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NM_000251.3(MSH2):c.2801C>A (p.Thr934Lys) AND Lynch syndrome

Germline classification:
Uncertain significance (1 submission)
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
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:
RCV001353614.1

Allele description [Variation Report for NM_000251.3(MSH2):c.2801C>A (p.Thr934Lys)]

NM_000251.3(MSH2):c.2801C>A (p.Thr934Lys)

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.2801C>A (p.Thr934Lys)
HGVS:
  • NC_000002.12:g.47482945C>A
  • NG_007110.2:g.84822C>A
  • NM_000251.3:c.2801C>AMANE SELECT
  • NM_001258281.1:c.2603C>A
  • NP_000242.1:p.Thr934Lys
  • NP_000242.1:p.Thr934Lys
  • NP_001245210.1:p.Thr868Lys
  • LRG_218t1:c.2801C>A
  • LRG_218:g.84822C>A
  • LRG_218p1:p.Thr934Lys
  • NC_000002.11:g.47710084C>A
  • NM_000251.1:c.2801C>A
  • NM_000251.2:c.2801C>A
Protein change:
T868K
Links:
dbSNP: rs587779969
NCBI 1000 Genomes Browser:
rs587779969
Molecular consequence:
  • NM_000251.3:c.2801C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001258281.1:c.2603C>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Lynch syndrome
Identifiers:
MONDO: MONDO:0005835; MedGen: C4552100

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000592557Department of Pathology and Laboratory Medicine, Sinai Health System - The Canadian Open Genetics Repository (COGR)

See additional submitters

no assertion criteria provided
Uncertain significanceunknownclinical testing

Help

Summary from all submissions

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

Details of each submission

From Department of Pathology and Laboratory Medicine, Sinai Health System - The Canadian Open Genetics Repository (COGR), SCV000592557.2

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

Description

The MSH2 p.Thr934Lys variant was not identified in the literature, nor has it been previous identified by our laboratory. The variant was identified in UMD (1X as an unclassified variant). The p.Thr934 residue is not conserved in mammals and four out of five computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) do not suggest a high likelihood of impact to the protein; in addition, in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) do not predict a difference in splicing. However, this information is not predictive enough to rule out pathogenicity. This substitution occurs in the last codon before the translational stop codon. In summary, based on the above information, the clinical significance of this variant cannot be determined with certainty at this time. This variant is classified as a variant of unknown significance.

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

Last Updated: Feb 20, 2024