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NM_024675.4(PALB2):c.2474G>C (p.Arg825Thr) AND Endometrial carcinoma

Germline classification:
Likely benign (1 submission)
Last evaluated:
Jul 20, 2020
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:
RCV001256975.3

Allele description [Variation Report for NM_024675.4(PALB2):c.2474G>C (p.Arg825Thr)]

NM_024675.4(PALB2):c.2474G>C (p.Arg825Thr)

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.2474G>C (p.Arg825Thr)
HGVS:
  • NC_000016.10:g.23629680C>G
  • NG_007406.1:g.16678G>C
  • NM_024675.4:c.2474G>CMANE SELECT
  • NP_078951.2:p.Arg825Thr
  • NP_078951.2:p.Arg825Thr
  • LRG_308t1:c.2474G>C
  • LRG_308:g.16678G>C
  • LRG_308p1:p.Arg825Thr
  • NC_000016.9:g.23641001C>G
  • NM_024675.3:c.2474G>C
  • p.R825T
Protein change:
R825T
Links:
dbSNP: rs146218439
NCBI 1000 Genomes Browser:
rs146218439
Molecular consequence:
  • NM_024675.4:c.2474G>C - missense variant - [Sequence Ontology: SO:0001583]
Observations:
1

Condition(s)

Name:
Endometrial carcinoma
Synonyms:
Endometrial carcinoma, somatic
Identifiers:
MONDO: MONDO:0002447; MedGen: C0476089; OMIM: 608089; Human Phenotype Ontology: HP:0012114

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001424575ACT Genomics,
criteria provided, single submitter

(ACMG Guidelines, 2015)		Likely benign
(Jul 20, 2020) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes1not 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 ACT Genomics,, SCV001424575.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
11not providednot providedclinical testing PubMed (1)

Description

The allele frequency of this variant c.2474G>C (p.Arg825Thr) is 0.0037 in East Asian of gnomAD and 0.004 in East Asian of 1000 Genomes, which is greater than expected for the disorder. There is a moderate physicochemical difference between arginine and threonine. The variant is predicted to be tolerated by both SIFT or PolyPhen2. For these reasons, this variant has been classified as Likely Benign.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided1not providednot providednot provided

Last Updated: Oct 20, 2024