NM_000179.3(MSH6):c.3568T>G (p.Phe1190Val) AND Hereditary nonpolyposis colorectal neoplasms

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: May 10, 2018
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:: RCV000705873.7

Allele description [Variation Report for NM_000179.3(MSH6):c.3568T>G (p.Phe1190Val)]

NM_000179.3(MSH6):c.3568T>G (p.Phe1190Val)

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.3568T>G (p.Phe1190Val)

HGVS:

NC_000002.12:g.47805629T>G
NG_007111.1:g.27483T>G
NG_008397.1:g.105047A>C
NM_000179.3:c.3568T>GMANE SELECT
NM_001281492.2:c.3178T>G
NM_001281493.2:c.2662T>G
NM_001281494.2:c.2662T>G
NP_000170.1:p.Phe1190Val
NP_000170.1:p.Phe1190Val
NP_001268421.1:p.Phe1060Val
NP_001268422.1:p.Phe888Val
NP_001268423.1:p.Phe888Val
LRG_219t1:c.3568T>G
LRG_219:g.27483T>G
LRG_219p1:p.Phe1190Val
NC_000002.11:g.48032768T>G
NM_000179.2:c.3568T>G

Protein change:

F1060V

Links:

dbSNP: rs778651272

NCBI 1000 Genomes Browser:

rs778651272

Molecular consequence:

NM_000179.3:c.3568T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001281492.2:c.3178T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001281493.2:c.2662T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001281494.2:c.2662T>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

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

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HS3ST6 [Ficedula albicollis]
HS3ST6 [Ficedula albicollis]
Gene ID:101806311

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000834890	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (May 10, 2018)	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

SCV000834890

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(May 10, 2018)

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	not provided	not provided	not provided	not provided	not provided	clinical 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, SCV000834890.4

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

Description

This sequence change replaces phenylalanine with valine at codon 1190 of the MSH6 protein (p.Phe1190Val). The phenylalanine residue is highly conserved and there is a small physicochemical difference between phenylalanine and valine. This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals with MSH6-related disease. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be disruptive, but these predictions have not been confirmed by published functional studies and their clinical significance is uncertain. 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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