reg.genome.network/gene/GN010588", "geneNCBI_id": 6326, "geneSymbol": "SCN2A", "hgvs": [ "NM_021007.2:c.3007C>A" ], "proteinEffect": { "hgvs": "NP_066287.2:p.Leu1003Ile", "hgvsWellDefined": "NP_066287.2:p.Leu1003Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS036761" }, { "coordinates": [ { "allele": "A", "end": 3187, "referenceAllele": "C", "start": 3186 } ], "gene": "http://reg.genome.network/gene/GN010588", "geneNCBI_id": 6326, "geneSymbol": "SCN2A", "hgvs": [ "XM_005246750.2:c.3007C>A" ], "proteinEffect": { "hgvs": "XP_005246807.1:p.Leu1003Ile", "hgvsWellDefined": "XP_005246807.1:p.Leu1003Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS057775" }, { "coordinates": [ { "allele": "A", "end": 3307, "referenceAllele": "C", "start": 3306 } ], "gene": "http://reg.genome.network/gene/GN010588", "geneNCBI_id": 6326, "geneSymbol": "SCN2A", "hgvs": [ "XM_005246753.2:c.3007C>A" ], "proteinEffect": { "hgvs": "XP_005246810.1:p.Leu1003Ile", "hgvsWellDefined": "XP_005246810.1:p.Leu1003Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS057776" }, { "coordinates": [ { "allele": "A", "end": 3200, "referenceAllele": "C", "start": 3199 } ], "gene": "http://reg.genome.network/gene/GN010588", "geneNCBI_id": 6326, "geneSymbol": "SCN2A", "hgvs": [ "XM_005246754.3:c.2977C>A" ], "proteinEffect": { "hgvs": "XP_005246811.1:p.Leu993Ile", "hgvsWellDefined": "XP_005246811.1:p.Leu993Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS057777" }, { "coordinates": [ { "allele": "A", "end": 2396, "referenceAllele": "C", "start": 2395 } ], "gene": "http://reg.genome.network/gene/GN010588", "geneNCBI_id": 6326, "geneSymbol": "SCN2A", "hgvs": [ "XM_005246755.3:c.2254C>A" ], "proteinEffect": { "hgvs": "XP_005246812.1:p.Leu752Ile", "hgvsWellDefined": "XP_005246812.1:p.Leu752Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS057778" }, { "coordinates": [ { "allele": "A", "end": 3447, "referenceAllele": "C", "start": 3446 } ], "gene": "http://reg.genome.network/gene/GN010588", "geneNCBI_id": 6326, "geneSymbol": "SCN2A", "hgvs": [ "XM_011511608.1:c.3007C>A" ], "proteinEffect": { "hgvs": "XP_011509910.1:p.Leu1003Ile", "hgvsWellDefined": "XP_011509910.1:p.Leu1003Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS078869" }, { "coordinates": [ { "allele": "A", "end": 3340, "referenceAllele": "C", "start": 3339 } ], "gene": "http://reg.genome.network/gene/GN010588", "geneNCBI_id": 6326, "geneSymbol": "SCN2A", "hgvs": [ "XM_011511609.1:c.3007C>A" ], "proteinEffect": { "hgvs": "XP_011509911.1:p.Leu1003Ile", "hgvsWellDefined": "XP_011509911.1:p.Leu1003Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS078870" }, { "coordinates": [ { "allele": "A", "end": 3313, "referenceAllele": "C", "start": 3312 } ], "gene": "http://reg.genome.network/gene/GN010588", "geneNCBI_id": 6326, "geneSymbol": "SCN2A", "hgvs": [ "XM_005246753.3:c.3007C>A" ], "proteinEffect": { "hgvs": "XP_005246810.1:p.Leu1003Ile", "hgvsWellDefined": "XP_005246810.1:p.Leu1003Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS532689" }, { "coordinates": [ { "allele": "A", "end": 3268, "referenceAllele": "C", "start": 3267 } ], "gene": "http://reg.genome.network/gene/GN010588", "geneNCBI_id": 6326, "geneSymbol": "SCN2A", "hgvs": [ "XM_017004656.1:c.3007C>A" ], "proteinEffect": { "hgvs": "XP_016860145.1:p.Leu1003Ile", "hgvsWellDefined": "XP_016860145.1:p.Leu1003Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS560106" }, { "coordinates": [ { "allele": "A", "end": 3165, "referenceAllele": "C", "start": 3164 } ], "gene": "http://reg.genome.network/gene/GN010588", "geneNCBI_id": 6326, "geneSymbol": "SCN2A", "hgvs": [ "XM_017004657.1:c.3007C>A" ], "proteinEffect": { "hgvs": "XP_016860146.1:p.Leu1003Ile", "hgvsWellDefined": "XP_016860146.1:p.Leu1003Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS560107" }, { "coordinates": [ { "allele": "A", "end": 3477, "referenceAllele": "C", "start": 3476 } ], "gene": "http://reg.genome.network/gene/GN010588", "geneNCBI_id": 6326, "geneSymbol": "SCN2A", "hgvs": [ "XM_017004658.1:c.2254C>A" ], "proteinEffect": { "hgvs": "XP_016860147.1:p.Leu752Ile", "hgvsWellDefined": "XP_016860147.1:p.Leu752Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS560108" }, { "coordinates": [ { "allele": "A", "end": 2395, "referenceAllele": "C", "start": 2394 } ], "gene": "http://reg.genome.network/gene/GN010588", "geneNCBI_id": 6326, "geneSymbol": "SCN2A", "hgvs": [ "XM_017004659.1:c.805C>A" ], "proteinEffect": { "hgvs": "XP_016860148.1:p.Leu269Ile", "hgvsWellDefined": "XP_016860148.1:p.Leu269Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS560109" }, { "coordinates": [ { "allele": "A", "end": 3221, "referenceAllele": "C", "start": 3220 } ], "gene": "http://reg.genome.network/gene/GN010588", "geneNCBI_id": 6326, "geneSymbol": "SCN2A", "hgvs": [ "XM_024453037.1:c.2254C>A" ], "proteinEffect": { "hgvs": "XP_024308805.1:p.Leu752Ile", "hgvsWellDefined": "XP_024308805.1:p.Leu752Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS586424" }, { "@id": "http://reg.genome.network/allele/PA094473", "coordinates": [ { "allele": "A", "end": 3285, "referenceAllele": "C", "start": 3284 } ], "gene": "http://reg.genome.network/gene/GN010588", "geneNCBI_id": 6326, "geneSymbol": "SCN2A", "hgvs": [ "NM_001040142.2:c.3007C>A" ], "proteinEffect": { "hgvs": "NP_001035232.1:p.Leu1003Ile", "hgvsWellDefined": "NP_001035232.1:p.Leu1003Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS663144", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Select", "nucleotide": { "Ensembl": { "hgvs": "ENST00000375437.7:c.3007C>A" }, "RefSeq": { "hgvs": "NM_001040142.2:c.3007C>A" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000364586.2:p.Leu1003Ile" }, "RefSeq": { "hgvs": "NP_001035232.1:p.Leu1003Ile" } } } }, { "@id": "http://reg.genome.network/allele/PA2825359192", "coordinates": [ { "allele": "A", "end": 3404, "referenceAllele": "C", "start": 3403 } ], "gene": "http://reg.genome.network/gene/GN010588", "geneNCBI_id": 6326, "geneSymbol": "SCN2A", "hgvs": [ "NM_001040143.2:c.3007C>A" ], "proteinEffect": { "hgvs": "NP_001035233.1:p.Leu1003Ile", "hgvsWellDefined": "NP_001035233.1:p.Leu1003Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS675962" }, { "@id": "http://reg.genome.network/allele/PA2828471741", "coordinates": [ { "allele": "A", "end": 3285, "referenceAllele": "C", "start": 3284 } ], "gene": "http://reg.genome.network/gene/GN010588", "geneNCBI_id": 6326, "geneSymbol": "SCN2A", "hgvs": [ "NM_001371246.1:c.3007C>A" ], "proteinEffect": { "hgvs": "NP_001358175.1:p.Leu1003Ile", "hgvsWellDefined": "NP_001358175.1:p.Leu1003Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS692751", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Plus Clinical", "nucleotide": { "Ensembl": { "hgvs": "ENST00000631182.3:c.3007C>A" }, "RefSeq": { "hgvs": "NM_001371246.1:c.3007C>A" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000486885.1:p.Leu1003Ile" }, "RefSeq": { "hgvs": "NP_001358175.1:p.Leu1003Ile" } } } }, { "@id": "http://reg.genome.network/allele/PA2828475169", "coordinates": [ { "allele": "A", "end": 3113, "referenceAllele": "C", "start": 3112 } ], "gene": "http://reg.genome.network/gene/GN010588", "geneNCBI_id": 6326, "geneSymbol": "SCN2A", "hgvs": [ "NM_001371247.1:c.3007C>A" ], "proteinEffect": { "hgvs": "NP_001358176.1:p.Leu1003Ile", "hgvsWellDefined": "NP_001358176.1:p.Leu1003Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS692752" }, { "@id": "http://reg.genome.network/allele/PA916055966", "coordinates": [ { "allele": "A", "end": 3139, "referenceAllele": "C", "start": 3138 } ], "gene": "http://reg.genome.network/gene/GN010588", "geneNCBI_id": 6326, "geneSymbol": "SCN2A", "hgvs": [ "NM_021007.3:c.3007C>A" ], "proteinEffect": { "hgvs": "NP_066287.2:p.Leu1003Ile", "hgvsWellDefined": "NP_066287.2:p.Leu1003Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS698348" } ], "type": "nucleotide" }