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NM_024675.4(PALB2):c.119G>A (p.Arg40Lys) AND not provided

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Mar 23, 2017
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:
RCV000523351.2

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)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000618348GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))		Uncertain significance
(Mar 23, 2017) 		germlineclinical testing

Citation Link

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Summary from all submissions

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

Details of each submission

From GeneDx, SCV000618348.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

This variant is denoted PALB2 c.119G>A at the cDNA level, p.Arg40Lys (R40K) at the protein level, and results in the change of an Arginine to a Lysine (AGA>AAA). This variant has not, to our knowledge, been published in the literature as pathogenic or benign. PALB2 Arg40Lys was not observed at a significant frequency in large population cohorts (NHLBI Exome Sequencing Project, The 1000 Genomes Consortium 2015, Lek 2016). Since Arginine and Lysine share similar properties, this is considered a conservative amino acid substitution. PALB2 Arg40Lys occurs at a position that is not conserved and is located in DNA binding domain as well as the region of interaction with RAD51 and BRCA1, which is required for its oligomerization and focal concentration at DNA damage sites (UniProt). In silico analyses are inconsistent regarding the effect this variant may have on protein structure and function. Based on currently available evidence, it is unclear whether PALB2 Arg40Lys is a pathogenic or benign variant. We consider it to be a variant of uncertain significance.

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

Last Updated: Sep 29, 2024