NM_000179.3(MSH6):c.1978A>G (p.Lys660Glu) AND Hereditary nonpolyposis colorectal neoplasms

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Sep 15, 2020
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:: RCV001369058.7

Allele description [Variation Report for NM_000179.3(MSH6):c.1978A>G (p.Lys660Glu)]

NM_000179.3(MSH6):c.1978A>G (p.Lys660Glu)

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.1978A>G (p.Lys660Glu)

HGVS:

NC_000002.12:g.47799961A>G
NG_007111.1:g.21815A>G
NM_000179.2:c.1978A>G
NM_000179.3:c.1978A>GMANE SELECT
NM_001281492.2:c.1588A>G
NM_001281493.2:c.1072A>G
NM_001281494.2:c.1072A>G
NP_000170.1:p.Lys660Glu
NP_001268421.1:p.Lys530Glu
NP_001268422.1:p.Lys358Glu
NP_001268423.1:p.Lys358Glu
LRG_219t1:c.1978A>G
LRG_219:g.21815A>G
NC_000002.11:g.48027100A>G

Protein change:

K358E

Links:

dbSNP: rs1060502894

NCBI 1000 Genomes Browser:

rs1060502894

Molecular consequence:

NM_000179.3:c.1978A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001281492.2:c.1588A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001281493.2:c.1072A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001281494.2:c.1072A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

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

Recent activity

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regulating synaptic membrane exocytosis protein 2 isoform X8 [Homo sapiens]
regulating synaptic membrane exocytosis protein 2 isoform X8 [Homo sapiens]
gi|2462621789|ref|XP_054217552.1|

Protein
Systrophia helicycloides isolate C3_Ami-Cic-cP65-6 cytochrome c oxidase subunit ...
Systrophia helicycloides isolate C3_Ami-Cic-cP65-6 cytochrome c oxidase subunit I (COI) gene, partial cds; mitochondrial
gi|328671879|gb|JF414808.1|

Nucleotide
Homo sapiens replication protein A4 (RPA4), mRNA
Homo sapiens replication protein A4 (RPA4), mRNA
gi|295148159|ref|NM_013347.4|

Nucleotide
recombination activating protein 1, partial [Arthroleptis variabilis]
recombination activating protein 1, partial [Arthroleptis variabilis]
gi|47500327|gb|AAT29041.1|

Protein
RecName: Full=Integral membrane protein GPR137B; AltName: Full=Transmembrane 7 s...
RecName: Full=Integral membrane protein GPR137B; AltName: Full=Transmembrane 7 superfamily member 1 protein
gi|38258405|sp|O60478.1|G137B_HUMAN

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001565486	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Sep 15, 2020)	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

SCV001565486

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Sep 15, 2020)

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, SCV001565486.4

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

Description

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. 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. This variant has not been reported in the literature in individuals with MSH6-related conditions. This variant is not present in population databases (ExAC no frequency). This sequence change replaces lysine with glutamic acid at codon 660 of the MSH6 protein (p.Lys660Glu). The lysine residue is highly conserved and there is a small physicochemical difference between lysine and glutamic acid.

#	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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