NM_000249.4(MLH1):c.44T>C (p.Val15Ala) AND Lynch syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Nov 30, 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:: RCV003997614.2

Allele description [Variation Report for NM_000249.4(MLH1):c.44T>C (p.Val15Ala)]

NM_000249.4(MLH1):c.44T>C (p.Val15Ala)

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.44T>C (p.Val15Ala)

HGVS:

NC_000003.12:g.36993591T>C
NG_007109.2:g.5242T>C
NG_008418.1:g.4714A>G
NM_000249.4:c.44T>CMANE SELECT
NM_001167617.3:c.-473T>C
NM_001167618.3:c.-902T>C
NM_001167619.3:c.-815T>C
NM_001258271.2:c.44T>C
NM_001258273.2:c.-589T>C
NM_001258274.3:c.-1052T>C
NM_001354615.2:c.-583T>C
NM_001354616.2:c.-583T>C
NM_001354617.2:c.-675T>C
NM_001354618.2:c.-907T>C
NM_001354619.2:c.-1031T>C
NM_001354620.2:c.-241T>C
NM_001354621.2:c.-1000T>C
NM_001354622.2:c.-1113T>C
NM_001354623.2:c.-1022T>C
NM_001354624.2:c.-783T>C
NM_001354625.2:c.-681T>C
NM_001354626.2:c.-778T>C
NM_001354627.2:c.-1010T>C
NM_001354628.2:c.44T>C
NM_001354629.2:c.44T>C
NM_001354630.2:c.44T>C
NP_000240.1:p.Val15Ala
NP_000240.1:p.Val15Ala
NP_001245200.1:p.Val15Ala
NP_001341557.1:p.Val15Ala
NP_001341558.1:p.Val15Ala
NP_001341559.1:p.Val15Ala
LRG_216t1:c.44T>C
LRG_216:g.5242T>C
LRG_216p1:p.Val15Ala
NC_000003.11:g.37035082T>C
NM_000249.3:c.44T>C

Protein change:

V15A

Links:

dbSNP: rs864622396

NCBI 1000 Genomes Browser:

rs864622396

Molecular consequence:

NM_001167617.3:c.-473T>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001167618.3:c.-902T>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001167619.3:c.-815T>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001258273.2:c.-589T>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001258274.3:c.-1052T>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354615.2:c.-583T>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354616.2:c.-583T>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354617.2:c.-675T>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354618.2:c.-907T>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354619.2:c.-1031T>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354620.2:c.-241T>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354621.2:c.-1000T>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354622.2:c.-1113T>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354623.2:c.-1022T>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354624.2:c.-783T>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354625.2:c.-681T>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354626.2:c.-778T>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354627.2:c.-1010T>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_000249.4:c.44T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001258271.2:c.44T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001354628.2:c.44T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001354629.2:c.44T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001354630.2:c.44T>C - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

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

Recent activity

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hypothetical protein M405DRAFT_771529 [Rhizopogon salebrosus TDB-379]
hypothetical protein M405DRAFT_771529 [Rhizopogon salebrosus TDB-379]
gi|2490681405|gb|KAJ8586522.1||gnl| AKEYD|M405DRAFT_771529

Protein
tetrapyrrole methylase [Rhizopogon vinicolor AM-OR11-026]
tetrapyrrole methylase [Rhizopogon vinicolor AM-OR11-026]
gi|1035373525|gb|OAX31299.1||gnl|WG I|K503DRAFT_777713

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004835218	All of Us Research Program, National Institutes of Health	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain Significance (Nov 30, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004835218

All of Us Research Program, National Institutes of Health

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain Significance
(Nov 30, 2023)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	2	not provided	not provided	108544	not provided	clinical testing

Citations

PubMed

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, SCV004835218.1

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

Description

This missense variant replaces valine with alanine at codon 15 of the MLH1 protein. Computational prediction suggests that this variant may have deleterious impact on protein structure and function (internally defined REVEL score threshold >= 0.7, PMID: 27666373). Splice site prediction tools suggest that this variant may not impact RNA splicing. To our knowledge, functional studies have not been performed for this variant. This variant has not been reported in individuals affected with hereditary cancer in the literature. This variant has been identified in 1/31380 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		2	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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