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NM_000179.3(MSH6):c.2555AGA[2] (p.Lys854del)

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Interpretation:
Uncertain significance​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
8 (Most recent: Jan 7, 2021)
Last evaluated:
Oct 27, 2020
Accession:
VCV000142970.11
Variation ID:
142970
Description:
3bp microsatellite
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NM_000179.3(MSH6):c.2555AGA[2] (p.Lys854del)

Allele ID
152684
Variant type
Microsatellite
Variant length
3 bp
Cytogenetic location
2p16.3
Genomic location
2: 47800537-47800539 (GRCh38) GRCh38 UCSC
2: 48027676-48027678 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000002.11:g.48027677AGA[2]
NC_000002.12:g.47800538AGA[2]
NM_000179.3:c.2555AGA[2] MANE Select NP_000170.1:p.Lys854del
... more HGVS
Protein change
K854del, K552del, K724del
Other names
-
Canonical SPDI
NC_000002.12:47800536:AAGAAGAAGA:AAGAAGA
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
-
Links
ClinGen: CA010414
dbSNP: rs587782858
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Uncertain significance 2 criteria provided, multiple submitters, no conflicts Mar 26, 2020 RCV000132477.10
Uncertain significance 2 criteria provided, multiple submitters, no conflicts May 15, 2018 RCV000656896.1
Uncertain significance 2 criteria provided, single submitter Sep 15, 2020 RCV000202234.3
Uncertain significance 1 criteria provided, single submitter Oct 27, 2020 RCV000226221.8
Lynch-like syndrome
Likely pathogenic 1 no assertion criteria provided Jul 1, 2019 RCV001249963.1
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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
5623 5657

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(May 15, 2018)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Quest Diagnostics Nichols Institute San Juan Capistrano
Accession: SCV000888259.1
Submitted: (Aug 31, 2018)
Evidence details
Uncertain significance
(Jan 12, 2018)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000565226.5
Submitted: (Jan 29, 2019)
Evidence details
Comment:
This deletion of three nucleotides in MSH6 is denoted c.2561_2563delAGA at the cDNA level and p.Lys854del at the protein level. The normal sequence, with the … (more)
Uncertain significance
(Feb 13, 2020)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Color Health, Inc
Accession: SCV000685296.3
Submitted: (May 19, 2020)
Comment:
This variant causes a deletion of 1 amino acid from the MSH6 protein. To our knowledge, functional studies have not been performed for this variant. … (more)
Evidence details
Uncertain significance
(Mar 26, 2020)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Ambry Genetics
Accession: SCV000187571.7
Submitted: (Nov 30, 2020)
Evidence details
Publications
PubMed (3)
Comment:
​The c.2561_2563delAGA variant (also known as p.K854del) is located in coding exon 4 of the MSH6 gene. This variant results from an in-frame AGA deletion … (more)
Uncertain significance
(Oct 27, 2020)
criteria provided, single submitter
Method: clinical testing
Hereditary nonpolyposis colorectal neoplasms
Allele origin: germline
Invitae
Accession: SCV000283756.8
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (2)
Comment:
This variant, c.2561_2563delAGA, results in the deletion of 1 amino acid of the MSH6 protein (p.Lys854del), but otherwise preserves the integrity of the reading frame. … (more)
Uncertain significance
(Sep 15, 2020)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV001437241.1
Submitted: (Oct 06, 2020)
Evidence details
Publications
PubMed (6)
Comment:
Variant summary: MSH6 c.2561_2563delAGA (p.Lys854del) results in an in-frame deletion that is predicted to remove one amino acid from the encoded protein. The variant allele … (more)
Uncertain significance
(-)
no assertion criteria provided
Method: research
not specified
Allele origin: unknown
Mayo Clinic Laboratories, Mayo Clinic
Accession: SCV000257223.1
Submitted: (Nov 19, 2015)
Evidence details
Likely pathogenic
(Jul 01, 2019)
no assertion criteria provided
Method: clinical testing
Lynch-like syndrome
Allele origin: somatic
Constitutional Genetics Lab,Leon Berard Cancer Center
Accession: SCV001423977.1
Submitted: (Jul 20, 2020)
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
Lynch Syndrome Germline Mutations in Breast Cancer: Next Generation Sequencing Case-Control Study of 1,263 Participants. Nikitin AG Frontiers in oncology 2020 PMID: 32547938
Comprehensive Paired Tumor/Germline Testing for Lynch Syndrome: Bringing Resolution to the Diagnostic Process. Salvador MU Journal of clinical oncology : official journal of the American Society of Clinical Oncology 2019 PMID: 30702970
TumorNext-Lynch-MMR: a comprehensive next generation sequencing assay for the detection of germline and somatic mutations in genes associated with mismatch repair deficiency and Lynch syndrome. Gray PN Oncotarget 2018 PMID: 29755653
Assessment of Tumor Sequencing as a Replacement for Lynch Syndrome Screening and Current Molecular Tests for Patients With Colorectal Cancer. Hampel H JAMA oncology 2018 PMID: 29596542
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
Constitutional mismatch repair deficiency syndrome: clinical description in a French cohort. Lavoine N Journal of medical genetics 2015 PMID: 26318770
Frequency of mutations in individuals with breast cancer referred for BRCA1 and BRCA2 testing using next-generation sequencing with a 25-gene panel. Tung N Cancer 2015 PMID: 25186627
Diversity of the clinical presentation of the MMR gene biallelic mutations. Bougeard G Familial cancer 2014 PMID: 24068316

Text-mined citations for rs587782858...

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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 Jun 14, 2021