NM_000249.4(MLH1):c.157G>A (p.Glu53Lys) AND Lynch syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Feb 5, 2024
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:: RCV003998631.2

Allele description [Variation Report for NM_000249.4(MLH1):c.157G>A (p.Glu53Lys)]

NM_000249.4(MLH1):c.157G>A (p.Glu53Lys)

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.157G>A (p.Glu53Lys)

HGVS:

NC_000003.12:g.36996659G>A
NG_007109.2:g.8310G>A
NG_008418.1:g.1646C>T
NM_000249.4:c.157G>AMANE SELECT
NM_001167617.3:c.-133G>A
NM_001167618.3:c.-567G>A
NM_001167619.3:c.-475G>A
NM_001258271.2:c.157G>A
NM_001258273.2:c.-517+2996G>A
NM_001258274.3:c.-712G>A
NM_001354615.2:c.-470G>A
NM_001354616.2:c.-475G>A
NM_001354617.2:c.-567G>A
NM_001354618.2:c.-567G>A
NM_001354619.2:c.-567G>A
NM_001354620.2:c.-133G>A
NM_001354621.2:c.-660G>A
NM_001354622.2:c.-773G>A
NM_001354623.2:c.-723+2769G>A
NM_001354624.2:c.-670G>A
NM_001354625.2:c.-573G>A
NM_001354626.2:c.-670G>A
NM_001354627.2:c.-670G>A
NM_001354628.2:c.157G>A
NM_001354629.2:c.157G>A
NM_001354630.2:c.157G>A
NP_000240.1:p.Glu53Lys
NP_000240.1:p.Glu53Lys
NP_001245200.1:p.Glu53Lys
NP_001341557.1:p.Glu53Lys
NP_001341558.1:p.Glu53Lys
NP_001341559.1:p.Glu53Lys
LRG_216t1:c.157G>A
LRG_216:g.8310G>A
LRG_216p1:p.Glu53Lys
NC_000003.11:g.37038150G>A
NM_000249.3:c.157G>A
NM_001167617.1:c.-133G>A

Protein change:

E53K

Links:

dbSNP: rs63751199

NCBI 1000 Genomes Browser:

rs63751199

Molecular consequence:

NM_001167617.3:c.-133G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001167618.3:c.-567G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001167619.3:c.-475G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001258274.3:c.-712G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354615.2:c.-470G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354616.2:c.-475G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354617.2:c.-567G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354618.2:c.-567G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354619.2:c.-567G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354620.2:c.-133G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354621.2:c.-660G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354622.2:c.-773G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354624.2:c.-670G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354625.2:c.-573G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354626.2:c.-670G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354627.2:c.-670G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001258273.2:c.-517+2996G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001354623.2:c.-723+2769G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_000249.4:c.157G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001258271.2:c.157G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354628.2:c.157G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354629.2:c.157G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354630.2:c.157G>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
SCV004835241	All of Us Research Program, National Institutes of Health	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain Significance (Feb 5, 2024)	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

SCV004835241

All of Us Research Program, National Institutes of Health

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain Significance
(Feb 5, 2024)

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	3	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, SCV004835241.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	3	not provided	not provided	clinical testing	PubMed (1)

Description

This missense variant replaces glutamic acid with lysine at codon 53 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 not been reported in individuals affected with MLH1-associated disease in the literature. This variant has not been identified 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		3	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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