NM_000249.4(MLH1):c.226G>A (p.Val76Ile) AND Lynch syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Dec 1, 2023
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:: RCV003998742.2

Allele description [Variation Report for NM_000249.4(MLH1):c.226G>A (p.Val76Ile)]

NM_000249.4(MLH1):c.226G>A (p.Val76Ile)

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.226G>A (p.Val76Ile)

HGVS:

NC_000003.12:g.37000973G>A
NG_007109.2:g.12624G>A
NM_000249.4:c.226G>AMANE SELECT
NM_001167617.3:c.-64G>A
NM_001167618.3:c.-498G>A
NM_001167619.3:c.-406G>A
NM_001258271.2:c.226G>A
NM_001258273.2:c.-498G>A
NM_001258274.3:c.-498G>A
NM_001354615.2:c.-401G>A
NM_001354616.2:c.-406G>A
NM_001354617.2:c.-498G>A
NM_001354618.2:c.-498G>A
NM_001354619.2:c.-498G>A
NM_001354620.2:c.-64G>A
NM_001354621.2:c.-591G>A
NM_001354622.2:c.-704G>A
NM_001354623.2:c.-704G>A
NM_001354624.2:c.-601G>A
NM_001354625.2:c.-504G>A
NM_001354626.2:c.-601G>A
NM_001354627.2:c.-601G>A
NM_001354628.2:c.226G>A
NM_001354629.2:c.208-3428G>A
NM_001354630.2:c.226G>A
NP_000240.1:p.Val76Ile
NP_000240.1:p.Val76Ile
NP_001245200.1:p.Val76Ile
NP_001341557.1:p.Val76Ile
NP_001341559.1:p.Val76Ile
LRG_216t1:c.226G>A
LRG_216:g.12624G>A
LRG_216p1:p.Val76Ile
NC_000003.11:g.37042464G>A
NM_000249.3:c.226G>A

Protein change:

V76I

Links:

dbSNP: rs878853788

NCBI 1000 Genomes Browser:

rs878853788

Molecular consequence:

NM_001167617.3:c.-64G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001167618.3:c.-498G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001167619.3:c.-406G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001258273.2:c.-498G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001258274.3:c.-498G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354615.2:c.-401G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354616.2:c.-406G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354617.2:c.-498G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354618.2:c.-498G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354619.2:c.-498G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354620.2:c.-64G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354621.2:c.-591G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354622.2:c.-704G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354623.2:c.-704G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354624.2:c.-601G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354625.2:c.-504G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354626.2:c.-601G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354627.2:c.-601G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354629.2:c.208-3428G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_000249.4:c.226G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001258271.2:c.226G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354628.2:c.226G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354630.2:c.226G>A - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

Name:: Lynch syndrome
Identifiers:: MONDO: MONDO:0005835; MedGen: C4552100

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004835256	All of Us Research Program, National Institutes of Health	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain Significance (Dec 1, 2023)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 26976419, 25741868

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004835256

All of Us Research Program, National Institutes of Health

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain Significance
(Dec 1, 2023)

germline

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	7	not provided	not provided	108544	not provided	clinical testing

Citations

PubMed

Frequency of Germline Mutations in 25 Cancer Susceptibility Genes in a Sequential Series of Patients With Breast Cancer.

Tung N, Lin NU, Kidd J, Allen BA, Singh N, Wenstrup RJ, Hartman AR, Winer EP, Garber JE.

J Clin Oncol. 2016 May 1;34(13):1460-8. doi: 10.1200/JCO.2015.65.0747. Epub 2016 Mar 14.

PubMed [citation]

PMID:: 26976419
PMCID:: PMC4872307

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 All of Us Research Program, National Institutes of Health, SCV004835256.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	7	not provided	not provided	clinical testing	PubMed (2)

Description

This missense variant replaces valine with isoleucine at codon 76 of the MLH1 protein. Computational prediction is inconclusive regarding the impact of this variant on protein structure and function (internally defined REVEL score threshold 0.5 < inconclusive < 0.7, PMID: 27666373). To our knowledge, functional studies have not been reported for this variant. This variant has been reported in an individual affected with breast cancer (PMID: 26976419). This variant has also been identified in 4/251370 chromosomes in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	108544	not provided	not provided		7	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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