NM_000179.3(MSH6):c.1995G>C (p.Glu665Asp) AND Hereditary nonpolyposis colorectal neoplasms

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Dec 23, 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:: RCV000199087.10

Allele description [Variation Report for NM_000179.3(MSH6):c.1995G>C (p.Glu665Asp)]

NM_000179.3(MSH6):c.1995G>C (p.Glu665Asp)

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.1995G>C (p.Glu665Asp)

HGVS:

NC_000002.12:g.47799978G>C
NG_007111.1:g.21832G>C
NM_000179.3:c.1995G>CMANE SELECT
NM_001281492.2:c.1605G>C
NM_001281493.2:c.1089G>C
NM_001281494.2:c.1089G>C
NP_000170.1:p.Glu665Asp
NP_000170.1:p.Glu665Asp
NP_001268421.1:p.Glu535Asp
NP_001268422.1:p.Glu363Asp
NP_001268423.1:p.Glu363Asp
LRG_219t1:c.1995G>C
LRG_219:g.21832G>C
LRG_219p1:p.Glu665Asp
NC_000002.11:g.48027117G>C
NM_000179.2:c.1995G>C

Protein change:

E363D

Links:

dbSNP: rs587778532

NCBI 1000 Genomes Browser:

rs587778532

Molecular consequence:

NM_000179.3:c.1995G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001281492.2:c.1605G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001281493.2:c.1089G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001281494.2:c.1089G>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

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

Recent activity

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cytochrome oxidase subunit I, partial (mitochondrion) [Mnestia sp. C TRO-2019]
cytochrome oxidase subunit I, partial (mitochondrion) [Mnestia sp. C TRO-2019]
gi|1798058036|gb|QHI07404.1|

Protein
Triticum urartu cultivar G1812 unplaced genomic scaffold scaffold54299, whole ge...
Triticum urartu cultivar G1812 unplaced genomic scaffold scaffold54299, whole genome shotgun sequence
gi|474227387|gb|KD120086.1||gnl|WGS 01|scaffold54299

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000254287	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Dec 23, 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

SCV000254287

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Dec 23, 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	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, SCV000254287.9

#	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 glutamic acid, which is acidic and polar, with aspartic acid, which is acidic and polar, at codon 665 of the MSH6 protein (p.Glu665Asp). This variant is present in population databases (rs587778532, gnomAD 0.0009%). 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: 134853). 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 with a negative predictive value of 95%. 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: Oct 8, 2024

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