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NM_000251.3(MSH2):c.198C>T (p.Tyr66=) AND Carcinoma of colon

Germline classification:
Likely benign (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:
RCV001354005.4

Allele description [Variation Report for NM_000251.3(MSH2):c.198C>T (p.Tyr66=)]

NM_000251.3(MSH2):c.198C>T (p.Tyr66=)

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.198C>T (p.Tyr66=)
Other names:
p.Y66Y:TAC>TAT
HGVS:
  • NC_000002.12:g.47403389C>T
  • NG_007110.2:g.5266C>T
  • NG_095167.1:g.593C>T
  • NM_000251.3:c.198C>TMANE SELECT
  • NM_001258281.1:c.-1C>T
  • NM_001406631.1:c.198C>T
  • NM_001406632.1:c.198C>T
  • NM_001406633.1:c.198C>T
  • NM_001406634.1:c.198C>T
  • NM_001406635.1:c.198C>T
  • NM_001406636.1:c.198C>T
  • NM_001406637.1:c.198C>T
  • NM_001406638.1:c.198C>T
  • NM_001406639.1:c.198C>T
  • NM_001406640.1:c.198C>T
  • NM_001406641.1:c.198C>T
  • NM_001406642.1:c.198C>T
  • NM_001406643.1:c.198C>T
  • NM_001406644.1:c.198C>T
  • NM_001406645.1:c.198C>T
  • NM_001406646.1:c.198C>T
  • NM_001406647.1:c.198C>T
  • NM_001406648.1:c.198C>T
  • NM_001406649.1:c.198C>T
  • NM_001406650.1:c.198C>T
  • NM_001406651.1:c.198C>T
  • NM_001406652.1:c.198C>T
  • NM_001406653.1:c.198C>T
  • NM_001406654.1:c.-143C>T
  • NM_001406655.1:c.198C>T
  • NM_001406656.1:c.-798C>T
  • NM_001406657.1:c.198C>T
  • NM_001406658.1:c.-1121C>T
  • NM_001406659.1:c.-1271C>T
  • NM_001406660.1:c.-1468C>T
  • NM_001406661.1:c.-1423C>T
  • NM_001406662.1:c.-1340C>T
  • NM_001406666.1:c.198C>T
  • NM_001406669.1:c.-1271C>T
  • NM_001406672.1:c.198C>T
  • NM_001406674.1:c.198C>T
  • NP_000242.1:p.Tyr66=
  • NP_000242.1:p.Tyr66=
  • NP_001393560.1:p.Tyr66=
  • NP_001393561.1:p.Tyr66=
  • NP_001393562.1:p.Tyr66=
  • NP_001393563.1:p.Tyr66=
  • NP_001393564.1:p.Tyr66=
  • NP_001393565.1:p.Tyr66=
  • NP_001393566.1:p.Tyr66=
  • NP_001393567.1:p.Tyr66=
  • NP_001393568.1:p.Tyr66=
  • NP_001393569.1:p.Tyr66=
  • NP_001393570.1:p.Tyr66=
  • NP_001393571.1:p.Tyr66=
  • NP_001393572.1:p.Tyr66=
  • NP_001393573.1:p.Tyr66=
  • NP_001393574.1:p.Tyr66=
  • NP_001393575.1:p.Tyr66=
  • NP_001393576.1:p.Tyr66=
  • NP_001393577.1:p.Tyr66=
  • NP_001393578.1:p.Tyr66=
  • NP_001393579.1:p.Tyr66=
  • NP_001393580.1:p.Tyr66=
  • NP_001393581.1:p.Tyr66=
  • NP_001393582.1:p.Tyr66=
  • NP_001393584.1:p.Tyr66=
  • NP_001393586.1:p.Tyr66=
  • NP_001393595.1:p.Tyr66=
  • NP_001393601.1:p.Tyr66=
  • NP_001393603.1:p.Tyr66=
  • LRG_218t1:c.198C>T
  • LRG_218:g.5266C>T
  • LRG_218p1:p.Tyr66=
  • NC_000002.11:g.47630528C>T
  • NM_000251.1:c.198C>T
  • NM_000251.2:c.198C>T
  • NM_001258281.1:c.-1C>T
  • NR_176230.1:n.234C>T
  • NR_176231.1:n.234C>T
  • NR_176232.1:n.234C>T
  • NR_176233.1:n.234C>T
  • NR_176234.1:n.234C>T
  • NR_176235.1:n.234C>T
  • NR_176236.1:n.234C>T
  • NR_176237.1:n.234C>T
  • NR_176238.1:n.234C>T
  • NR_176239.1:n.234C>T
  • NR_176240.1:n.234C>T
  • NR_176241.1:n.234C>T
  • NR_176242.1:n.234C>T
  • NR_176243.1:n.234C>T
  • NR_176244.1:n.234C>T
  • NR_176245.1:n.234C>T
  • NR_176246.1:n.234C>T
  • NR_176247.1:n.234C>T
  • NR_176248.1:n.234C>T
  • NR_176249.1:n.234C>T
  • NR_176250.1:n.234C>T
  • p.Y66Y
Links:
dbSNP: rs730881784
NCBI 1000 Genomes Browser:
rs730881784
Molecular consequence:
  • NM_001258281.1:c.-1C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001406654.1:c.-143C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001406656.1:c.-798C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001406658.1:c.-1121C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001406659.1:c.-1271C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001406660.1:c.-1468C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001406661.1:c.-1423C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001406662.1:c.-1340C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001406669.1:c.-1271C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NR_176230.1:n.234C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_176231.1:n.234C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_176232.1:n.234C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_176233.1:n.234C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_176234.1:n.234C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_176235.1:n.234C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_176236.1:n.234C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_176237.1:n.234C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_176238.1:n.234C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_176239.1:n.234C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_176240.1:n.234C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_176241.1:n.234C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_176242.1:n.234C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_176243.1:n.234C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_176244.1:n.234C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_176245.1:n.234C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_176246.1:n.234C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_176247.1:n.234C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_176248.1:n.234C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_176249.1:n.234C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_176250.1:n.234C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NM_000251.3:c.198C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406631.1:c.198C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406632.1:c.198C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406633.1:c.198C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406634.1:c.198C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406635.1:c.198C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406636.1:c.198C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406637.1:c.198C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406638.1:c.198C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406639.1:c.198C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406640.1:c.198C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406641.1:c.198C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406642.1:c.198C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406643.1:c.198C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406644.1:c.198C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406645.1:c.198C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406646.1:c.198C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406647.1:c.198C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406648.1:c.198C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406649.1:c.198C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406650.1:c.198C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406651.1:c.198C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406652.1:c.198C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406653.1:c.198C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406655.1:c.198C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406657.1:c.198C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406666.1:c.198C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406672.1:c.198C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406674.1:c.198C>T - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Name:
Carcinoma of colon (CRC)
Synonyms:
Colonic carcinoma; Colon carcinoma
Identifiers:
MONDO: MONDO:0002032; MedGen: C0699790

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000592454Department of Pathology and Laboratory Medicine, Sinai Health System - The Canadian Open Genetics Repository (COGR)

See additional submitters

no assertion criteria provided
Likely benignunknownclinical 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), SCV000592454.2

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

Description

MSH2, EXON01, c.198C>T, p.= (p.Tyr66Tyr), Heterozygous, Likely benign rnrnThe MSH2 c.198C>T variant was not identified in the literature nor was it identified in the COSMIC, “Mismatch Repair Genes Variant Database”, “MMR Gene Unclassified Variants Database”, InSiGHT Colon Cancer Gene Variant Database (LOVD), Zhejiang Colon Cancer Database (LOVD) and GeneInsight - COGR database. The variant was identified in dbSNP (ID: rs730881784) as “With Likely benign allele”, ClinVar database (classified as benign by GeneDx and likely benign by Ambry Genetics and Invitae) and UMD (1x with an “unclassified variant” classification). This variant was identified in the Exome Aggregation Consortium database (August 8, 2016) in 11 of 83058 chromosomes (freq. 0.0001) in the following populations: European in 11 of 47956 chromosomes (freq. 0.0002), increasing the likelihood that this may be a low frequency benign variant in certain populations of origin. The p.Tyr66Tyr variant is not expected to have clinical significance because it does not result in a change of amino acid and is not located in a known consensus splice site. The variant occurs outside of the splicing consensus sequence and 2 of 5 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) predict a greater than 10% difference in splicing; this is not very predictive of pathogenicity. In summary, based on the above information, the clinical significance of this variant cannot be determined with certainty at this time although we would lean towards a more benign role for this variant. This variant is classified as likely benign.

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

Last Updated: Jul 29, 2024