NM_000179.3(MSH6):c.16A>C (p.Thr6Pro) AND MSH6-related disorder

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Feb 6, 2024
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

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:: RCV004535548.2

Allele description [Variation Report for NM_000179.3(MSH6):c.16A>C (p.Thr6Pro)]

NM_000179.3(MSH6):c.16A>C (p.Thr6Pro)

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.16A>C (p.Thr6Pro)

HGVS:

NC_000002.12:g.47783249A>C
NG_007111.1:g.5103A>C
NM_000179.3:c.16A>CMANE SELECT
NM_001281492.2:c.16A>C
NM_001281493.2:c.-721A>C
NP_000170.1:p.Thr6Pro
NP_000170.1:p.Thr6Pro
NP_001268421.1:p.Thr6Pro
LRG_219t1:c.16A>C
LRG_219:g.5103A>C
LRG_219p1:p.Thr6Pro
NC_000002.11:g.48010388A>C
NM_000179.2:c.16A>C

Protein change:

T6P

Links:

dbSNP: rs200944853

NCBI 1000 Genomes Browser:

rs200944853

Molecular consequence:

NM_001281493.2:c.-721A>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_000179.3:c.16A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001281492.2:c.16A>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: MSH6-related disorder
Synonyms:: MSH6-related disorders; MSH6-related condition
Identifiers:

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004717661	PreventionGenetics, part of Exact Sciences	no assertion criteria provided	Uncertain significance (Feb 6, 2024)	germline	clinical testing

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004717661

PreventionGenetics, part of Exact Sciences

no assertion criteria provided

Uncertain significance
(Feb 6, 2024)

germline

clinical testing

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 PreventionGenetics, part of Exact Sciences, SCV004717661.2

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

Description

The MSH6 c.16A>C variant is predicted to result in the amino acid substitution p.Thr6Pro. This variant has been reported in an individual with high grade glioma (Zhang et al. 2015. PubMed ID: 26580448, Table S4a, Case SJHGG073) and in at least one individual with Cowden syndrome or Bannayan-Riley-Ruvalcaba syndrome (Yehia et al. 2018. PubMed ID: 29684080, Table S9). This variant is reported in 0.0084% of alleles in individuals of African descent in gnomAD and is interpreted as uncertain in ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/variation/428380/). At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.

#	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: Nov 10, 2024

ClinVar

Relating variation to medicine