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NM_000179.3(MSH6):c.3246G>A (p.Pro1082=)

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(3);Likely benign(3);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
9 (Most recent: Jul 20, 2021)
Last evaluated:
Dec 6, 2020
Accession:
VCV000184530.9
Variation ID:
184530
Description:
single nucleotide variant
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NM_000179.3(MSH6):c.3246G>A (p.Pro1082=)

Allele ID
182142
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
2p16.3
Genomic location
2: 47803493 (GRCh38) GRCh38 UCSC
2: 48030632 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_219:g.25347G>A
LRG_219t1:c.3246G>A LRG_219p1:p.Pro1082=
NC_000002.11:g.48030632G>A
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000002.12:47803492:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.00140 (T)

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00007
Links
ClinGen: CA012143
dbSNP: rs3136351
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely benign 3 criteria provided, multiple submitters, no conflicts Apr 8, 2015 RCV000163801.2
Benign 2 criteria provided, single submitter Aug 13, 2018 RCV000202109.4
Likely benign 1 criteria provided, single submitter Oct 7, 2016 RCV000410558.1
Benign 1 criteria provided, single submitter Dec 6, 2020 RCV001085889.2
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations Mar 3, 2015 RCV000724321.5
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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
5678 5712

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Oct 30, 2014)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000230868.5
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Likely benign
(Dec 28, 2014)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Ambry Genetics
Accession: SCV000214384.6
Submitted: (Nov 30, 2020)
Evidence details
Comment:
This alteration is classified as likely benign based on a combination of the following: population frequency, intact protein function, lack of segregation with disease, co-occurrence, … (more)
Benign
(Dec 06, 2020)
criteria provided, single submitter
Method: clinical testing
Hereditary nonpolyposis colorectal neoplasms
Allele origin: germline
Invitae
Accession: SCV000260070.8
Submitted: (Jan 07, 2021)
Evidence details
Likely benign
(Oct 07, 2016)
criteria provided, single submitter
Method: clinical testing
Hereditary nonpolyposis colorectal cancer type 5
Allele origin: unknown
Counsyl
Accession: SCV000489464.1
Submitted: (Nov 23, 2016)
Evidence details
Publications
PubMed (1)
Likely benign
(Apr 08, 2015)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Color Health, Inc
Accession: SCV000685371.1
Submitted: (Oct 26, 2017)
Evidence details
Benign
(Aug 13, 2018)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV000917772.1
Submitted: (Apr 24, 2019)
Evidence details
Comment:
Variant summary: MSH6 c.3246G>A alters a non-conserved nucleotide resulting in a synonymous change. 5/5 computational tools predict no significant impact on normal splicing. However, these … (more)
Benign
(Mar 03, 2015)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV001757089.1
Submitted: (Jul 20, 2021)
Evidence details
Uncertain significance
(-)
no assertion criteria provided
Method: research
not specified
Allele origin: unknown
Mayo Clinic Laboratories, Mayo Clinic
Accession: SCV000257245.1
Submitted: (Nov 19, 2015)
Evidence details
Likely benign
(Jul 13, 2018)
no assertion criteria provided
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
True Health Diagnostics
Accession: SCV000886689.1
Submitted: (Nov 27, 2018)
Evidence details

Functional evidence

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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

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Title Author Journal Year Link
Mutational analysis of the hMSH6 gene in familial and early-onset colorectal and endometrial cancer in Israeli patients. Figer A Genetic testing 2002 PMID: 12537658
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=MSH6 - - - -

Text-mined citations for rs3136351...

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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 Oct 30, 2021