NM_000251.3(MSH2):c.115C>A (p.Arg39=) AND Hereditary nonpolyposis colorectal neoplasms

Clinical significance:Uncertain significance (Last evaluated: Oct 19, 2020)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV000233469.7

Allele description [Variation Report for NM_000251.3(MSH2):c.115C>A (p.Arg39=)]

NM_000251.3(MSH2):c.115C>A (p.Arg39=)

Gene:
MSH2:mutS homolog 2 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
2p21
Genomic location:
Preferred name:
NM_000251.3(MSH2):c.115C>A (p.Arg39=)
HGVS:
  • NC_000002.12:g.47403306C>A
  • NG_007110.2:g.5183C>A
  • NM_000251.2:c.115C>A
  • NM_000251.3:c.115C>AMANE SELECT
  • NM_001258281.1:c.-30-54C>A
  • NP_000242.1:p.Arg39=
  • NP_000242.1:p.Arg39=
  • LRG_218t1:c.115C>A
  • LRG_218:g.5183C>A
  • LRG_218p1:p.Arg39=
  • NC_000002.11:g.47630445C>A
  • NM_000251.1:c.115C>A
  • p.R39R
Links:
dbSNP: rs786202334
NCBI 1000 Genomes Browser:
rs786202334
Molecular consequence:
  • NM_001258281.1:c.-30-54C>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_000251.2:c.115C>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_000251.3:c.115C>A - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Name:
Hereditary nonpolyposis colorectal neoplasms
Identifiers:
MedGen: C0009405; Orphanet: 443090

Recent activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...

Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000284093Invitaecriteria provided, single submitter
Uncertain significance
(Oct 19, 2020)
germlineclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot 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):240-242.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Invitae, SCV000284093.7

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

Description

This sequence change affects codon 39 of the MSH2 mRNA. It is a 'silent' change, meaning that it does not change the encoded amino acid sequence of the MSH2 protein. This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals with MSH2-related disease. ClinVar contains an entry for this variant (Variation ID: 185640). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site, but this prediction has not been confirmed by published transcriptional studies. 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.

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

Last Updated: Oct 30, 2021

Support Center