NM_000249.4(MLH1):c.1897-2A>G AND not provided

Clinical significance:Likely pathogenic (Last evaluated: Mar 29, 2021)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV000487325.2

Allele description [Variation Report for NM_000249.4(MLH1):c.1897-2A>G]

NM_000249.4(MLH1):c.1897-2A>G

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.1897-2A>G
HGVS:
  • NC_000003.12:g.37048515A>G
  • NG_007109.2:g.60166A>G
  • NM_000249.3:c.1897-2A>G
  • NM_000249.4:c.1897-2A>GMANE SELECT
  • NM_001167617.3:c.1603-2A>G
  • NM_001167618.3:c.1174-2A>G
  • NM_001167619.3:c.1174-2A>G
  • NM_001258271.2:c.1896+832A>G
  • NM_001258273.2:c.1174-2A>G
  • NM_001258274.3:c.1174-2A>G
  • NM_001354615.2:c.1174-2A>G
  • NM_001354616.2:c.1174-2A>G
  • NM_001354617.2:c.1174-2A>G
  • NM_001354618.2:c.1174-2A>G
  • NM_001354619.2:c.1174-2A>G
  • NM_001354620.2:c.1603-2A>G
  • NM_001354621.2:c.874-2A>G
  • NM_001354622.2:c.874-2A>G
  • NM_001354623.2:c.874-2A>G
  • NM_001354624.2:c.823-2A>G
  • NM_001354625.2:c.823-2A>G
  • NM_001354626.2:c.823-2A>G
  • NM_001354627.2:c.823-2A>G
  • NM_001354628.2:c.1897-389A>G
  • NM_001354629.2:c.1798-2A>G
  • NM_001354630.2:c.1732-2A>G
  • LRG_216t1:c.1897-2A>G
  • LRG_216:g.60166A>G
  • NC_000003.11:g.37090006A>G
Links:
dbSNP: rs267607871
NCBI 1000 Genomes Browser:
rs267607871
Molecular consequence:
  • NM_001258271.2:c.1896+832A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354628.2:c.1897-389A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_000249.3:c.1897-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_000249.4:c.1897-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001167617.3:c.1603-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001167618.3:c.1174-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001167619.3:c.1174-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001258273.2:c.1174-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001258274.3:c.1174-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001354615.2:c.1174-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001354616.2:c.1174-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001354617.2:c.1174-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001354618.2:c.1174-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001354619.2:c.1174-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001354620.2:c.1603-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001354621.2:c.874-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001354622.2:c.874-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001354623.2:c.874-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001354624.2:c.823-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001354625.2:c.823-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001354626.2:c.823-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001354627.2:c.823-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001354629.2:c.1798-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001354630.2:c.1732-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000565163GeneDxcriteria provided, single submitter
Likely pathogenic
(Mar 29, 2021)
germlineclinical testing

Citation Link

Summary from all submissions

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

Details of each submission

From GeneDx, SCV000565163.2

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

Description

Canonical splice site variant predicted to result in an in-frame deletion of the critical regions of interaction with EXO1, PMS2/MLH3/PMS1 (Plotz 2003, Kosinski 2010, Andersen 2012); Not observed at a significant frequency in large population cohorts (Lek 2016); Observed in individuals with colon cancer (Rajkumar 2004, Pearlman 2017, Yurgelun 2017); This variant is associated with the following publications: (PMID: 28135145, 27978560, 15345113, 22753075, 20533529, 12799449, 30720243)

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

Last Updated: Oct 30, 2021

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