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NM_000251.3(MSH2):c.198del (p.Lys65_Tyr66insTer) AND Lynch syndrome 1

Germline classification:
Likely pathogenic (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:
RCV003337717.2

Allele description [Variation Report for NM_000251.3(MSH2):c.198del (p.Lys65_Tyr66insTer)]

NM_000251.3(MSH2):c.198del (p.Lys65_Tyr66insTer)

Gene:
MSH2:mutS homolog 2 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
2p21
Genomic location:
Preferred name:
NM_000251.3(MSH2):c.198del (p.Lys65_Tyr66insTer)
HGVS:
  • NC_000002.12:g.47403389del
  • NG_007110.2:g.5266del
  • NG_095167.1:g.593del
  • NM_000251.3:c.198delMANE SELECT
  • NM_001258281.1:c.-1del
  • NM_001406631.1:c.198del
  • NM_001406632.1:c.198del
  • NM_001406633.1:c.198del
  • NM_001406634.1:c.198del
  • NM_001406635.1:c.198del
  • NM_001406636.1:c.198del
  • NM_001406637.1:c.198del
  • NM_001406638.1:c.198del
  • NM_001406639.1:c.198del
  • NM_001406640.1:c.198del
  • NM_001406641.1:c.198del
  • NM_001406642.1:c.198del
  • NM_001406643.1:c.198del
  • NM_001406644.1:c.198del
  • NM_001406645.1:c.198del
  • NM_001406646.1:c.198del
  • NM_001406647.1:c.198del
  • NM_001406648.1:c.198del
  • NM_001406649.1:c.198del
  • NM_001406650.1:c.198del
  • NM_001406651.1:c.198del
  • NM_001406652.1:c.198del
  • NM_001406653.1:c.198del
  • NM_001406654.1:c.-143del
  • NM_001406655.1:c.198del
  • NM_001406656.1:c.-798del
  • NM_001406657.1:c.198del
  • NM_001406658.1:c.-1121del
  • NM_001406659.1:c.-1271del
  • NM_001406660.1:c.-1468del
  • NM_001406661.1:c.-1423del
  • NM_001406662.1:c.-1340del
  • NM_001406666.1:c.198del
  • NM_001406669.1:c.-1271del
  • NM_001406672.1:c.198del
  • NM_001406674.1:c.198del
  • NP_000242.1:p.Lys65_Tyr66insTer
  • NP_000242.1:p.Tyr66Terfs
  • NP_001393560.1:p.Lys65_Tyr66insTer
  • NP_001393561.1:p.Lys65_Tyr66insTer
  • NP_001393562.1:p.Lys65_Tyr66insTer
  • NP_001393563.1:p.Lys65_Tyr66insTer
  • NP_001393564.1:p.Lys65_Tyr66insTer
  • NP_001393565.1:p.Lys65_Tyr66insTer
  • NP_001393566.1:p.Lys65_Tyr66insTer
  • NP_001393567.1:p.Lys65_Tyr66insTer
  • NP_001393568.1:p.Lys65_Tyr66insTer
  • NP_001393569.1:p.Lys65_Tyr66insTer
  • NP_001393570.1:p.Lys65_Tyr66insTer
  • NP_001393571.1:p.Lys65_Tyr66insTer
  • NP_001393572.1:p.Lys65_Tyr66insTer
  • NP_001393573.1:p.Lys65_Tyr66insTer
  • NP_001393574.1:p.Lys65_Tyr66insTer
  • NP_001393575.1:p.Lys65_Tyr66insTer
  • NP_001393576.1:p.Lys65_Tyr66insTer
  • NP_001393577.1:p.Lys65_Tyr66insTer
  • NP_001393578.1:p.Lys65_Tyr66insTer
  • NP_001393579.1:p.Lys65_Tyr66insTer
  • NP_001393580.1:p.Lys65_Tyr66insTer
  • NP_001393581.1:p.Lys65_Tyr66insTer
  • NP_001393582.1:p.Lys65_Tyr66insTer
  • NP_001393584.1:p.Lys65_Tyr66insTer
  • NP_001393586.1:p.Lys65_Tyr66insTer
  • NP_001393595.1:p.Lys65_Tyr66insTer
  • NP_001393601.1:p.Lys65_Tyr66insTer
  • NP_001393603.1:p.Lys65_Tyr66insTer
  • LRG_218t1:c.198del
  • LRG_218:g.5266del
  • LRG_218p1:p.Tyr66Terfs
  • NC_000002.11:g.47630528del
  • NM_000251.2:c.198delC
  • NR_176230.1:n.234del
  • NR_176231.1:n.234del
  • NR_176232.1:n.234del
  • NR_176233.1:n.234del
  • NR_176234.1:n.234del
  • NR_176235.1:n.234del
  • NR_176236.1:n.234del
  • NR_176237.1:n.234del
  • NR_176238.1:n.234del
  • NR_176239.1:n.234del
  • NR_176240.1:n.234del
  • NR_176241.1:n.234del
  • NR_176242.1:n.234del
  • NR_176243.1:n.234del
  • NR_176244.1:n.234del
  • NR_176245.1:n.234del
  • NR_176246.1:n.234del
  • NR_176247.1:n.234del
  • NR_176248.1:n.234del
  • NR_176249.1:n.234del
  • NR_176250.1:n.234del
Molecular consequence:
  • NM_001258281.1:c.-1del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001406654.1:c.-143del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001406656.1:c.-798del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001406658.1:c.-1121del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001406659.1:c.-1271del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001406660.1:c.-1468del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001406661.1:c.-1423del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001406662.1:c.-1340del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001406669.1:c.-1271del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NR_176230.1:n.234del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_176231.1:n.234del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_176232.1:n.234del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_176233.1:n.234del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_176234.1:n.234del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_176235.1:n.234del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_176236.1:n.234del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_176237.1:n.234del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_176238.1:n.234del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_176239.1:n.234del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_176240.1:n.234del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_176241.1:n.234del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_176242.1:n.234del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_176243.1:n.234del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_176244.1:n.234del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_176245.1:n.234del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_176246.1:n.234del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_176247.1:n.234del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_176248.1:n.234del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_176249.1:n.234del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_176250.1:n.234del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NM_000251.3:c.198del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001406631.1:c.198del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001406632.1:c.198del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001406633.1:c.198del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001406634.1:c.198del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001406635.1:c.198del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001406636.1:c.198del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001406637.1:c.198del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001406638.1:c.198del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001406639.1:c.198del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001406640.1:c.198del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001406641.1:c.198del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001406642.1:c.198del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001406643.1:c.198del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001406644.1:c.198del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001406645.1:c.198del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001406646.1:c.198del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001406647.1:c.198del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001406648.1:c.198del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001406649.1:c.198del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001406650.1:c.198del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001406651.1:c.198del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001406652.1:c.198del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001406653.1:c.198del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001406655.1:c.198del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001406657.1:c.198del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001406666.1:c.198del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001406672.1:c.198del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001406674.1:c.198del - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:
Lynch syndrome 1
Synonyms:
COLON CANCER, FAMILIAL NONPOLYPOSIS, TYPE 1; MSH2-Related Hereditary Non-Polyposis Colon Cancer; Lynch syndrome I; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0007356; MedGen: C2936783; Orphanet: 144; OMIM: 120435

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004047932Neuberg Centre For Genomic Medicine, NCGM
criteria provided, single submitter

(ACMG Guidelines, 2015)		Likely pathogenicgermlineclinical 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, SCV004047932.1

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

Description

The frame shift c.198del(p.Tyr66Ter) variant has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. The c.198del variant is novel (not in any individuals) in gnomAD Exomes and 1000 Genomes. This variant has not been reported to the ClinVar database. This variant is predicted to cause loss of normal protein function through protein truncation. Loss of function variants have been previously reported to be disease causing. For these reasons, this variant has been classified as Likely Pathogenic

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

Last Updated: Jun 9, 2024