NM_000249.4(MLH1):c.453+1G>T AND not provided

Clinical significance:Likely pathogenic (Last evaluated: Sep 18, 2018)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV000160522.5

Allele description [Variation Report for NM_000249.4(MLH1):c.453+1G>T]

NM_000249.4(MLH1):c.453+1G>T

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.453+1G>T
HGVS:
  • NC_000003.12:g.37007064G>T
  • NG_007109.2:g.18715G>T
  • NM_000249.4:c.453+1G>TMANE SELECT
  • NM_001167617.3:c.159+1G>T
  • NM_001167618.3:c.-271+1G>T
  • NM_001167619.3:c.-179+1G>T
  • NM_001258271.2:c.453+1G>T
  • NM_001258273.2:c.-271+1G>T
  • NM_001258274.3:c.-271+1G>T
  • NM_001354615.2:c.-179+1G>T
  • NM_001354616.2:c.-179+1G>T
  • NM_001354617.2:c.-271+1G>T
  • NM_001354618.2:c.-271+1G>T
  • NM_001354619.2:c.-271+1G>T
  • NM_001354620.2:c.159+1G>T
  • NM_001354621.2:c.-364+1G>T
  • NM_001354622.2:c.-477+1G>T
  • NM_001354623.2:c.-477+1G>T
  • NM_001354624.2:c.-374+1G>T
  • NM_001354625.2:c.-282+1G>T
  • NM_001354626.2:c.-374+1G>T
  • NM_001354627.2:c.-374+1G>T
  • NM_001354628.2:c.453+1G>T
  • NM_001354629.2:c.354+1G>T
  • NM_001354630.2:c.453+1G>T
  • LRG_216t1:c.453+1G>T
  • LRG_216:g.18715G>T
  • NC_000003.11:g.37048555G>T
  • NM_000249.3:c.453+1G>T
Links:
dbSNP: rs267607750
NCBI 1000 Genomes Browser:
rs267607750
Molecular consequence:
  • NM_000249.4:c.453+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001167617.3:c.159+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001167618.3:c.-271+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001167619.3:c.-179+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001258271.2:c.453+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001258273.2:c.-271+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001258274.3:c.-271+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001354615.2:c.-179+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001354616.2:c.-179+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001354617.2:c.-271+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001354618.2:c.-271+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001354619.2:c.-271+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001354620.2:c.159+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001354621.2:c.-364+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001354622.2:c.-477+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001354623.2:c.-477+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001354624.2:c.-374+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001354625.2:c.-282+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001354626.2:c.-374+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001354627.2:c.-374+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001354628.2:c.453+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001354629.2:c.354+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001354630.2:c.453+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000211088GeneDxcriteria provided, single submitter
Likely pathogenic
(Sep 18, 2018)
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, SCV000211088.13

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

Description

This variant is denoted MLH1 c.453+1G>T or IVS5+1G>T and consists of a G>T nucleotide substitution at the +1 position of intron 5 of the MLH1 gene. The variant destroys a canonical splice donor site and is predicted to cause abnormal gene splicing, leading to either an abnormal message that is subject to nonsense-mediated mRNA decay or to an abnormal protein product. This variant has been reported in at least one individual who was reported to have colon, jejunum and renal cancer all under the age of 50 (Zhang 2015). We consider this variant to be likely pathogenic.

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

Last Updated: Nov 27, 2021

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