{ "@context": "http://reg.genome.network/schema/allele.jsonld", "@id": "http://reg.genome.network/allele/CA248339", "communityStandardTitle": [ "NM_001013693.3(LDLRAD2):c.*1931C>T", "NM_005529.7(HSPG2):c.12874G>A (p.Glu4292Lys)" ], "externalRecords": { "ClinVarAlleles": [ { "@id": "http://www.ncbi.nlm.nih.gov/clinvar/?term=196393[alleleid]", "alleleId": 196393, "preferredName": "NM_005529.7(HSPG2):c.12874G>A (p.Glu4292Lys)" } ], "ClinVarVariations": [ { "@id": "http://www.ncbi.nlm.nih.gov/clinvar/variation/199234", "RCV": [ "RCV000711912", "RCV001101422", "RCV001101423", "RCV004539697" ], "variationId": 199234 } ], "ExAC": [ { "@id": "http://exac.broadinstitute.org/variant/1-22150639-C-T", "id": "1-22150639-C-T", "variant": "1:22150639 C / T" } ], "MyVariantInfo_hg19": [ { "@id": "http://myvariant.info/v1/variant/chr1:g.22150639C>T?assembly=hg19", "id": "chr1:g.22150639C>T" } ], "MyVariantInfo_hg38": [ { "@id": "http://myvariant.info/v1/variant/chr1:g.21824146C>T?assembly=hg38", "id": "chr1:g.21824146C>T" } ], "dbSNP": [ { "@id": "http://www.ncbi.nlm.nih.gov/snp/141280063", "rs": 141280063 } ], "gnomAD_2": [ { "@id": "http://gnomad.broadinstitute.org/variant/1-22150639-C-T?dataset=gnomad_r2_1", "id": "1-22150639-C-T", "variant": "1:22150639 C / T" } ], "gnomAD_3": [ { "@id": "http://gnomad.broadinstitute.org/variant/1-21824146-C-T?dataset=gnomad_r3", "id": "1-21824146-C-T", "variant": "1:21824146 C / T" } ], "gnomAD_4": [ { "@id": "http://gnomad.broadinstitute.org/variant/1-21824146-C-T?dataset=gnomad_r4", "id": "1-21824146-C-T", "variant": "1:21824146 C / T" } ] }, "genomicAlleles": [ { "chromosome": "1", "coordinates": [ { "allele": "T", "end": 21824146, "referenceAllele": "C", "start": 21824145 } ], "hgvs": [ "NC_000001.11:g.21824146C>T", "CM000663.2:g.21824146C>T" ], "referenceGenome": "GRCh38", "referenceSequence": "http://reg.genome.network/refseq/RS000049" }, { "chromosome": "1", "coordinates": [ { "allele": "T", "end": 22150639, "referenceAllele": "C", "start": 22150638 } ], "hgvs": [ "NC_000001.10:g.22150639C>T", "CM000663.1:g.22150639C>T" ], "referenceGenome": "GRCh37", "referenceSequence": "http://reg.genome.network/refseq/RS000025" }, { "chromosome": "1", "coordinates": [ { "allele": "T", "end": 22023226, "referenceAllele": "C", "start": 22023225 } ], "hgvs": [ "NC_000001.9:g.22023226C>T" ], "referenceGenome": "NCBI36", "referenceSequence": "http://reg.genome.network/refseq/RS000001" }, { "coordinates": [ { "allele": "A", "end": 118112, "referenceAllele": "G", "start": 118111 } ], "hgvs": [ "NG_016740.1:g.118112G>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS003265" } ], "transcriptAlleles": [ { "coordinates": [ { "allele": "T", "end": 2937, "referenceAllele": "C", "start": 2936 } ], "gene": "http://reg.genome.network/gene/GN032071", "geneNCBI_id": 401944, "geneSymbol": "LDLRAD2", "hgvs": [ "ENST00000344642.7:c.*1931C>T" ], "proteinEffect": { "hgvs": "ENSP00000340988.2:n.*1931C>T" }, "referenceSequence": "http://reg.genome.network/refseq/RS748236", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Select", "nucleotide": { "Ensembl": { "hgvs": "ENST00000344642.7:c.*1931C>T" }, "RefSeq": { "hgvs": "NM_001013693.3:c.*1931C>T" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000340988.2:n.*1931C>T" }, "RefSeq": { "hgvs": "NP_001013715.2:n.*1931C>T" } } } }, { "coordinates": [ { "allele": "A", "end": 12967, "referenceAllele": "G", "start": 12966 } ], "gene": "http://reg.genome.network/gene/GN005273", "geneNCBI_id": 3339, "geneSymbol": "HSPG2", "hgvs": [ "ENST00000374695.8:c.12874G>A" ], "proteinEffect": { "hgvs": "ENSP00000363827.3:p.Glu4292Lys", "hgvsWellDefined": "ENSP00000363827.3:p.Glu4292Lys" }, "referenceSequence": "http://reg.genome.network/refseq/RS751480", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Select", "nucleotide": { "Ensembl": { "hgvs": "ENST00000374695.8:c.12874G>A" }, "RefSeq": { "hgvs": "NM_005529.7:c.12874G>A" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000363827.3:p.Glu4292Lys" }, "RefSeq": { "hgvs": "NP_005520.4:p.Glu4292Lys" } } } }, { "coordinates": [ { "allele": "T", "end": 2937, "referenceAllele": "C", "start": 2936 } ], "gene": "http://reg.genome.network/gene/GN032071", "geneNCBI_id": 401944, "geneSymbol": "LDLRAD2", "hgvs": [ "ENST00000344642.6:c.*1931C>T" ], "proteinEffect": { "hgvs": "ENSP00000340988.2:n.*1931C>T" }, "referenceSequence": "http://reg.genome.network/refseq/RS262023" }, { "coordinates": [ { "allele": "A", "end": 12954, "referenceAllele": "G", "start": 12953 } ], "gene": "http://reg.genome.network/gene/GN005273", "geneNCBI_id": 3339, "geneSymbol": "HSPG2", "hgvs": [ "ENST00000374695.7:c.12874G>A" ], "proteinEffect": { "hgvs": "ENSP00000363827.3:p.Glu4292Lys", "hgvsWellDefined": "ENSP00000363827.3:p.Glu4292Lys" }, "referenceSequence": "http://reg.genome.network/refseq/RS270365" }, { "coordinates": [ { "allele": "A", "end": 121, "referenceAllele": "G", "start": 120 } ], "gene": "http://reg.genome.network/gene/GN005273", "geneNCBI_id": 3339, "geneSymbol": "HSPG2", "hgvs": [ "ENST00000481644.1:n.121G>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS321513" }, { "coordinates": [ { "allele": "A", "end": 2213, "referenceAllele": "G", "start": 2212 } ], "gene": "http://reg.genome.network/gene/GN005273", "geneNCBI_id": 3339, "geneSymbol": "HSPG2", "hgvs": [ "ENST00000486901.1:n.2213G>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS325595" }, { "coordinates": [ { "allele": "T", "end": 2937, "referenceAllele": "C", "start": 2936 } ], "gene": "http://reg.genome.network/gene/GN032071", "geneNCBI_id": 401944, "geneSymbol": "LDLRAD2", "hgvs": [ "NM_001013693.2:c.*1931C>T" ], "proteinEffect": { "hgvs": "NP_001013715.2:n.*1931C>T" }, "referenceSequence": "http://reg.genome.network/refseq/RS008442" }, { "@id": "http://reg.genome.network/allele/PA916018162", "coordinates": [ { "allele": "A", "end": 12957, "referenceAllele": "G", "start": 12956 } ], "gene": "http://reg.genome.network/gene/GN005273", "geneNCBI_id": 3339, "geneSymbol": "HSPG2", "hgvs": [ "NM_001291860.1:c.12877G>A" ], "proteinEffect": { "hgvs": "NP_001278789.1:p.Glu4293Lys", "hgvsWellDefined": "NP_001278789.1:p.Glu4293Lys" }, "referenceSequence": "http://reg.genome.network/refseq/RS024346" }, { "@id": "http://reg.genome.network/allele/PA248340", "coordinates": [ { "allele": "A", "end": 12954, "referenceAllele": "G", "start": 12953 } ], "gene": "http://reg.genome.network/gene/GN005273", "geneNCBI_id": 3339, "geneSymbol": "HSPG2", "hgvs": [ "NM_005529.6:c.12874G>A" ], "proteinEffect": { "hgvs": "NP_005520.4:p.Glu4292Lys", "hgvsWellDefined": "NP_005520.4:p.Glu4292Lys" }, "referenceSequence": "http://reg.genome.network/refseq/RS030620" }, { "coordinates": [ { "allele": "A", "end": 13453, "referenceAllele": "G", "start": 13452 } ], "gene": "http://reg.genome.network/gene/GN005273", "geneNCBI_id": 3339, "geneSymbol": "HSPG2", "hgvs": [ "XM_006710594.2:c.13438G>A" ], "proteinEffect": { "hgvs": "XP_006710657.1:p.Glu4480Lys", "hgvsWellDefined": "XP_006710657.1:p.Glu4480Lys" }, "referenceSequence": "http://reg.genome.network/refseq/RS068699" }, { "coordinates": [ { "allele": "A", "end": 13405, "referenceAllele": "G", "start": 13404 } ], "gene": "http://reg.genome.network/gene/GN005273", "geneNCBI_id": 3339, "geneSymbol": "HSPG2", "hgvs": [ "XM_006710595.2:c.13390G>A" ], "proteinEffect": { "hgvs": "XP_006710658.1:p.Glu4464Lys", "hgvsWellDefined": "XP_006710658.1:p.Glu4464Lys" }, "referenceSequence": "http://reg.genome.network/refseq/RS068700" }, { "coordinates": [ { "allele": "A", "end": 13384, "referenceAllele": "G", "start": 13383 } ], "gene": "http://reg.genome.network/gene/GN005273", "geneNCBI_id": 3339, "geneSymbol": "HSPG2", "hgvs": [ "XM_006710596.2:c.13369G>A" ], "proteinEffect": { "hgvs": "XP_006710659.1:p.Glu4457Lys", "hgvsWellDefined": "XP_006710659.1:p.Glu4457Lys" }, "referenceSequence": "http://reg.genome.network/refseq/RS068701" }, { "coordinates": [ { "allele": "A", "end": 12907, "referenceAllele": "G", "start": 12906 } ], "gene": "http://reg.genome.network/gene/GN005273", "geneNCBI_id": 3339, "geneSymbol": "HSPG2", "hgvs": [ "XM_006710597.2:c.12892G>A" ], "proteinEffect": { "hgvs": "XP_006710660.1:p.Glu4298Lys", "hgvsWellDefined": "XP_006710660.1:p.Glu4298Lys" }, "referenceSequence": "http://reg.genome.network/refseq/RS068702" }, { "coordinates": [ { "allele": "A", "end": 13456, "referenceAllele": "G", "start": 13455 } ], "gene": "http://reg.genome.network/gene/GN005273", "geneNCBI_id": 3339, "geneSymbol": "HSPG2", "hgvs": [ "XM_011541317.1:c.13441G>A" ], "proteinEffect": { "hgvs": "XP_011539619.1:p.Glu4481Lys", "hgvsWellDefined": "XP_011539619.1:p.Glu4481Lys" }, "referenceSequence": "http://reg.genome.network/refseq/RS108259" }, { "coordinates": [ { "allele": "A", "end": 13438, "referenceAllele": "G", "start": 13437 } ], "gene": "http://reg.genome.network/gene/GN005273", "geneNCBI_id": 3339, "geneSymbol": "HSPG2", "hgvs": [ "XM_011541318.1:c.13423G>A" ], "proteinEffect": { "hgvs": "XP_011539620.1:p.Glu4475Lys", "hgvsWellDefined": "XP_011539620.1:p.Glu4475Lys" }, "referenceSequence": "http://reg.genome.network/refseq/RS108260" }, { "coordinates": [ { "allele": "A", "end": 13333, "referenceAllele": "G", "start": 13332 } ], "gene": "http://reg.genome.network/gene/GN005273", "geneNCBI_id": 3339, "geneSymbol": "HSPG2", "hgvs": [ "XM_011541319.1:c.13318G>A" ], "proteinEffect": { "hgvs": "XP_011539621.1:p.Glu4440Lys", "hgvsWellDefined": "XP_011539621.1:p.Glu4440Lys" }, "referenceSequence": "http://reg.genome.network/refseq/RS108261" }, { "coordinates": [ { "allele": "A", "end": 13177, "referenceAllele": "G", "start": 13176 } ], "gene": "http://reg.genome.network/gene/GN005273", "geneNCBI_id": 3339, "geneSymbol": "HSPG2", "hgvs": [ "XM_011541320.1:c.13162G>A" ], "proteinEffect": { "hgvs": "XP_011539622.1:p.Glu4388Lys", "hgvsWellDefined": "XP_011539622.1:p.Glu4388Lys" }, "referenceSequence": "http://reg.genome.network/refseq/RS108262" }, { "coordinates": [ { "allele": "A", "end": 12961, "referenceAllele": "G", "start": 12960 } ], "gene": "http://reg.genome.network/gene/GN005273", "geneNCBI_id": 3339, "geneSymbol": "HSPG2", "hgvs": [ "XM_011541321.1:c.12946G>A" ], "proteinEffect": { "hgvs": "XP_011539623.1:p.Glu4316Lys", "hgvsWellDefined": "XP_011539623.1:p.Glu4316Lys" }, "referenceSequence": "http://reg.genome.network/refseq/RS108263" }, { "coordinates": [ { "allele": "A", "end": 13438, "referenceAllele": "G", "start": 13437 } ], "gene": "http://reg.genome.network/gene/GN005273", "geneNCBI_id": 3339, "geneSymbol": "HSPG2", "hgvs": [ "XM_011541318.2:c.13423G>A" ], "proteinEffect": { "hgvs": "XP_011539620.1:p.Glu4475Lys", "hgvsWellDefined": "XP_011539620.1:p.Glu4475Lys" }, "referenceSequence": "http://reg.genome.network/refseq/RS554390" }, { "coordinates": [ { "allele": "A", "end": 13084, "referenceAllele": "G", "start": 13083 } ], "gene": "http://reg.genome.network/gene/GN005273", "geneNCBI_id": 3339, "geneSymbol": "HSPG2", "hgvs": [ "XM_017001120.1:c.13069G>A" ], "proteinEffect": { "hgvs": "XP_016856609.1:p.Glu4357Lys", "hgvsWellDefined": "XP_016856609.1:p.Glu4357Lys" }, "referenceSequence": "http://reg.genome.network/refseq/RS557347" }, { "coordinates": [ { "allele": "A", "end": 13033, "referenceAllele": "G", "start": 13032 } ], "gene": "http://reg.genome.network/gene/GN005273", "geneNCBI_id": 3339, "geneSymbol": "HSPG2", "hgvs": [ "XM_017001121.1:c.13018G>A" ], "proteinEffect": { "hgvs": "XP_016856610.1:p.Glu4340Lys", "hgvsWellDefined": "XP_016856610.1:p.Glu4340Lys" }, "referenceSequence": "http://reg.genome.network/refseq/RS557348" }, { "coordinates": [ { "allele": "A", "end": 13030, "referenceAllele": "G", "start": 13029 } ], "gene": "http://reg.genome.network/gene/GN005273", "geneNCBI_id": 3339, "geneSymbol": "HSPG2", "hgvs": [ "XM_017001122.1:c.13015G>A" ], "proteinEffect": { "hgvs": "XP_016856611.1:p.Glu4339Lys", "hgvsWellDefined": "XP_016856611.1:p.Glu4339Lys" }, "referenceSequence": "http://reg.genome.network/refseq/RS557349" }, { "@id": "http://reg.genome.network/allele/PA248340", "coordinates": [ { "allele": "A", "end": 12967, "referenceAllele": "G", "start": 12966 } ], "gene": "http://reg.genome.network/gene/GN005273", "geneNCBI_id": 3339, "geneSymbol": "HSPG2", "hgvs": [ "NM_005529.7:c.12874G>A" ], "proteinEffect": { "hgvs": "NP_005520.4:p.Glu4292Lys", "hgvsWellDefined": "NP_005520.4:p.Glu4292Lys" }, "referenceSequence": "http://reg.genome.network/refseq/RS667014", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Select", "nucleotide": { "Ensembl": { "hgvs": "ENST00000374695.8:c.12874G>A" }, "RefSeq": { "hgvs": "NM_005529.7:c.12874G>A" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000363827.3:p.Glu4292Lys" }, "RefSeq": { "hgvs": "NP_005520.4:p.Glu4292Lys" } } } }, { "coordinates": [ { "allele": "T", "end": 2937, "referenceAllele": "C", "start": 2936 } ], "gene": "http://reg.genome.network/gene/GN032071", "geneNCBI_id": 401944, "geneSymbol": "LDLRAD2", "hgvs": [ "NM_001013693.3:c.*1931C>T" ], "proteinEffect": { "hgvs": "NP_001013715.2:n.*1931C>T" }, "referenceSequence": "http://reg.genome.network/refseq/RS675482", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Select", "nucleotide": { "Ensembl": { "hgvs": "ENST00000344642.7:c.*1931C>T" }, "RefSeq": { "hgvs": "NM_001013693.3:c.*1931C>T" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000340988.2:n.*1931C>T" }, "RefSeq": { "hgvs": "NP_001013715.2:n.*1931C>T" } } } }, { "@id": "http://reg.genome.network/allele/PA916018162", "coordinates": [ { "allele": "A", "end": 12970, "referenceAllele": "G", "start": 12969 } ], "gene": "http://reg.genome.network/gene/GN005273", "geneNCBI_id": 3339, "geneSymbol": "HSPG2", "hgvs": [ "NM_001291860.2:c.12877G>A" ], "proteinEffect": { "hgvs": "NP_001278789.1:p.Glu4293Lys", "hgvsWellDefined": "NP_001278789.1:p.Glu4293Lys" }, "referenceSequence": "http://reg.genome.network/refseq/RS682883" } ], "type": "nucleotide" }