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NM_024675.4(PALB2):c.119G>A (p.Arg40Lys) AND Breast-ovarian cancer, familial, susceptibility to, 5

Germline classification:
Uncertain significance (1 submission)
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:
RCV003446134.2

Allele description [Variation Report for NM_024675.4(PALB2):c.119G>A (p.Arg40Lys)]

NM_024675.4(PALB2):c.119G>A (p.Arg40Lys)

Gene:
PALB2:partner and localizer of BRCA2 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
16p12.2
Genomic location:
Preferred name:
NM_024675.4(PALB2):c.119G>A (p.Arg40Lys)
HGVS:
  • NC_000016.10:g.23637942C>T
  • NG_007406.1:g.8416G>A
  • NM_024675.4:c.119G>AMANE SELECT
  • NP_078951.2:p.Arg40Lys
  • NP_078951.2:p.Arg40Lys
  • LRG_308t1:c.119G>A
  • LRG_308:g.8416G>A
  • LRG_308p1:p.Arg40Lys
  • NC_000016.9:g.23649263C>T
  • NM_024675.3:c.119G>A
Protein change:
R40K
Links:
dbSNP: rs573118236
NCBI 1000 Genomes Browser:
rs573118236
Molecular consequence:
  • NM_024675.4:c.119G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Breast-ovarian cancer, familial, susceptibility to, 5 (BROVCA5)
Identifiers:
MONDO: MONDO:0957530; MedGen: C5830615; OMIM: 620442

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004171863Neuberg Centre For Genomic Medicine, NCGM
criteria provided, single submitter

(ACMG Guidelines, 2015)		Uncertain significancegermlineclinical testing

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

Help

Summary from all submissions

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

Citations

PubMed

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 Neuberg Centre For Genomic Medicine, NCGM, SCV004171863.1

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

Description

The missense c.119G>A(p.Arg40Lys) variant in PALB2 gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. The variant is reported with an allele frequency of 0.0008% in the gnomAD exomes database and is novel (not in any individuals) in 1000 Genomes database. This variant has been reported to the ClinVar database as Uncertain Significance (multiple submission). The amino acid change p.Arg40Lys in PALB2 is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. The amino acid Arg at position 40 is changed to a Lys changing protein sequence and it might alter its composition and physico-chemical properties. For these reasons, this variant has been classified as Variant of Uncertain Significance (VUS).

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

Last Updated: Sep 29, 2024