NM_000179.3(MSH6):c.3268G>C (p.Glu1090Gln) AND Hereditary cancer-predisposing syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Sep 16, 2016
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:: RCV000575395.3

Allele description [Variation Report for NM_000179.3(MSH6):c.3268G>C (p.Glu1090Gln)]

NM_000179.3(MSH6):c.3268G>C (p.Glu1090Gln)

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.3268G>C (p.Glu1090Gln)

HGVS:

NC_000002.12:g.47803515G>C
NG_007111.1:g.25369G>C
NM_000179.3:c.3268G>CMANE SELECT
NM_001281492.2:c.2878G>C
NM_001281493.2:c.2362G>C
NM_001281494.2:c.2362G>C
NP_000170.1:p.Glu1090Gln
NP_000170.1:p.Glu1090Gln
NP_001268421.1:p.Glu960Gln
NP_001268422.1:p.Glu788Gln
NP_001268423.1:p.Glu788Gln
LRG_219t1:c.3268G>C
LRG_219:g.25369G>C
LRG_219p1:p.Glu1090Gln
NC_000002.11:g.48030654G>C
NM_000179.2:c.3268G>C

Protein change:

E1090Q

Links:

dbSNP: rs143477948

NCBI 1000 Genomes Browser:

rs143477948

Molecular consequence:

NM_000179.3:c.3268G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001281492.2:c.2878G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001281493.2:c.2362G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001281494.2:c.2362G>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Hereditary cancer-predisposing syndrome
Synonyms:: Neoplastic Syndromes, Hereditary; Tumor predisposition; Cancer predisposition; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0015356; MeSH: D009386; MedGen: C0027672

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000662519	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Uncertain significance (Sep 16, 2016)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000662519

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Uncertain significance
(Sep 16, 2016)

germline

clinical testing

Citation Link

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

Details of each submission

From Ambry Genetics, SCV000662519.5

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

Description

The p.E1090Q variant (also known as c.3268G>C), located in coding exon 5 of the MSH6 gene, results from a G to C substitution at nucleotide position 3268. The glutamic acid at codon 1090 is replaced by glutamine, an amino acid with highly similar properties. This variant was not reported in population based cohorts in the following databases: Database of Single Nucleotide Polymorphisms (dbSNP), NHLBI Exome Sequencing Project (ESP), and 1000 Genomes Project. In the ESP, this variant was not observed in 6503 samples (13006 alleles) with coverage at this position. To date, this alteration has been detected with an allele frequency of approximately 0.001% (greater than 150000 alleles tested) in our clinical cohort. This amino acid position is poorly conserved in available vertebrate species. In addition, the in silico prediction for this alteration is inconclusive. In addition, the CoDP in silico tool predicts this alteration to have a minor impact on molecular function, with a score of 0.014 (Terui H et al. J. Biomed. Sci. 2013;20:25). Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.

#	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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