NM_000249.4(MLH1):c.380+2T>C AND not provided

Clinical significance:Pathogenic (Last evaluated: Apr 19, 2021)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
2 submissions [Details]
Record status:
current
Accession:
RCV001356725.2

Allele description [Variation Report for NM_000249.4(MLH1):c.380+2T>C]

NM_000249.4(MLH1):c.380+2T>C

Gene:
MLH1:mutL homolog 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
3p22.2
Genomic location:
Preferred name:
NM_000249.4(MLH1):c.380+2T>C
HGVS:
  • NC_000003.12:g.37004476T>C
  • NG_007109.2:g.16127T>C
  • NM_000249.4:c.380+2T>CMANE SELECT
  • NM_001167617.3:c.86+2T>C
  • NM_001167618.3:c.-344+2T>C
  • NM_001167619.3:c.-252+2T>C
  • NM_001258271.2:c.380+2T>C
  • NM_001258273.2:c.-344+2T>C
  • NM_001258274.3:c.-344+2T>C
  • NM_001354615.2:c.-252+2T>C
  • NM_001354616.2:c.-252+2T>C
  • NM_001354617.2:c.-344+2T>C
  • NM_001354618.2:c.-344+2T>C
  • NM_001354619.2:c.-344+2T>C
  • NM_001354620.2:c.86+2T>C
  • NM_001354621.2:c.-437+2T>C
  • NM_001354622.2:c.-550+2T>C
  • NM_001354623.2:c.-550+2T>C
  • NM_001354624.2:c.-447+2T>C
  • NM_001354625.2:c.-355+2T>C
  • NM_001354626.2:c.-447+2T>C
  • NM_001354627.2:c.-447+2T>C
  • NM_001354628.2:c.380+2T>C
  • NM_001354629.2:c.281+2T>C
  • NM_001354630.2:c.380+2T>C
  • LRG_216t1:c.380+2T>C
  • LRG_216:g.16127T>C
  • NC_000003.11:g.37045967T>C
  • NM_000249.3:c.380+2T>C
Links:
dbSNP: rs267607742
NCBI 1000 Genomes Browser:
rs267607742
Molecular consequence:
  • NM_000249.4:c.380+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001167617.3:c.86+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001167618.3:c.-344+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001167619.3:c.-252+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001258271.2:c.380+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001258273.2:c.-344+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001258274.3:c.-344+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001354615.2:c.-252+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001354616.2:c.-252+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001354617.2:c.-344+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001354618.2:c.-344+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001354619.2:c.-344+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001354620.2:c.86+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001354621.2:c.-437+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001354622.2:c.-550+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001354623.2:c.-550+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001354624.2:c.-447+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001354625.2:c.-355+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001354626.2:c.-447+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001354627.2:c.-447+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001354628.2:c.380+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001354629.2:c.281+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001354630.2:c.380+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
Observations:
2

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001551969Department of Pathology and Laboratory Medicine,Sinai Health System - The Canadian Open Genetics Repository (COGR)

See additional submitters

no assertion criteria providedUncertain significanceunknownclinical testing

SCV001983877GeneDxcriteria provided, single submitter
Pathogenic
(Apr 19, 2021)
germlineclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownyes2not providednot providednot providednot providedclinical testing
not providedgermlineyesnot 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), SCV001551969.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided2not providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyesnot providednot providednot provided2not providednot providednot provided

From GeneDx, SCV001983877.1

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

Description

Canonical splice site variant predicted to result in a null allele in a gene for which loss-of-function is a known mechanism of disease; Observed in patients with Lynch-related cancers consistent with pathogenic variants in this gene (Lee 2005, DeRycke 2017); Not observed in large population cohorts (Lek 2016); This variant is associated with the following publications: (PMID: 32906206, 25525159, 15996210, 18726168, 28944238)

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

Last Updated: Nov 27, 2021

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