NM_000179.3(MSH6):c.944C>T (p.Ser315Phe) AND Hereditary nonpolyposis colorectal neoplasms

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Sep 14, 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:: RCV001223820.7

Allele description [Variation Report for NM_000179.3(MSH6):c.944C>T (p.Ser315Phe)]

NM_000179.3(MSH6):c.944C>T (p.Ser315Phe)

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.944C>T (p.Ser315Phe)

HGVS:

NC_000002.12:g.47798927C>T
NG_007111.1:g.20781C>T
NM_000179.3:c.944C>TMANE SELECT
NM_001281492.2:c.554C>T
NM_001281493.2:c.38C>T
NM_001281494.2:c.38C>T
NP_000170.1:p.Ser315Phe
NP_001268421.1:p.Ser185Phe
NP_001268422.1:p.Ser13Phe
NP_001268423.1:p.Ser13Phe
LRG_219t1:c.944C>T
LRG_219:g.20781C>T
NC_000002.11:g.48026066C>T
NM_000179.2:c.944C>T

Protein change:

S13F

Links:

dbSNP: rs63750491

NCBI 1000 Genomes Browser:

rs63750491

Molecular consequence:

NM_000179.3:c.944C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001281492.2:c.554C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001281493.2:c.38C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001281494.2:c.38C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Hereditary nonpolyposis colorectal neoplasms
Identifiers:: MeSH: D003123; MedGen: C0009405

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001395986	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Sep 14, 2023)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 21437237, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001395986

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Sep 14, 2023)

germline

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Cooperative nuclear localization sequences lend a novel role to the N-terminal region of MSH6.

Gassman NR, Clodfelter JE, McCauley AK, Bonin K, Salsbury FR Jr, Scarpinato KD.

PLoS One. 2011 Mar 17;6(3):e17907. doi: 10.1371/journal.pone.0017907.

PubMed [citation]

PMID:: 21437237
PMCID:: PMC3060103

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, SCV001395986.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

This sequence change replaces serine, which is neutral and polar, with phenylalanine, which is neutral and non-polar, at codon 315 of the MSH6 protein (p.Ser315Phe). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with MSH6-related conditions. ClinVar contains an entry for this variant (Variation ID: 951825). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt MSH6 protein function. Experimental studies have shown that this missense change affects MSH6 function (PMID: 21437237). 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.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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