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NM_004656.4(BAP1):c.1777C>T (p.Gln593Ter) AND Hereditary cancer-predisposing syndrome

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Mar 11, 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:
RCV001013141.3

Allele description [Variation Report for NM_004656.4(BAP1):c.1777C>T (p.Gln593Ter)]

NM_004656.4(BAP1):c.1777C>T (p.Gln593Ter)

Gene:
BAP1:BRCA1 associated deubiquitinase 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
3p21.1
Genomic location:
Preferred name:
NM_004656.4(BAP1):c.1777C>T (p.Gln593Ter)
HGVS:
  • NC_000003.12:g.52403251G>A
  • NG_031859.1:g.11743C>T
  • NM_004656.4:c.1777C>TMANE SELECT
  • NP_004647.1:p.Gln593Ter
  • LRG_529t1:c.1777C>T
  • LRG_529:g.11743C>T
  • NC_000003.11:g.52437267G>A
  • NM_004656.2:c.1777C>T
  • NM_004656.3:c.1777C>T
Protein change:
Q593*
Links:
dbSNP: rs1064795638
NCBI 1000 Genomes Browser:
rs1064795638
Molecular consequence:
  • NM_004656.4:c.1777C>T - nonsense - [Sequence Ontology: SO:0001587]

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
SCV001173685Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)		Pathogenic
(Mar 11, 2021) 		germlineclinical testing

PubMed (3)
[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

A novel BAP1 mutation is associated with melanocytic neoplasms and thyroid cancer.

McDonnell KJ, Gallanis GT, Heller KA, Melas M, Idos GE, Culver JO, Martin SE, Peng DH, Gruber SB.

Cancer Genet. 2016 Mar;209(3):75-81. doi: 10.1016/j.cancergen.2015.12.007. Epub 2015 Dec 22.

PubMed [citation]
PMID:
26774355
PMCID:
PMC6447287

Histomorphologic spectrum of germline-related and sporadic BAP1-inactivated melanocytic tumors.

Garfield EM, Walton KE, Quan VL, VandenBoom T, Zhang B, Kong BY, Isales MC, Panah E, Kim G, Gerami P.

J Am Acad Dermatol. 2018 Sep;79(3):525-534. doi: 10.1016/j.jaad.2018.05.005. Epub 2018 May 10.

PubMed [citation]
PMID:
29753057
See all PubMed Citations (3)

Details of each submission

From Ambry Genetics, SCV001173685.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)

Description

The p.Q593* pathogenic mutation (also known as c.1777C>T), located in coding exon 14 of the BAP1 gene, results from a C to T substitution at nucleotide position 1777. This changes the amino acid from a glutamine to a stop codon within coding exon 14. This mutation has been described multiple individuals with BAP1-related cancers (McDonnell KJ et al. Cancer Genet, 2016 Mar;209:75-81; Garfield EM et al. J Am Acad Dermatol, 2018 Sep;79:525-534; Guo R et al. J Thorac Oncol, 2020 04;15:655-660). 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: Jul 15, 2024