{ "@context": "http://reg.genome.network/schema/allele.jsonld", "@id": "http://reg.genome.network/allele/CA3271846009", "communityStandardTitle": [ "NM_024675.4(PALB2):c.3547_3549del (p.Tyr1183del)" ], "genomicAlleles": [ { "chromosome": "16", "coordinates": [ { "allele": "", "end": 23603473, "referenceAllele": "GTA", "start": 23603470 } ], "hgvs": [ "NC_000016.10:g.23603471_23603473del", "CM000678.2:g.23603471_23603473del" ], "referenceGenome": "GRCh38", "referenceSequence": "http://reg.genome.network/refseq/RS000064" }, { "chromosome": "16", "coordinates": [ { "allele": "", "end": 23614794, "referenceAllele": "GTA", "start": 23614791 } ], "hgvs": [ "NC_000016.9:g.23614792_23614794del", "CM000678.1:g.23614792_23614794del" ], "referenceGenome": "GRCh37", "referenceSequence": "http://reg.genome.network/refseq/RS000040" }, { "chromosome": "16", "coordinates": [ { "allele": "", "end": 23522295, "referenceAllele": "GTA", "start": 23522292 } ], "hgvs": [ "NC_000016.8:g.23522293_23522295del" ], "referenceGenome": "NCBI36", "referenceSequence": "http://reg.genome.network/refseq/RS000016" }, { "coordinates": [ { "allele": "", "end": 42887, "referenceAllele": "TAC", "start": 42884 } ], "hgvs": [ "NG_007406.1:g.42885_42887del", "LRG_308:g.42885_42887del" ], "referenceSequence": "http://reg.genome.network/refseq/RS000571" } ], "transcriptAlleles": [ { "coordinates": [ { "allele": "", "end": 4554, "referenceAllele": "TAC", "start": 4551 } ], "gene": "http://reg.genome.network/gene/GN026144", "geneNCBI_id": 79728, "geneSymbol": "PALB2", "hgvs": [ "ENST00000561514.3:c.3553_3555del" ], "proteinEffect": { "hgvs": "ENSP00000460666.3:p.Tyr1185del", "hgvsWellDefined": "ENSP00000460666.3:p.Tyr1185del" }, "referenceSequence": "http://reg.genome.network/refseq/RS914287" }, { "coordinates": [ { "allele": "", "end": 1324, "referenceAllele": "TAC", "start": 1321 } ], "gene": "http://reg.genome.network/gene/GN026144", "geneNCBI_id": 79728, "geneSymbol": "PALB2", "hgvs": [ "ENST00000565038.2:c.*1032_*1034del" ], "proteinEffect": { "hgvs": "ENSP00000459882.2:n.*1032_*1034del" }, "referenceSequence": "http://reg.genome.network/refseq/RS914301" }, { "coordinates": [ { "allele": "", "end": 3539, "referenceAllele": "TAC", "start": 3536 } ], "gene": "http://reg.genome.network/gene/GN026144", "geneNCBI_id": 79728, "geneSymbol": "PALB2", "hgvs": [ "ENST00000566069.6:c.*182_*184del" ], "proteinEffect": { "hgvs": "ENSP00000459237.2:n.*182_*184del" }, "referenceSequence": "http://reg.genome.network/refseq/RS914305" }, { "coordinates": [ { "allele": "", "end": 3786, "referenceAllele": "TAC", "start": 3783 } ], "gene": "http://reg.genome.network/gene/GN026144", "geneNCBI_id": 79728, "geneSymbol": "PALB2", "hgvs": [ "ENST00000697377.2:c.3391_3393del" ], "proteinEffect": { "hgvs": "ENSP00000513286.2:p.Tyr1131del", "hgvsWellDefined": "ENSP00000513286.2:p.Tyr1131del" }, "referenceSequence": "http://reg.genome.network/refseq/RS914472" }, { "coordinates": [ { "allele": "", "end": 3854, "referenceAllele": "TAC", "start": 3851 } ], "gene": "http://reg.genome.network/gene/GN026144", "geneNCBI_id": 79728, "geneSymbol": "PALB2", "hgvs": [ "ENST00000697379.2:c.3553_3555del" ], "proteinEffect": { "hgvs": "ENSP00000513287.2:p.Tyr1185del", "hgvsWellDefined": "ENSP00000513287.2:p.Tyr1185del" }, "referenceSequence": "http://reg.genome.network/refseq/RS914473" }, { "coordinates": [ { "allele": "", "end": 4554, "referenceAllele": "TAC", "start": 4551 } ], "gene": "http://reg.genome.network/gene/GN026144", "geneNCBI_id": 79728, "geneSymbol": "PALB2", "hgvs": [ "ENST00000561514.2:c.2662_2664del" ], "proteinEffect": { "hgvs": "ENSP00000460666.2:p.Tyr888del", "hgvsWellDefined": "ENSP00000460666.2:p.Tyr888del" }, "referenceSequence": "http://reg.genome.network/refseq/RS905930" }, { "coordinates": [ { "allele": "", "end": 4072, "referenceAllele": "TAC", "start": 4069 } ], "gene": "http://reg.genome.network/gene/GN026144", "geneNCBI_id": 79728, "geneSymbol": "PALB2", "hgvs": [ "ENST00000697374.1:c.2662_2664del" ], "proteinEffect": { "hgvs": "ENSP00000513284.1:p.Tyr888del", "hgvsWellDefined": "ENSP00000513284.1:p.Tyr888del" }, "referenceSequence": "http://reg.genome.network/refseq/RS908744" }, { "coordinates": [ { "allele": "", "end": 4896, "referenceAllele": "TAC", "start": 4893 } ], "gene": "http://reg.genome.network/gene/GN026144", "geneNCBI_id": 79728, "geneSymbol": "PALB2", "hgvs": [ "ENST00000697375.1:n.4894_4896del" ], "referenceSequence": "http://reg.genome.network/refseq/RS908745" }, { "coordinates": [ { "allele": "", "end": 3702, "referenceAllele": "TAC", "start": 3699 } ], "gene": "http://reg.genome.network/gene/GN026144", "geneNCBI_id": 79728, "geneSymbol": "PALB2", "hgvs": [ "ENST00000697376.1:c.*182_*184del" ], "proteinEffect": { "hgvs": "ENSP00000513285.1:n.*182_*184del" }, "referenceSequence": "http://reg.genome.network/refseq/RS908746" }, { "coordinates": [ { "allele": "", "end": 3786, "referenceAllele": "TAC", "start": 3783 } ], "gene": "http://reg.genome.network/gene/GN026144", "geneNCBI_id": 79728, "geneSymbol": "PALB2", "hgvs": [ "ENST00000697377.1:c.2500_2502del" ], "proteinEffect": { "hgvs": "ENSP00000513286.1:p.Tyr834del", "hgvsWellDefined": "ENSP00000513286.1:p.Tyr834del" }, "referenceSequence": "http://reg.genome.network/refseq/RS908747" }, { "coordinates": [ { "allele": "", "end": 4069, "referenceAllele": "TAC", "start": 4066 } ], "gene": "http://reg.genome.network/gene/GN026144", "geneNCBI_id": 79728, "geneSymbol": "PALB2", "hgvs": [ "ENST00000697378.1:n.4067_4069del" ], "referenceSequence": "http://reg.genome.network/refseq/RS908748" }, { "coordinates": [ { "allele": "", "end": 3854, "referenceAllele": "TAC", "start": 3851 } ], "gene": "http://reg.genome.network/gene/GN026144", "geneNCBI_id": 79728, "geneSymbol": "PALB2", "hgvs": [ "ENST00000697379.1:c.2662_2664del" ], "proteinEffect": { "hgvs": "ENSP00000513287.1:p.Tyr888del", "hgvsWellDefined": "ENSP00000513287.1:p.Tyr888del" }, "referenceSequence": "http://reg.genome.network/refseq/RS908749" }, { "coordinates": [ { "allele": "", "end": 2753, "referenceAllele": "TAC", "start": 2750 } ], "gene": "http://reg.genome.network/gene/GN026144", "geneNCBI_id": 79728, "geneSymbol": "PALB2", "hgvs": [ "ENST00000697380.1:n.2751_2753del" ], "referenceSequence": "http://reg.genome.network/refseq/RS908750" }, { "coordinates": [ { "allele": "", "end": 2244, "referenceAllele": "TAC", "start": 2241 } ], "gene": "http://reg.genome.network/gene/GN026144", "geneNCBI_id": 79728, "geneSymbol": "PALB2", "hgvs": [ "ENST00000697381.1:n.2242_2244del" ], "referenceSequence": "http://reg.genome.network/refseq/RS908751" }, { "coordinates": [ { "allele": "", "end": 4489, "referenceAllele": "TAC", "start": 4486 } ], "gene": "http://reg.genome.network/gene/GN026144", "geneNCBI_id": 79728, "geneSymbol": "PALB2", "hgvs": [ "ENST00000697382.1:c.*324_*326del" ], "proteinEffect": { "hgvs": "ENSP00000513288.1:n.*324_*326del" }, "referenceSequence": "http://reg.genome.network/refseq/RS908752" }, { "coordinates": [ { "allele": "", "end": 1247, "referenceAllele": "TAC", "start": 1244 } ], "gene": "http://reg.genome.network/gene/GN026144", "geneNCBI_id": 79728, "geneSymbol": "PALB2", "hgvs": [ "ENST00000697383.1:c.1081_1083del" ], "proteinEffect": { "hgvs": "ENSP00000513289.1:p.Tyr361del", "hgvsWellDefined": "ENSP00000513289.1:p.Tyr361del" }, "referenceSequence": "http://reg.genome.network/refseq/RS908753" }, { "coordinates": [ { "allele": "", "end": 3702, "referenceAllele": "TAC", "start": 3699 } ], "gene": "http://reg.genome.network/gene/GN026144", "geneNCBI_id": 79728, "geneSymbol": "PALB2", "hgvs": [ "ENST00000261584.9:c.3547_3549del" ], "proteinEffect": { "hgvs": "ENSP00000261584.4:p.Tyr1183del", "hgvsWellDefined": "ENSP00000261584.4:p.Tyr1183del" }, "referenceSequence": "http://reg.genome.network/refseq/RS742164", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Select", "nucleotide": { "Ensembl": { "hgvs": "ENST00000261584.9:c.3547_3549del" }, "RefSeq": { "hgvs": "NM_024675.4:c.3547_3549del" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000261584.4:p.Tyr1183del" }, "RefSeq": { "hgvs": "NP_078951.2:p.Tyr1183del" } } } }, { "coordinates": [ { "allele": "", "end": 3702, "referenceAllele": "TAC", "start": 3699 } ], "gene": "http://reg.genome.network/gene/GN026144", "geneNCBI_id": 79728, "geneSymbol": "PALB2", "hgvs": [ "ENST00000261584.8:c.3547_3549del" ], "proteinEffect": { "hgvs": "ENSP00000261584.4:p.Tyr1183del", "hgvsWellDefined": "ENSP00000261584.4:p.Tyr1183del" }, "referenceSequence": "http://reg.genome.network/refseq/RS250784" }, { "coordinates": [ { "allele": "", "end": 315, "referenceAllele": "TAC", "start": 312 } ], "gene": "http://reg.genome.network/gene/GN026144", "geneNCBI_id": 79728, "geneSymbol": "PALB2", "hgvs": [ "ENST00000566069.5:c.313_315del" ], "referenceSequence": "http://reg.genome.network/refseq/RS379166" }, { "coordinates": [ { "allele": "", "end": 3660, "referenceAllele": "TAC", "start": 3657 } ], "gene": "http://reg.genome.network/gene/GN026144", "geneNCBI_id": 79728, "geneSymbol": "PALB2", "hgvs": [ "ENST00000568219.5:c.2662_2664del" ], "proteinEffect": { "hgvs": "ENSP00000454703.2:p.Tyr888del", "hgvsWellDefined": "ENSP00000454703.2:p.Tyr888del" }, "referenceSequence": "http://reg.genome.network/refseq/RS380628" }, { "coordinates": [ { "allele": "", "end": 3749, "referenceAllele": "TAC", "start": 3746 } ], "gene": "http://reg.genome.network/gene/GN026144", "geneNCBI_id": 79728, "geneSymbol": "PALB2", "hgvs": [ "NM_024675.3:c.3547_3549del", "LRG_308t1:c.3547_3549del" ], "proteinEffect": { "hgvs": "NP_078951.2:p.Tyr1183del", "hgvsWellDefined": "NP_078951.2:p.Tyr1183del" }, "referenceSequence": "http://reg.genome.network/refseq/RS037924" }, { "coordinates": [ { "allele": "", "end": 4344, "referenceAllele": "TAC", "start": 4341 } ], "gene": "http://reg.genome.network/gene/GN026144", "geneNCBI_id": 79728, "geneSymbol": "PALB2", "hgvs": [ "XM_011545946.1:c.3553_3555del" ], "proteinEffect": { "hgvs": "XP_011544248.1:p.Tyr1185del", "hgvsWellDefined": "XP_011544248.1:p.Tyr1185del" }, "referenceSequence": "http://reg.genome.network/refseq/RS112826" }, { "coordinates": [ { "allele": "", "end": 4196, "referenceAllele": "TAC", "start": 4193 } ], "gene": "http://reg.genome.network/gene/GN026144", "geneNCBI_id": 79728, "geneSymbol": "PALB2", "hgvs": [ "XM_011545947.1:c.*182_*184del" ], "proteinEffect": { "hgvs": "XP_011544249.1:n.*182_*184del" }, "referenceSequence": "http://reg.genome.network/refseq/RS112827" }, { "coordinates": [ { "allele": "", "end": 3805, "referenceAllele": "TAC", "start": 3802 } ], "gene": "http://reg.genome.network/gene/GN026144", "geneNCBI_id": 79728, "geneSymbol": "PALB2", "hgvs": [ "XM_011545948.1:c.2662_2664del" ], "proteinEffect": { "hgvs": "XP_011544250.1:p.Tyr888del", "hgvsWellDefined": "XP_011544250.1:p.Tyr888del" }, "referenceSequence": "http://reg.genome.network/refseq/RS112828" }, { "coordinates": [ { "allele": "", "end": 4257, "referenceAllele": "TAC", "start": 4254 } ], "gene": "http://reg.genome.network/gene/GN026144", "geneNCBI_id": 79728, "geneSymbol": "PALB2", "hgvs": [ "XR_950851.1:n.4255_4257del" ], "referenceSequence": "http://reg.genome.network/refseq/RS143781" }, { "coordinates": [ { "allele": "", "end": 4554, "referenceAllele": "TAC", "start": 4551 } ], "gene": "http://reg.genome.network/gene/GN026144", "geneNCBI_id": 79728, "geneSymbol": "PALB2", "hgvs": [ "XM_011545946.2:c.3553_3555del" ], "proteinEffect": { "hgvs": "XP_011544248.1:p.Tyr1185del", "hgvsWellDefined": "XP_011544248.1:p.Tyr1185del" }, "referenceSequence": "http://reg.genome.network/refseq/RS556315" }, { "coordinates": [ { "allele": "", "end": 4370, "referenceAllele": "TAC", "start": 4367 } ], "gene": "http://reg.genome.network/gene/GN026144", "geneNCBI_id": 79728, "geneSymbol": "PALB2", "hgvs": [ "XM_011545947.2:c.*182_*184del" ], "proteinEffect": { "hgvs": "XP_011544249.1:n.*182_*184del" }, "referenceSequence": "http://reg.genome.network/refseq/RS556316" }, { "coordinates": [ { "allele": "", "end": 3841, "referenceAllele": "TAC", "start": 3838 } ], "gene": "http://reg.genome.network/gene/GN026144", "geneNCBI_id": 79728, "geneSymbol": "PALB2", "hgvs": [ "XM_011545948.2:c.2662_2664del" ], "proteinEffect": { "hgvs": "XP_011544250.1:p.Tyr888del", "hgvsWellDefined": "XP_011544250.1:p.Tyr888del" }, "referenceSequence": "http://reg.genome.network/refseq/RS556317" }, { "coordinates": [ { "allele": "", "end": 4282, "referenceAllele": "TAC", "start": 4279 } ], "gene": "http://reg.genome.network/gene/GN026144", "geneNCBI_id": 79728, "geneSymbol": "PALB2", "hgvs": [ "XM_017023671.1:c.3316_3318del" ], "proteinEffect": { "hgvs": "XP_016879160.1:p.Tyr1106del", "hgvsWellDefined": "XP_016879160.1:p.Tyr1106del" }, "referenceSequence": "http://reg.genome.network/refseq/RS574393" }, { "coordinates": [ { "allele": "", "end": 3492, "referenceAllele": "TAC", "start": 3489 } ], "gene": "http://reg.genome.network/gene/GN026144", "geneNCBI_id": 79728, "geneSymbol": "PALB2", "hgvs": [ "XM_017023672.2:c.3310_3312del" ], "proteinEffect": { "hgvs": "XP_016879161.1:p.Tyr1104del", "hgvsWellDefined": "XP_016879161.1:p.Tyr1104del" }, "referenceSequence": "http://reg.genome.network/refseq/RS574394" }, { "coordinates": [ { "allele": "", "end": 3580, "referenceAllele": "TAC", "start": 3577 } ], "gene": "http://reg.genome.network/gene/GN026144", "geneNCBI_id": 79728, "geneSymbol": "PALB2", "hgvs": [ "XM_017023673.2:c.*182_*184del" ], "proteinEffect": { "hgvs": "XP_016879162.1:n.*182_*184del" }, "referenceSequence": "http://reg.genome.network/refseq/RS574395" }, { "coordinates": [ { "allele": "", "end": 3702, "referenceAllele": "TAC", "start": 3699 } ], "gene": "http://reg.genome.network/gene/GN026144", "geneNCBI_id": 79728, "geneSymbol": "PALB2", "hgvs": [ "NM_024675.4:c.3547_3549del" ], "proteinEffect": { "hgvs": "NP_078951.2:p.Tyr1183del", "hgvsWellDefined": "NP_078951.2:p.Tyr1183del" }, "referenceSequence": "http://reg.genome.network/refseq/RS698739", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Select", "nucleotide": { "Ensembl": { "hgvs": "ENST00000261584.9:c.3547_3549del" }, "RefSeq": { "hgvs": "NM_024675.4:c.3547_3549del" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000261584.4:p.Tyr1183del" }, "RefSeq": { "hgvs": "NP_078951.2:p.Tyr1183del" } } } } ], "type": "nucleotide" }