ClinVar Miner

Submissions for variant NM_004656.4(BAP1):c.1358_1359del (p.Lys453fs)

dbSNP: rs1351986946
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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Genetic Services Laboratory, University of Chicago RCV000501537 SCV000593576 pathogenic BAP1-related tumor predisposition syndrome 2016-04-01 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV000501537 SCV000771606 pathogenic BAP1-related tumor predisposition syndrome 2023-12-26 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Lys453Argfs*15) in the BAP1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in BAP1 are known to be pathogenic (PMID: 21874000, 23684012). This variant is present in population databases (no rsID available, gnomAD 0.0009%). This variant has not been reported in the literature in individuals affected with BAP1-related conditions. ClinVar contains an entry for this variant (Variation ID: 434478). For these reasons, this variant has been classified as Pathogenic.
Ambry Genetics RCV002383963 SCV002689317 pathogenic Hereditary cancer-predisposing syndrome 2021-12-20 criteria provided, single submitter clinical testing The c.1358_1359delAA pathogenic mutation, located in coding exon 13 of the BAP1 gene, results from a deletion of two nucleotides at nucleotide positions 1358 to 1359, causing a translational frameshift with a predicted alternate stop codon (p.K453Rfs*15). This alteration was detected in an individual with uveal melanoma (Huang KL et al. Cell, 2018 04;173:355-370.e14) and has also been observed in an individual with breast cancer (Hong JH et al. NPJ Genom Med, 2020 Nov;5:50). In addition to the clinical data presented in the literature, this alteration is expected to result in loss of function by premature protein truncation or nonsense-mediated mRNA decay. As such, this alteration is interpreted as a disease-causing mutation.
Molecular Genetics and NGS Laboratory, Hospital Fundacion Valle Del Lili RCV003492083 SCV004242253 pathogenic Melanoma, uveal, susceptibility to, 2; BAP1-related tumor predisposition syndrome; Kury-Isidor syndrome 2024-01-31 criteria provided, single submitter clinical testing
Myriad Genetics, Inc. RCV000501537 SCV004930977 pathogenic BAP1-related tumor predisposition syndrome 2024-03-15 criteria provided, single submitter clinical testing This variant is considered pathogenic. This variant creates a frameshift predicted to result in premature protein truncation.
Baylor Genetics RCV000501537 SCV005053242 pathogenic BAP1-related tumor predisposition syndrome 2024-03-27 criteria provided, single submitter clinical testing
Clinical Genetics Laboratory, Skane University Hospital Lund RCV004696923 SCV005197019 pathogenic not provided 2024-02-29 criteria provided, single submitter clinical testing

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