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NM_004656.4(BAP1):c.1873G>A (p.Glu625Lys) AND BAP1-related tumor predisposition syndrome

Germline classification:
Uncertain significance (2 submissions)
Last evaluated:
Oct 9, 2023
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
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:
RCV000692761.6

Allele description [Variation Report for NM_004656.4(BAP1):c.1873G>A (p.Glu625Lys)]

NM_004656.4(BAP1):c.1873G>A (p.Glu625Lys)

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.1873G>A (p.Glu625Lys)
HGVS:
  • NC_000003.12:g.52403155C>T
  • NG_031859.1:g.11839G>A
  • NM_004656.4:c.1873G>AMANE SELECT
  • NP_004647.1:p.Glu625Lys
  • LRG_529t1:c.1873G>A
  • LRG_529:g.11839G>A
  • NC_000003.11:g.52437171C>T
  • NM_004656.2:c.1873G>A
  • NM_004656.3:c.1873G>A
Protein change:
E625K
Links:
dbSNP: rs1482404545
NCBI 1000 Genomes Browser:
rs1482404545
Molecular consequence:
  • NM_004656.4:c.1873G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
BAP1-related tumor predisposition syndrome (TPDS1)
Synonyms:
Tumor predisposition syndrome; Tumor susceptibility linked to germline BAP1 mutations; BAP1 tumor predisposition syndrome; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0013692; MedGen: C3280492; Orphanet: 289539; OMIM: 614327

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000820603Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Aug 25, 2023) 		germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV004213200Baylor Genetics
criteria provided, single submitter

(ACMG Guidelines, 2015)		Uncertain significance
(Oct 9, 2023) 		unknownclinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

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

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From Invitae, SCV000820603.5

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

Description

In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt BAP1 protein function. ClinVar contains an entry for this variant (Variation ID: 485294). This variant has not been reported in the literature in individuals affected with BAP1-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces glutamic acid, which is acidic and polar, with lysine, which is basic and polar, at codon 625 of the BAP1 protein (p.Glu625Lys).

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

From Baylor Genetics, SCV004213200.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Jul 15, 2024