Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

ClinVar Genomic variation as it relates to human health

Advanced search

NM_000179.2(MSH6):c.3079G>C (p.Val1027Leu)

Help
Interpretation:
Conflicting interpretations of pathogenicity​

Likely benign(2);Uncertain significance(2)

Review status:
criteria provided, conflicting interpretations
Submissions:
5 (Most recent: Mar 31, 2021)
Last evaluated:
Nov 23, 2020
Accession:
VCV000230117.9
Variation ID:
230117
Description:
single nucleotide variant
Help

NM_000179.2(MSH6):c.3079G>C (p.Val1027Leu)

Allele ID
232800
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
2p16.3
Genomic location
2: 47801062 (GRCh38) GRCh38 UCSC
2: 48028201 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000002.12:g.47801062G>C
NC_000002.11:g.48028201G>C
NM_000179.2:c.3079G>C NP_000170.1:p.Val1027Leu missense
... more HGVS
Protein change
V1027L, V725L, V897L
Other names
-
Canonical SPDI
NC_000002.12:47801061:G:C
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
-
Links
ClinGen: CA10578129
dbSNP: rs876658397
Varsome
Help

Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Uncertain significance 1 criteria provided, single submitter Aug 13, 2018 RCV000227272.7
Likely benign 1 criteria provided, single submitter Nov 23, 2020 RCV001080207.2
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations Dec 16, 2019 RCV000216842.3
Uncertain significance 1 no assertion criteria provided - RCV000503628.2
Help
Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
MSH6 Sufficient evidence for dosage pathogenicity No evidence available GRCh38
GRCh37
5633 5667

Submitted interpretations and evidence

Help
Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely benign
(May 24, 2018)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Ambry Genetics
Accession: SCV000273550.5
Submitted: (Nov 30, 2020)
Evidence details
Comment:
In silico models in agreement (benign);Other data supporting benign classification
Uncertain significance
(Aug 13, 2018)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Quest Diagnostics Nichols Institute San Juan Capistrano
Accession: SCV001134420.2
Submitted: (Mar 06, 2020)
Evidence details
Publications
PubMed (1)
Uncertain significance
(Dec 16, 2019)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Color Health, Inc
Accession: SCV001359122.1
Submitted: (May 19, 2020)
Comment:
This missense variant replaces valine with leucine at codon 1027 of the MSH6 protein. Computational prediction suggests that this variant may not impact protein structure … (more)
Evidence details
Likely benign
(Nov 23, 2020)
criteria provided, single submitter
Method: clinical testing
Hereditary nonpolyposis colorectal neoplasms
Allele origin: germline
Invitae
Accession: SCV000283782.7
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (1)
Uncertain significance
(-)
no assertion criteria provided
Method: clinical testing
Carcinoma of colon
Allele origin: unknown
Department of Pathology and Laboratory Medicine,Sinai Health System
Additional submitter:
Franklin by Genoox
Study: The Canadian Open Genetics Repository (COGR)
Accession: SCV000592621.2
Submitted: (Mar 31, 2021)
Evidence details
Comment:
The MSH6 p.Val1027Leu variant was not identified in the literature, nor was it identified in the dbSNP, NHLBI Exome Sequencing Project, Exome Aggregation Consortium (March … (more)

Functional evidence

Help
There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

Help
Title Author Journal Year Link
Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. Nykamp K Genetics in medicine : official journal of the American College of Medical Genetics 2017 PMID: 28492532
Prevalence of germline mutations in cancer predisposition genes in patients with pancreatic cancer. Grant RC Gastroenterology 2015 PMID: 25479140

Text-mined citations for rs876658397...

Help
These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Jun 06, 2021