NM_000179.3(MSH6):c.1634_1635del (p.Lys545fs) AND not provided

Clinical significance:Pathogenic (Last evaluated: Jun 15, 2020)

Review status:2 stars out of maximum of 4 stars

criteria provided, multiple submitters, no conflicts

Based on:
3 submissions [Details]
Record status:
current
Accession:
RCV000202281.5

Allele description [Variation Report for NM_000179.3(MSH6):c.1634_1635del (p.Lys545fs)]

NM_000179.3(MSH6):c.1634_1635del (p.Lys545fs)

Gene:
MSH6:mutS homolog 6 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
2p16.3
Genomic location:
Preferred name:
NM_000179.3(MSH6):c.1634_1635del (p.Lys545fs)
HGVS:
  • NC_000002.12:g.47799617_47799618del
  • NG_007111.1:g.21471_21472del
  • NM_000179.3:c.1634_1635delMANE SELECT
  • NM_001281492.2:c.1244_1245del
  • NM_001281493.2:c.728_729del
  • NM_001281494.2:c.728_729del
  • NP_000170.1:p.Lys545fs
  • NP_001268421.1:p.Lys415fs
  • NP_001268422.1:p.Lys243fs
  • NP_001268423.1:p.Lys243fs
  • LRG_219:g.21471_21472del
  • NC_000002.11:g.48026753_48026754del
  • NC_000002.11:g.48026753_48026754delAA
  • NC_000002.11:g.48026753_48026754delAA
  • NC_000002.11:g.48026756_48026757del
  • NC_000002.11:g.48026756_48026757delAA
  • NM_000179.2:c.1634_1635delAA
  • p.K545RFS*17
  • p.Lys545Argfs*17
Protein change:
K243fs
Links:
dbSNP: rs267608064
NCBI 1000 Genomes Browser:
rs267608064
Molecular consequence:
  • NM_000179.3:c.1634_1635del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001281492.2:c.1244_1245del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001281493.2:c.728_729del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001281494.2:c.728_729del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000257215Mayo Clinic Laboratories, Mayo Clinicno assertion criteria providedPathogenicunknownresearch

SCV000565783GeneDxcriteria provided, single submitter
Pathogenic
(Jun 15, 2020)
germlineclinical testing

Citation Link,

SCV000601511Quest Diagnostics Nichols Institute San Juan Capistranocriteria provided, single submitter
Pathogenic
(Feb 26, 2015)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing
not providedunknownunknown2not providednot providednot providednot providedresearch

Citations

PubMed

A Standardized DNA Variant Scoring System for Pathogenicity Assessments in Mendelian Disorders.

Karbassi I, Maston GA, Love A, DiVincenzo C, Braastad CD, Elzinga CD, Bright AR, Previte D, Zhang K, Rowland CM, McCarthy M, Lapierre JL, Dubois F, Medeiros KA, Batish SD, Jones J, Liaquat K, Hoffman CA, Jaremko M, Wang Z, Sun W, Buller-Burckle A, et al.

Hum Mutat. 2016 Jan;37(1):127-34. doi: 10.1002/humu.22918. Epub 2015 Oct 29.

PubMed [citation]
PMID:
26467025
PMCID:
PMC4737317

Details of each submission

From Mayo Clinic Laboratories, Mayo Clinic, SCV000257215.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided2not providednot providedresearchnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot provided2not providednot providednot provided

From GeneDx, SCV000565783.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

Frameshift variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; Not observed in large population cohorts (Lek 2016); Truncating variants in this gene are considered pathogenic by a well-established clinical consortium and/or database; Observed in individuals with Lynch syndrome-associated cancer and/or colon polyps (Yurgelun 2015, Ring 2016); This variant is associated with the following publications: (PMID: 26681312, 21674763, 28152038, 25980754, 27443514, 19194194)

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Quest Diagnostics Nichols Institute San Juan Capistrano, SCV000601511.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Oct 24, 2021

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