NM_000179.3(MSH6):c.2118T>A (p.Phe706Leu) AND Lynch syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Nov 20, 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:: RCV004006826.2

Allele description [Variation Report for NM_000179.3(MSH6):c.2118T>A (p.Phe706Leu)]

NM_000179.3(MSH6):c.2118T>A (p.Phe706Leu)

Gene:

MSH6:mutS homolog 6 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

2p16.3

Genomic location:

Preferred name:

NM_000179.3(MSH6):c.2118T>A (p.Phe706Leu)

HGVS:

NC_000002.12:g.47800101T>A
NG_007111.1:g.21955T>A
NM_000179.2:c.2118T>A
NM_000179.3:c.2118T>AMANE SELECT
NM_001281492.2:c.1728T>A
NM_001281493.2:c.1212T>A
NM_001281494.2:c.1212T>A
NP_000170.1:p.Phe706Leu
NP_001268421.1:p.Phe576Leu
NP_001268422.1:p.Phe404Leu
NP_001268423.1:p.Phe404Leu
LRG_219t1:c.2118T>A
LRG_219:g.21955T>A
NC_000002.11:g.48027240T>A

Protein change:

F404L

Links:

dbSNP: rs2104389604

NCBI 1000 Genomes Browser:

rs2104389604

Molecular consequence:

NM_000179.3:c.2118T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001281492.2:c.1728T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001281493.2:c.1212T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001281494.2:c.1212T>A - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

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

Recent activity

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Ndel1 nudE neurodevelopment protein 1-like 1 [Rattus norvegicus]
Ndel1 nudE neurodevelopment protein 1-like 1 [Rattus norvegicus]
Gene ID:170845

Gene
170845[uid] AND (alive[prop]) (1)
Gene
Erigeron epiroticus (0)
Nucleotide
PREDICTED: Mus musculus predicted gene, 30515 (Gm30515), transcript variant X7, ...
PREDICTED: Mus musculus predicted gene, 30515 (Gm30515), transcript variant X7, ncRNA
gi|1039742512|ref|XR_001780583.1|

Nucleotide
Homo sapiens bone morphogenetic protein 4 (BMP4), transcript variant 5, mRNA
Homo sapiens bone morphogenetic protein 4 (BMP4), transcript variant 5, mRNA
gi|1122781518|ref|NM_001347913.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004835599	All of Us Research Program, National Institutes of Health	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain Significance (Nov 20, 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

SCV004835599

All of Us Research Program, National Institutes of Health

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain Significance
(Nov 20, 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	1	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, SCV004835599.1

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

Description

This missense variant replaces phenylalanine with leucine at codon 706 of the MSH6 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). To our knowledge, functional studies have not been reported for this variant. This variant has not been reported in individuals affected with MSH6-related disorders in the literature. A different missense variant occurring at the same codon, p.Phe706Ser, is known to be disease-causing (ClinVar variation ID: 89254). 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		1	not provided	not provided	not provided

Last Updated: Sep 29, 2024

ClinVar

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