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NM_001040108.2(MLH3):c.2425A>G (p.Met809Val) AND Colorectal cancer, hereditary nonpolyposis, type 7

Germline classification:
Conflicting interpretations of pathogenicity (3 submissions)
Last evaluated:
Jan 29, 2024
Review status:
criteria provided, conflicting classifications
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:
RCV001119882.17

Allele description [Variation Report for NM_001040108.2(MLH3):c.2425A>G (p.Met809Val)]

NM_001040108.2(MLH3):c.2425A>G (p.Met809Val)

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.2425A>G (p.Met809Val)
HGVS:
  • NC_000014.9:g.75047231T>C
  • NG_008649.1:g.9302A>G
  • NM_001040108.2:c.2425A>GMANE SELECT
  • NM_014381.3:c.2425A>G
  • NP_001035197.1:p.Met809Val
  • NP_001035197.1:p.Met809Val
  • NP_055196.2:p.Met809Val
  • LRG_217t1:c.2425A>G
  • LRG_217:g.9302A>G
  • LRG_217p1:p.Met809Val
  • NC_000014.8:g.75513934T>C
  • NM_001040108.1:c.2425A>G
Protein change:
M809V
Links:
dbSNP: rs61752722
NCBI 1000 Genomes Browser:
rs61752722
Molecular consequence:
  • NM_001040108.2:c.2425A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_014381.3:c.2425A>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
SCV000562044Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Likely benign
(Jan 29, 2024) 		germlineclinical testing

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

SCV001278333Illumina Laboratory Services, Illumina
criteria provided, single submitter

(ICSL Variant Classification Criteria 13 December 2019)		Uncertain significance
(Apr 27, 2017) 		germlineclinical testing

Citation Link,

SCV004015904KCCC/NGS Laboratory, Kuwait Cancer Control Center
criteria provided, single submitter

(ACMG Guidelines, 2015)		Likely benign
(Jul 7, 2023) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing
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

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 Labcorp Genetics (formerly Invitae), Labcorp, SCV000562044.9

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Illumina Laboratory Services, Illumina, SCV001278333.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance.

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

From KCCC/NGS Laboratory, Kuwait Cancer Control Center, SCV004015904.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Oct 26, 2024