{ "@context": "http://reg.genome.network/schema/allele.jsonld", "@id": "http://reg.genome.network/allele/CA16603923", "communityStandardTitle": [ "NM_001040142.2(SCN2A):c.4904G>A (p.Arg1635Gln)" ], "externalRecords": { "COSMIC": [ { "@id": "http://cancer.sanger.ac.uk/cosmic/mutation/overview?id=263534", "active": true, "id": "COSM263534" }, { "@id": "http://cancer.sanger.ac.uk/cosmic/mutation/overview?id=263535", "active": true, "id": "COSM263535" } ], "ClinVarAlleles": [ { "@id": "http://www.ncbi.nlm.nih.gov/clinvar/?term=365825[alleleid]", "alleleId": 365825, "preferredName": "NM_001040142.2(SCN2A):c.4904G>A (p.Arg1635Gln)" } ], "ClinVarVariations": [ { "@id": "http://www.ncbi.nlm.nih.gov/clinvar/variation/380389", "RCV": [ "RCV000433186", "RCV001265330", "RCV003985332", "RCV002524873", "RCV003126721" ], "variationId": 380389 } ], "MyVariantInfo_hg19": [ { "@id": "http://myvariant.info/v1/variant/chr2:g.166245220G>A?assembly=hg19", "id": "chr2:g.166245220G>A" } ], "MyVariantInfo_hg38": [ { "@id": "http://myvariant.info/v1/variant/chr2:g.165388710G>A?assembly=hg38", "id": "chr2:g.165388710G>A" } ], "dbSNP": [ { "@id": "http://www.ncbi.nlm.nih.gov/snp/1057520844", "rs": 1057520844 } ], "gnomAD_2": [ { "@id": "http://gnomad.broadinstitute.org/variant/2-166245220-G-A?dataset=gnomad_r2_1", "id": "2-166245220-G-A", "variant": "2:166245220 G / A" } ], "gnomAD_4": [ { "@id": "http://gnomad.broadinstitute.org/variant/2-165388710-G-A?dataset=gnomad_r4", "id": "2-165388710-G-A", "variant": "2:165388710 G / A" } ] }, "genomicAlleles": [ { "chromosome": "2", "coordinates": [ { "allele": "A", "end": 165388710, "referenceAllele": "G", "start": 165388709 } ], "hgvs": [ "NC_000002.12:g.165388710G>A", "CM000664.2:g.165388710G>A" ], "referenceGenome": "GRCh38", "referenceSequence": "http://reg.genome.network/refseq/RS000050" }, { "chromosome": "2", "coordinates": [ { "allele": "A", "end": 166245220, "referenceAllele": "G", "start": 166245219 } ], "hgvs": [ "NC_000002.11:g.166245220G>A", "CM000664.1:g.166245220G>A" ], "referenceGenome": "GRCh37", "referenceSequence": "http://reg.genome.network/refseq/RS000026" }, { "chromosome": "2", "coordinates": [ { "allele": "A", "end": 165953466, "referenceAllele": "G", "start": 165953465 } ], "hgvs": [ "NC_000002.10:g.165953466G>A" ], "referenceGenome": "NCBI36", "referenceSequence": "http://reg.genome.network/refseq/RS000002" }, { "coordinates": [ { "allele": "A", "end": 154309, "referenceAllele": "G", "start": 154308 } ], "hgvs": [ "NG_008143.1:g.154309G>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS000889" } ], "transcriptAlleles": [ { "coordinates": [ { "allele": "A", "end": 5182, "referenceAllele": "G", "start": 5181 } ], "gene": "http://reg.genome.network/gene/GN010588", "geneNCBI_id": 6326, "geneSymbol": "SCN2A", "hgvs": [ "ENST00000631182.3:c.4904G>A" ], "proteinEffect": { "hgvs": "ENSP00000486885.1:p.Arg1635Gln", "hgvsWellDefined": "ENSP00000486885.1:p.Arg1635Gln" }, "referenceSequence": "http://reg.genome.network/refseq/RS826623", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Plus Clinical", "nucleotide": { "Ensembl": { "hgvs": "ENST00000631182.3:c.4904G>A" }, "RefSeq": { "hgvs": "NM_001371246.1:c.4904G>A" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000486885.1:p.Arg1635Gln" }, "RefSeq": { "hgvs": "NP_001358175.1:p.Arg1635Gln" } } } }, { "coordinates": [ { "allele": "A", "end": 5182, "referenceAllele": "G", "start": 5181 } ], "gene": "http://reg.genome.network/gene/GN010588", "geneNCBI_id": 6326, "geneSymbol": "SCN2A", "hgvs": [ "ENST00000375437.7:c.4904G>A" ], "proteinEffect": { "hgvs": "ENSP00000364586.2:p.Arg1635Gln", "hgvsWellDefined": "ENSP00000364586.2:p.Arg1635Gln" }, "referenceSequence": "http://reg.genome.network/refseq/RS751612", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Select", "nucleotide": { "Ensembl": { "hgvs": "ENST00000375437.7:c.4904G>A" }, "RefSeq": { "hgvs": "NM_001040142.2:c.4904G>A" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000364586.2:p.Arg1635Gln" }, "RefSeq": { "hgvs": "NP_001035232.1:p.Arg1635Gln" } } } }, { "coordinates": [ { "allele": "A", "end": 5281, "referenceAllele": "G", "start": 5280 } ], "gene": "http://reg.genome.network/gene/GN010588", "geneNCBI_id": 6326, "geneSymbol": "SCN2A", "hgvs": [ "ENST00000636071.2:c.4904G>A" ], "proteinEffect": { "hgvs": "ENSP00000490107.1:p.Arg1635Gln", "hgvsWellDefined": "ENSP00000490107.1:p.Arg1635Gln" }, "referenceSequence": "http://reg.genome.network/refseq/RS762851" }, { "coordinates": [ { "allele": "A", "end": 5203, "referenceAllele": "G", "start": 5202 } ], "gene": "http://reg.genome.network/gene/GN010588", "geneNCBI_id": 6326, "geneSymbol": "SCN2A", "hgvs": [ "ENST00000636135.1:c.*3223G>A" ], "proteinEffect": { "hgvs": "ENSP00000489821.1:n.*3223G>A" }, "referenceSequence": "http://reg.genome.network/refseq/RS762897" }, { "coordinates": [ { "allele": "A", "end": 5407, "referenceAllele": "G", "start": 5406 } ], "gene": "http://reg.genome.network/gene/GN010588", "geneNCBI_id": 6326, "geneSymbol": "SCN2A", "hgvs": [ "ENST00000636384.2:c.*2891G>A" ], "proteinEffect": { "hgvs": "ENSP00000490765.1:n.*2891G>A" }, "referenceSequence": "http://reg.genome.network/refseq/RS763075" }, { "coordinates": [ { "allele": "A", "end": 5856, "referenceAllele": "G", "start": 5855 } ], "gene": "http://reg.genome.network/gene/GN010588", "geneNCBI_id": 6326, "geneSymbol": "SCN2A", "hgvs": [ "ENST00000636662.2:c.*5427G>A" ], "proteinEffect": { "hgvs": "ENSP00000489873.1:n.*5427G>A" }, "referenceSequence": "http://reg.genome.network/refseq/RS763290" }, { "coordinates": [ { "allele": "A", "end": 5137, "referenceAllele": "G", "start": 5136 } ], "gene": "http://reg.genome.network/gene/GN010588", "geneNCBI_id": 6326, "geneSymbol": "SCN2A", "hgvs": [ "ENST00000636769.1:c.*2846G>A" ], "proteinEffect": { "hgvs": "ENSP00000490800.1:n.*2846G>A" }, "referenceSequence": "http://reg.genome.network/refseq/RS763366" }, { "coordinates": [ { "allele": "A", "end": 5256, "referenceAllele": "G", "start": 5255 } ], "gene": "http://reg.genome.network/gene/GN010588", "geneNCBI_id": 6326, "geneSymbol": "SCN2A", "hgvs": [ "ENST00000636985.2:c.4508G>A" ], "proteinEffect": { "hgvs": "ENSP00000490849.1:p.Arg1503Gln", "hgvsWellDefined": "ENSP00000490849.1:p.Arg1503Gln" }, "referenceSequence": "http://reg.genome.network/refseq/RS763522" }, { "coordinates": [ { "allele": "A", "end": 5010, "referenceAllele": "G", "start": 5009 } ], "gene": "http://reg.genome.network/gene/GN010588", "geneNCBI_id": 6326, "geneSymbol": "SCN2A", "hgvs": [ "ENST00000637266.2:c.4904G>A" ], "proteinEffect": { "hgvs": "ENSP00000490866.1:p.Arg1635Gln", "hgvsWellDefined": "ENSP00000490866.1:p.Arg1635Gln" }, "referenceSequence": "http://reg.genome.network/refseq/RS763740" }, { "coordinates": [ { "allele": "A", "end": 5060, "referenceAllele": "G", "start": 5059 } ], "gene": "http://reg.genome.network/gene/GN010588", "geneNCBI_id": 6326, "geneSymbol": "SCN2A", "hgvs": [ "ENST00000283256.10:c.4904G>A" ], "proteinEffect": { "hgvs": "ENSP00000283256.6:p.Arg1635Gln", "hgvsWellDefined": "ENSP00000283256.6:p.Arg1635Gln" }, "referenceSequence": "http://reg.genome.network/refseq/RS253151" }, { "coordinates": [ { "allele": "A", "end": 4955, "referenceAllele": "G", "start": 4954 } ], "gene": "http://reg.genome.network/gene/GN010588", "geneNCBI_id": 6326, "geneSymbol": "SCN2A", "hgvs": [ "ENST00000375427.4:c.4904G>A" ], "proteinEffect": { "hgvs": "ENSP00000364576.2:p.Arg1635Gln", "hgvsWellDefined": "ENSP00000364576.2:p.Arg1635Gln" }, "referenceSequence": "http://reg.genome.network/refseq/RS270704" }, { "coordinates": [ { "allele": "A", "end": 5194, "referenceAllele": "G", "start": 5193 } ], "gene": "http://reg.genome.network/gene/GN010588", "geneNCBI_id": 6326, "geneSymbol": "SCN2A", "hgvs": [ "ENST00000375437.6:c.4904G>A" ], "proteinEffect": { "hgvs": "ENSP00000364586.2:p.Arg1635Gln", "hgvsWellDefined": "ENSP00000364586.2:p.Arg1635Gln" }, "referenceSequence": "http://reg.genome.network/refseq/RS270710" }, { "coordinates": [ { "allele": "A", "end": 8335, "referenceAllele": "G", "start": 8334 } ], "gene": "http://reg.genome.network/gene/GN010588", "geneNCBI_id": 6326, "geneSymbol": "SCN2A", "hgvs": [ "ENST00000480032.4:n.8335G>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS320280" }, { "coordinates": [ { "allele": "A", "end": 5108, "referenceAllele": "G", "start": 5107 } ], "gene": "http://reg.genome.network/gene/GN010588", "geneNCBI_id": 6326, "geneSymbol": "SCN2A", "hgvs": [ "ENST00000631182.2:c.4904G>A" ], "proteinEffect": { "hgvs": "ENSP00000486885.1:p.Arg1635Gln", "hgvsWellDefined": "ENSP00000486885.1:p.Arg1635Gln" }, "referenceSequence": "http://reg.genome.network/refseq/RS407485" }, { "@id": "http://reg.genome.network/allele/PA2825356925", "coordinates": [ { "allele": "A", "end": 5194, "referenceAllele": "G", "start": 5193 } ], "gene": "http://reg.genome.network/gene/GN010588", "geneNCBI_id": 6326, "geneSymbol": "SCN2A", "hgvs": [ "NM_001040142.1:c.4904G>A" ], "proteinEffect": { "hgvs": "NP_001035232.1:p.Arg1635Gln", "hgvsWellDefined": "NP_001035232.1:p.Arg1635Gln" }, "referenceSequence": "http://reg.genome.network/refseq/RS009521" }, { "@id": "http://reg.genome.network/allele/PA2825360323", "coordinates": [ { "allele": "A", "end": 4955, "referenceAllele": "G", "start": 4954 } ], "gene": "http://reg.genome.network/gene/GN010588", "geneNCBI_id": 6326, "geneSymbol": "SCN2A", "hgvs": [ "NM_001040143.1:c.4904G>A" ], "proteinEffect": { "hgvs": "NP_001035233.1:p.Arg1635Gln", "hgvsWellDefined": "NP_001035233.1:p.Arg1635Gln" }, "referenceSequence": "http://reg.genome.network/refseq/RS009522" }, { "@id": "http://reg.genome.network/allele/PA645407759", "coordinates": [ { "allele": "A", "end": 5260, "referenceAllele": "G", "start": 5259 } ], "gene": "http://reg.genome.network/gene/GN010588", "geneNCBI_id": 6326, "geneSymbol": "SCN2A", "hgvs": [ "NM_021007.2:c.4904G>A" ], "proteinEffect": { "hgvs": "NP_066287.2:p.Arg1635Gln", "hgvsWellDefined": "NP_066287.2:p.Arg1635Gln" }, "referenceSequence": "http://reg.genome.network/refseq/RS036761" }, { "coordinates": [ { "allele": "A", "end": 5084, "referenceAllele": "G", "start": 5083 } ], "gene": "http://reg.genome.network/gene/GN010588", "geneNCBI_id": 6326, "geneSymbol": "SCN2A", "hgvs": [ "XM_005246750.2:c.4904G>A" ], "proteinEffect": { "hgvs": "XP_005246807.1:p.Arg1635Gln", "hgvsWellDefined": "XP_005246807.1:p.Arg1635Gln" }, "referenceSequence": "http://reg.genome.network/refseq/RS057775" }, { "coordinates": [ { "allele": "A", "end": 5204, "referenceAllele": "G", "start": 5203 } ], "gene": "http://reg.genome.network/gene/GN010588", "geneNCBI_id": 6326, "geneSymbol": "SCN2A", "hgvs": [ "XM_005246753.2:c.4904G>A" ], "proteinEffect": { "hgvs": "XP_005246810.1:p.Arg1635Gln", "hgvsWellDefined": "XP_005246810.1:p.Arg1635Gln" }, "referenceSequence": "http://reg.genome.network/refseq/RS057776" }, { "coordinates": [ { "allele": "A", "end": 5097, "referenceAllele": "G", "start": 5096 } ], "gene": "http://reg.genome.network/gene/GN010588", "geneNCBI_id": 6326, "geneSymbol": "SCN2A", "hgvs": [ "XM_005246754.3:c.4874G>A" ], "proteinEffect": { "hgvs": "XP_005246811.1:p.Arg1625Gln", "hgvsWellDefined": "XP_005246811.1:p.Arg1625Gln" }, "referenceSequence": "http://reg.genome.network/refseq/RS057777" }, { "coordinates": [ { "allele": "A", "end": 4293, "referenceAllele": "G", "start": 4292 } ], "gene": "http://reg.genome.network/gene/GN010588", "geneNCBI_id": 6326, "geneSymbol": "SCN2A", "hgvs": [ "XM_005246755.3:c.4151G>A" ], "proteinEffect": { "hgvs": "XP_005246812.1:p.Arg1384Gln", "hgvsWellDefined": "XP_005246812.1:p.Arg1384Gln" }, "referenceSequence": "http://reg.genome.network/refseq/RS057778" }, { "coordinates": [ { "allele": "A", "end": 5344, "referenceAllele": "G", "start": 5343 } ], "gene": "http://reg.genome.network/gene/GN010588", "geneNCBI_id": 6326, "geneSymbol": "SCN2A", "hgvs": [ "XM_011511608.1:c.4904G>A" ], "proteinEffect": { "hgvs": "XP_011509910.1:p.Arg1635Gln", "hgvsWellDefined": "XP_011509910.1:p.Arg1635Gln" }, "referenceSequence": "http://reg.genome.network/refseq/RS078869" }, { "coordinates": [ { "allele": "A", "end": 5237, "referenceAllele": "G", "start": 5236 } ], "gene": "http://reg.genome.network/gene/GN010588", "geneNCBI_id": 6326, "geneSymbol": "SCN2A", "hgvs": [ "XM_011511609.1:c.4904G>A" ], "proteinEffect": { "hgvs": "XP_011509911.1:p.Arg1635Gln", "hgvsWellDefined": "XP_011509911.1:p.Arg1635Gln" }, "referenceSequence": "http://reg.genome.network/refseq/RS078870" }, { "coordinates": [ { "allele": "A", "end": 5210, "referenceAllele": "G", "start": 5209 } ], "gene": "http://reg.genome.network/gene/GN010588", "geneNCBI_id": 6326, "geneSymbol": "SCN2A", "hgvs": [ "XM_005246753.3:c.4904G>A" ], "proteinEffect": { "hgvs": "XP_005246810.1:p.Arg1635Gln", "hgvsWellDefined": "XP_005246810.1:p.Arg1635Gln" }, "referenceSequence": "http://reg.genome.network/refseq/RS532689" }, { "coordinates": [ { "allele": "A", "end": 5165, "referenceAllele": "G", "start": 5164 } ], "gene": "http://reg.genome.network/gene/GN010588", "geneNCBI_id": 6326, "geneSymbol": "SCN2A", "hgvs": [ "XM_017004656.1:c.4904G>A" ], "proteinEffect": { "hgvs": "XP_016860145.1:p.Arg1635Gln", "hgvsWellDefined": "XP_016860145.1:p.Arg1635Gln" }, "referenceSequence": "http://reg.genome.network/refseq/RS560106" }, { "coordinates": [ { "allele": "A", "end": 5062, "referenceAllele": "G", "start": 5061 } ], "gene": "http://reg.genome.network/gene/GN010588", "geneNCBI_id": 6326, "geneSymbol": "SCN2A", "hgvs": [ "XM_017004657.1:c.4904G>A" ], "proteinEffect": { "hgvs": "XP_016860146.1:p.Arg1635Gln", "hgvsWellDefined": "XP_016860146.1:p.Arg1635Gln" }, "referenceSequence": "http://reg.genome.network/refseq/RS560107" }, { "coordinates": [ { "allele": "A", "end": 5374, "referenceAllele": "G", "start": 5373 } ], "gene": "http://reg.genome.network/gene/GN010588", "geneNCBI_id": 6326, "geneSymbol": "SCN2A", "hgvs": [ "XM_017004658.1:c.4151G>A" ], "proteinEffect": { "hgvs": "XP_016860147.1:p.Arg1384Gln", "hgvsWellDefined": "XP_016860147.1:p.Arg1384Gln" }, "referenceSequence": "http://reg.genome.network/refseq/RS560108" }, { "coordinates": [ { "allele": "A", "end": 4292, "referenceAllele": "G", "start": 4291 } ], "gene": "http://reg.genome.network/gene/GN010588", "geneNCBI_id": 6326, "geneSymbol": "SCN2A", "hgvs": [ "XM_017004659.1:c.2702G>A" ], "proteinEffect": { "hgvs": "XP_016860148.1:p.Arg901Gln", "hgvsWellDefined": "XP_016860148.1:p.Arg901Gln" }, "referenceSequence": "http://reg.genome.network/refseq/RS560109" }, { "coordinates": [ { "allele": "A", "end": 5118, "referenceAllele": "G", "start": 5117 } ], "gene": "http://reg.genome.network/gene/GN010588", "geneNCBI_id": 6326, "geneSymbol": "SCN2A", "hgvs": [ "XM_024453037.1:c.4151G>A" ], "proteinEffect": { "hgvs": "XP_024308805.1:p.Arg1384Gln", "hgvsWellDefined": "XP_024308805.1:p.Arg1384Gln" }, "referenceSequence": "http://reg.genome.network/refseq/RS586424" }, { "@id": "http://reg.genome.network/allele/PA2825356925", "coordinates": [ { "allele": "A", "end": 5182, "referenceAllele": "G", "start": 5181 } ], "gene": "http://reg.genome.network/gene/GN010588", "geneNCBI_id": 6326, "geneSymbol": "SCN2A", "hgvs": [ "NM_001040142.2:c.4904G>A" ], "proteinEffect": { "hgvs": "NP_001035232.1:p.Arg1635Gln", "hgvsWellDefined": "NP_001035232.1:p.Arg1635Gln" }, "referenceSequence": "http://reg.genome.network/refseq/RS663144", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Select", "nucleotide": { "Ensembl": { "hgvs": "ENST00000375437.7:c.4904G>A" }, "RefSeq": { "hgvs": "NM_001040142.2:c.4904G>A" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000364586.2:p.Arg1635Gln" }, "RefSeq": { "hgvs": "NP_001035232.1:p.Arg1635Gln" } } } }, { "@id": "http://reg.genome.network/allele/PA2825360323", "coordinates": [ { "allele": "A", "end": 5301, "referenceAllele": "G", "start": 5300 } ], "gene": "http://reg.genome.network/gene/GN010588", "geneNCBI_id": 6326, "geneSymbol": "SCN2A", "hgvs": [ "NM_001040143.2:c.4904G>A" ], "proteinEffect": { "hgvs": "NP_001035233.1:p.Arg1635Gln", "hgvsWellDefined": "NP_001035233.1:p.Arg1635Gln" }, "referenceSequence": "http://reg.genome.network/refseq/RS675962" }, { "@id": "http://reg.genome.network/allele/PA2828472900", "coordinates": [ { "allele": "A", "end": 5182, "referenceAllele": "G", "start": 5181 } ], "gene": "http://reg.genome.network/gene/GN010588", "geneNCBI_id": 6326, "geneSymbol": "SCN2A", "hgvs": [ "NM_001371246.1:c.4904G>A" ], "proteinEffect": { "hgvs": "NP_001358175.1:p.Arg1635Gln", "hgvsWellDefined": "NP_001358175.1:p.Arg1635Gln" }, "referenceSequence": "http://reg.genome.network/refseq/RS692751", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Plus Clinical", "nucleotide": { "Ensembl": { "hgvs": "ENST00000631182.3:c.4904G>A" }, "RefSeq": { "hgvs": "NM_001371246.1:c.4904G>A" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000486885.1:p.Arg1635Gln" }, "RefSeq": { "hgvs": "NP_001358175.1:p.Arg1635Gln" } } } }, { "@id": "http://reg.genome.network/allele/PA2828476458", "coordinates": [ { "allele": "A", "end": 5010, "referenceAllele": "G", "start": 5009 } ], "gene": "http://reg.genome.network/gene/GN010588", "geneNCBI_id": 6326, "geneSymbol": "SCN2A", "hgvs": [ "NM_001371247.1:c.4904G>A" ], "proteinEffect": { "hgvs": "NP_001358176.1:p.Arg1635Gln", "hgvsWellDefined": "NP_001358176.1:p.Arg1635Gln" }, "referenceSequence": "http://reg.genome.network/refseq/RS692752" }, { "@id": "http://reg.genome.network/allele/PA645407759", "coordinates": [ { "allele": "A", "end": 5036, "referenceAllele": "G", "start": 5035 } ], "gene": "http://reg.genome.network/gene/GN010588", "geneNCBI_id": 6326, "geneSymbol": "SCN2A", "hgvs": [ "NM_021007.3:c.4904G>A" ], "proteinEffect": { "hgvs": "NP_066287.2:p.Arg1635Gln", "hgvsWellDefined": "NP_066287.2:p.Arg1635Gln" }, "referenceSequence": "http://reg.genome.network/refseq/RS698348" } ], "type": "nucleotide" }