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NM_001040108.2(MLH3):c.1493A>G (p.Glu498Gly) AND Colorectal cancer, hereditary nonpolyposis, type 7

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
May 28, 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:
RCV001295921.7

Allele description [Variation Report for NM_001040108.2(MLH3):c.1493A>G (p.Glu498Gly)]

NM_001040108.2(MLH3):c.1493A>G (p.Glu498Gly)

Gene:
MLH3:mutL homolog 3 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
14q24.3
Genomic location:
Preferred name:
NM_001040108.2(MLH3):c.1493A>G (p.Glu498Gly)
HGVS:
  • NC_000014.9:g.75048163T>C
  • NG_008649.1:g.8370A>G
  • NM_001040108.2:c.1493A>GMANE SELECT
  • NM_014381.3:c.1493A>G
  • NP_001035197.1:p.Glu498Gly
  • NP_055196.2:p.Glu498Gly
  • LRG_217:g.8370A>G
  • NC_000014.8:g.75514866T>C
Protein change:
E498G
Links:
dbSNP: rs1892394467
NCBI 1000 Genomes Browser:
rs1892394467
Molecular consequence:
  • NM_001040108.2:c.1493A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_014381.3:c.1493A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Colorectal cancer, hereditary nonpolyposis, type 7
Identifiers:
MONDO: MONDO:0013725; MedGen: C1858380; Orphanet: 144; OMIM: 614385

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001484873Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(May 28, 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

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001484873.4

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

Description

In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The glycine amino acid residue is found in multiple mammalian species, suggesting that this missense change does not adversely affect protein function. These predictions have not been confirmed by published functional studies and their clinical significance is uncertain. This variant has not been reported in the literature in individuals with MLH3-related conditions. This variant is not present in population databases (ExAC no frequency). This sequence change replaces glutamic acid with glycine at codon 498 of the MLH3 protein (p.Glu498Gly). The glutamic acid residue is weakly conserved and there is a moderate physicochemical difference between glutamic acid and glycine.

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

Last Updated: Sep 29, 2024