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NM_000249.4(MLH1):c.159G>T (p.Glu53Asp) AND Hereditary cancer-predisposing syndrome

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jan 2, 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:
RCV001190375.4

Allele description [Variation Report for NM_000249.4(MLH1):c.159G>T (p.Glu53Asp)]

NM_000249.4(MLH1):c.159G>T (p.Glu53Asp)

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.159G>T (p.Glu53Asp)
HGVS:
  • NC_000003.12:g.36996661G>T
  • NG_007109.2:g.8312G>T
  • NG_008418.1:g.1644C>A
  • NM_000249.4:c.159G>TMANE SELECT
  • NM_001167617.3:c.-131G>T
  • NM_001167618.3:c.-565G>T
  • NM_001167619.3:c.-473G>T
  • NM_001258271.2:c.159G>T
  • NM_001258273.2:c.-517+2998G>T
  • NM_001258274.3:c.-710G>T
  • NM_001354615.2:c.-468G>T
  • NM_001354616.2:c.-473G>T
  • NM_001354617.2:c.-565G>T
  • NM_001354618.2:c.-565G>T
  • NM_001354619.2:c.-565G>T
  • NM_001354620.2:c.-131G>T
  • NM_001354621.2:c.-658G>T
  • NM_001354622.2:c.-771G>T
  • NM_001354623.2:c.-723+2771G>T
  • NM_001354624.2:c.-668G>T
  • NM_001354625.2:c.-571G>T
  • NM_001354626.2:c.-668G>T
  • NM_001354627.2:c.-668G>T
  • NM_001354628.2:c.159G>T
  • NM_001354629.2:c.159G>T
  • NM_001354630.2:c.159G>T
  • NP_000240.1:p.Glu53Asp
  • NP_001245200.1:p.Glu53Asp
  • NP_001341557.1:p.Glu53Asp
  • NP_001341558.1:p.Glu53Asp
  • NP_001341559.1:p.Glu53Asp
  • LRG_216t1:c.159G>T
  • LRG_216:g.8312G>T
  • NC_000003.11:g.37038152G>T
  • NM_000249.3:c.159G>T
Protein change:
E53D
Links:
dbSNP: rs1060504012
NCBI 1000 Genomes Browser:
rs1060504012
Molecular consequence:
  • NM_001167617.3:c.-131G>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001167618.3:c.-565G>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001167619.3:c.-473G>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001258274.3:c.-710G>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001354615.2:c.-468G>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001354616.2:c.-473G>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001354617.2:c.-565G>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001354618.2:c.-565G>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001354619.2:c.-565G>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001354620.2:c.-131G>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001354621.2:c.-658G>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001354622.2:c.-771G>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001354624.2:c.-668G>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001354625.2:c.-571G>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001354626.2:c.-668G>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001354627.2:c.-668G>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001258273.2:c.-517+2998G>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354623.2:c.-723+2771G>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_000249.4:c.159G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001258271.2:c.159G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354628.2:c.159G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354629.2:c.159G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354630.2:c.159G>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Hereditary cancer-predisposing syndrome
Synonyms:
Neoplastic Syndromes, Hereditary; Tumor predisposition; Cancer predisposition; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0015356; MeSH: D009386; MedGen: C0027672

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001357838Color Diagnostics, LLC DBA Color Health
criteria provided, single submitter

(ACMG Guidelines, 2015)		Uncertain significance
(Jan 2, 2020) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical 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 Color Diagnostics, LLC DBA Color Health, SCV001357838.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

This missense variant replaces glutamic acid with aspartic acid at codon 53 of the MLH1 protein. Computational prediction tool suggests that this variant may not impact protein structure and function (internally defined REVEL score threshold ≤0.5, 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 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.

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

Last Updated: Jun 23, 2024