NM_000179.3(MSH6):c.3850dup (p.Thr1284fs) AND not provided

Clinical significance:Pathogenic/Likely pathogenic (Last evaluated: Nov 16, 2020)

Review status:2 stars out of maximum of 4 stars

criteria provided, multiple submitters, no conflicts

Based on:
2 submissions [Details]
Record status:
current
Accession:
RCV000657421.2

Allele description [Variation Report for NM_000179.3(MSH6):c.3850dup (p.Thr1284fs)]

NM_000179.3(MSH6):c.3850dup (p.Thr1284fs)

Gene:
MSH6:mutS homolog 6 [Gene - OMIM - HGNC]
Variant type:
Duplication
Cytogenetic location:
2p16.3
Genomic location:
Preferred name:
NM_000179.3(MSH6):c.3850dup (p.Thr1284fs)
HGVS:
  • NC_000002.12:g.47806500dup
  • NG_007111.1:g.28354dup
  • NG_008397.1:g.104176dup
  • NM_000179.2:c.3850dup
  • NM_000179.3:c.3850dupMANE SELECT
  • NM_001281492.2:c.3460dup
  • NM_001281493.2:c.2944dup
  • NM_001281494.2:c.2944dup
  • NP_000170.1:p.Thr1284fs
  • NP_000170.1:p.Thr1284fs
  • NP_001268421.1:p.Thr1154fs
  • NP_001268422.1:p.Thr982fs
  • NP_001268423.1:p.Thr982fs
  • LRG_219t1:c.3850dup
  • LRG_219:g.28354dup
  • LRG_219p1:p.Thr1284fs
  • NC_000002.11:g.48033638_48033639insA
  • NC_000002.11:g.48033639dup
  • NM_000179.2:c.3850dupA
Protein change:
T1154fs
Links:
dbSNP: rs1553333421
NCBI 1000 Genomes Browser:
rs1553333421
Molecular consequence:
  • NM_000179.3:c.3850dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001281492.2:c.3460dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001281493.2:c.2944dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001281494.2:c.2944dup - 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
SCV000779156GeneDxcriteria provided, single submitter
Pathogenic
(Nov 16, 2020)
germlineclinical testing

Citation Link,

SCV000889497Quest Diagnostics Nichols Institute San Juan Capistranocriteria provided, single submitter
Likely pathogenic
(Dec 15, 2017)
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

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 GeneDx, SCV000779156.3

#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 et al., 2016); Truncating variants in this gene are considered pathogenic by a well-established clinical consortium and/or database; Reported as a pathogenic variant in healthy individuals enrolled in screening studies (Capalbo 2019, eMERGE Consortium 2019); This variant is associated with the following publications: (PMID: 31447099, 31589614)

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

From Quest Diagnostics Nichols Institute San Juan Capistrano, SCV000889497.1

#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: Nov 27, 2021

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