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NM_004656.4(BAP1):c.1358_1359del (p.Lys453fs) AND Hereditary cancer-predisposing syndrome

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Dec 20, 2021
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV002383963.2

Allele description [Variation Report for NM_004656.4(BAP1):c.1358_1359del (p.Lys453fs)]

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

Gene:
BAP1:BRCA1 associated protein 1 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
3p21.1
Genomic location:
Preferred name:
NM_004656.4(BAP1):c.1358_1359del (p.Lys453fs)
Other names:
p.Lys453fs
HGVS:
  • NC_000003.12:g.52403787_52403788del
  • NG_031859.1:g.11207_11208del
  • NM_004656.4:c.1358_1359delMANE SELECT
  • NP_004647.1:p.Lys453fs
  • LRG_529t1:c.1358_1359del
  • LRG_529:g.11207_11208del
  • NC_000003.11:g.52437802_52437803del
  • NC_000003.11:g.52437803_52437804del
  • NM_004656.2:c.1358_1359delAA
  • NM_004656.3:c.1358_1359delAA
Protein change:
K453fs
Links:
dbSNP: rs1351986946
NCBI 1000 Genomes Browser:
rs1351986946
Molecular consequence:
  • NM_004656.4:c.1358_1359del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:
Hereditary cancer-predisposing syndrome
Synonyms:
Neoplastic Syndromes, Hereditary; Tumor predisposition; Cancer predisposition; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0015356; MeSH: D009386; MedGen: C0027672

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002689317Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)		Pathogenic
(Dec 20, 2021) 		germlineclinical testing

PubMed (2)
[See all records that cite these PMIDs]

Citation Link

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Pathogenic Germline Variants in 10,389 Adult Cancers.

Huang KL, Mashl RJ, Wu Y, Ritter DI, Wang J, Oh C, Paczkowska M, Reynolds S, Wyczalkowski MA, Oak N, Scott AD, Krassowski M, Cherniack AD, Houlahan KE, Jayasinghe R, Wang LB, Zhou DC, Liu D, Cao S, Kim YW, Koire A, McMichael JF, et al.

Cell. 2018 Apr 5;173(2):355-370.e14. doi: 10.1016/j.cell.2018.03.039.

PubMed [citation]
PMID:
29625052
PMCID:
PMC5949147

Functional characterisation guides classification of novel BAP1 germline variants.

Hong JH, Chong ST, Lee PH, Tan J, Heng HL, Ishak NDB, Chan SH, Teh BT, Ngeow J.

NPJ Genom Med. 2020;5:50. doi: 10.1038/s41525-020-00157-6.

PubMed [citation]
PMID:
33240524
PMCID:
PMC7678838

Details of each submission

From Ambry Genetics, SCV002689317.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)

Description

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.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: May 7, 2024