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NM_002439.5(MSH3):c.2396T>G (p.Leu799Arg) AND Familial adenomatous polyposis 4

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:
RCV003338797.2

Allele description [Variation Report for NM_002439.5(MSH3):c.2396T>G (p.Leu799Arg)]

NM_002439.5(MSH3):c.2396T>G (p.Leu799Arg)

Gene:
MSH3:mutS homolog 3 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
5q14.1
Genomic location:
Preferred name:
NM_002439.5(MSH3):c.2396T>G (p.Leu799Arg)
HGVS:
  • NC_000005.10:g.80778797T>G
  • NG_016607.2:g.129323T>G
  • NM_002439.5:c.2396T>GMANE SELECT
  • NP_002430.3:p.Leu799Arg
  • NC_000005.9:g.80074616T>G
  • NG_016607.1:g.129323T>G
  • NM_002439.3:c.2396T>G
  • NM_002439.4:c.2396T>G
Protein change:
L799R
Links:
dbSNP: rs555670202
NCBI 1000 Genomes Browser:
rs555670202
Molecular consequence:
  • NM_002439.5:c.2396T>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Familial adenomatous polyposis 4 (FAP4)
Identifiers:
MONDO: MONDO:0044300; MedGen: C4310719; OMIM: 617100

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004048026Neuberg 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, SCV004048026.1

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

Description

The missense variant c.2396T>G (p.Leu799Arg) in MSH3 has been submitted to ClinVar as a Variant of Uncertain Significance. This p.Leu799Arg variant has allele frequency of 0.002787% in the gnomAD and novel (not in any individuals) in 1000 genome database. The amino acid Leu at position 799 is changed to a Arg changing protein sequence and it might alter its composition and physico-chemical properties. The amino acid change p.Leu799Arg in MSH3 is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. For these reasons, this variant has been classified as Uncertain Significance (VUS).

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

Last Updated: May 7, 2024