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NM_000179.3(MSH6):c.3716_3717del (p.Ile1239fs)

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Interpretation:
Pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
6 (Most recent: Nov 30, 2020)
Last evaluated:
Aug 7, 2018
Accession:
VCV000420268.4
Variation ID:
420268
Description:
2bp microsatellite
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NM_000179.3(MSH6):c.3716_3717del (p.Ile1239fs)

Allele ID
405951
Variant type
Microsatellite
Variant length
2 bp
Cytogenetic location
2p16.3
Genomic location
2: 47806271-47806272 (GRCh38) GRCh38 UCSC
2: 48033410-48033411 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000002.11:g.48033410TA[1]
NC_000002.12:g.47806271TA[1]
NM_000179.3:c.3716_3717del MANE Select NP_000170.1:p.Ile1239fs frameshift
... more HGVS
Protein change
I937fs, I1109fs, I1239fs
Other names
-
Canonical SPDI
NC_000002.12:47806270:TATA:TA
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
-
Links
ClinGen: CA16617707
dbSNP: rs1064794384
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic 4 criteria provided, multiple submitters, no conflicts Jun 11, 2018 RCV000482291.3
Pathogenic 1 criteria provided, single submitter Aug 7, 2018 RCV000561455.1
Pathogenic 1 criteria provided, single submitter May 1, 2018 RCV000697841.1
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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
5633 5667

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Pathogenic
(May 01, 2018)
criteria provided, single submitter
Method: clinical testing
Hereditary nonpolyposis colon cancer
Allele origin: germline
Invitae
Accession: SCV000826473.1
Submitted: (Aug 29, 2018)
Evidence details
Publications
PubMed (1)
Comment:
This sequence change creates a premature translational stop signal (p.Ile1239Lysfs*35) in the MSH6 gene. It is expected to result in an absent or disrupted protein … (more)
Pathogenic
(Jun 11, 2018)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Quest Diagnostics Nichols Institute San Juan Capistrano
Accession: SCV000889491.1
Submitted: (Aug 31, 2018)
Evidence details
Pathogenic
(Dec 21, 2015)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000569026.3
Submitted: (Jan 29, 2019)
Evidence details
Comment:
This deletion of 2 nucleotides in MSH6 is denoted c.3716_3717delTA at the cDNA level and p.Ile1239LysfsX35 (I1239KfsX35) at the protein level. The normal sequence, with … (more)
Pathogenic
(Aug 07, 2018)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Ambry Genetics
Accession: SCV000673947.3
Submitted: (Nov 30, 2020)
Evidence details
Comment:
The c.3716_3717delTA pathogenic mutation, located in coding exon 8 of the MSH6 gene, results from a deletion of two nucleotides at nucleotide positions 3716 to … (more)
Likely pathogenic
(Feb 20, 2018)
no assertion criteria provided
Method: clinical testing
not provided
Allele origin: unknown
Mayo Clinic Laboratories, Mayo Clinic
Accession: SCV000778624.1
Submitted: (Mar 09, 2018)
Evidence details
Pathogenic
(Sep 16, 2018)
no assertion criteria provided
Method: research
not provided
Allele origin: germline
Gharavi Laboratory,Columbia University
Accession: SCV000809467.1
Submitted: (Sep 24, 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
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

Text-mined citations for rs1064794384...

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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 Aug 27, 2021