U.S. flag

An official website of the United States government

NM_000249.4(MLH1):c.55A>T (p.Ile19Phe) AND not provided

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Sep 1, 2020
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:
RCV000483320.3

Allele description [Variation Report for NM_000249.4(MLH1):c.55A>T (p.Ile19Phe)]

NM_000249.4(MLH1):c.55A>T (p.Ile19Phe)

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.55A>T (p.Ile19Phe)
HGVS:
  • NC_000003.12:g.36993602A>T
  • NG_007109.2:g.5253A>T
  • NG_008418.1:g.4703T>A
  • NM_000249.4:c.55A>TMANE SELECT
  • NM_001167617.3:c.-462A>T
  • NM_001167618.3:c.-891A>T
  • NM_001167619.3:c.-804A>T
  • NM_001258271.2:c.55A>T
  • NM_001258273.2:c.-578A>T
  • NM_001258274.3:c.-1041A>T
  • NM_001354615.2:c.-572A>T
  • NM_001354616.2:c.-572A>T
  • NM_001354617.2:c.-664A>T
  • NM_001354618.2:c.-896A>T
  • NM_001354619.2:c.-1020A>T
  • NM_001354620.2:c.-230A>T
  • NM_001354621.2:c.-989A>T
  • NM_001354622.2:c.-1102A>T
  • NM_001354623.2:c.-1011A>T
  • NM_001354624.2:c.-772A>T
  • NM_001354625.2:c.-670A>T
  • NM_001354626.2:c.-767A>T
  • NM_001354627.2:c.-999A>T
  • NM_001354628.2:c.55A>T
  • NM_001354629.2:c.55A>T
  • NM_001354630.2:c.55A>T
  • NP_000240.1:p.Ile19Phe
  • NP_000240.1:p.Ile19Phe
  • NP_001245200.1:p.Ile19Phe
  • NP_001341557.1:p.Ile19Phe
  • NP_001341558.1:p.Ile19Phe
  • NP_001341559.1:p.Ile19Phe
  • LRG_216t1:c.55A>T
  • LRG_216:g.5253A>T
  • LRG_216p1:p.Ile19Phe
  • NC_000003.11:g.37035093A>T
  • NM_000249.3:c.55A>T
  • P40692:p.Ile19Phe
  • p.I19F
Protein change:
I19F
Links:
UniProtKB: P40692#VAR_043383; dbSNP: rs63750648
NCBI 1000 Genomes Browser:
rs63750648
Molecular consequence:
  • NM_001167617.3:c.-462A>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001167618.3:c.-891A>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001167619.3:c.-804A>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001258273.2:c.-578A>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001258274.3:c.-1041A>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001354615.2:c.-572A>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001354616.2:c.-572A>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001354617.2:c.-664A>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001354618.2:c.-896A>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001354619.2:c.-1020A>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001354620.2:c.-230A>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001354621.2:c.-989A>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001354622.2:c.-1102A>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001354623.2:c.-1011A>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001354624.2:c.-772A>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001354625.2:c.-670A>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001354626.2:c.-767A>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001354627.2:c.-999A>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_000249.4:c.55A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001258271.2:c.55A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354628.2:c.55A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354629.2:c.55A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354630.2:c.55A>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...

Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000565139GeneDx
criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)		Likely pathogenic
(Sep 1, 2020) 		germlineclinical testing

Citation Link

Help

Summary from all submissions

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

Details of each submission

From GeneDx, SCV000565139.4

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

Description

Observed in individuals with colorectal or other Lynch-associated cancers meeting revised Bethesda or Amsterdam II criteria (Andrew 2002, Kurzawski 2002, Perera 2010, Yurgleun 2017); Not observed in large population cohorts (Lek 2016); Published functional studies demonstrate partial loss of mismatch repair function (Ellison 2004); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 18383312, 30212499, 15475387, 29478780, 20864636, 12362047, 12537657, 28135145, 26333163, 26248088, 31857677, 31391288)

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

Last Updated: Feb 28, 2024