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NM_000179.2(MSH6):c.3699_3702delAGAA (p.Lys1233Asnfs) AND not provided

Germline classification:
Pathogenic (2 submissions)
Last evaluated:
Mar 8, 2016
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV000202074.2

Allele description

NM_000179.2(MSH6):c.3699_3702delAGAA (p.Lys1233Asnfs)

Gene:
MSH6:mutS homolog 6 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
2p16.3
Genomic location:
Preferred name:
NM_000179.2(MSH6):c.3699_3702delAGAA (p.Lys1233Asnfs)
HGVS:
  • NC_000002.12:g.47806256_47806259delAGAA
  • NG_007111.1:g.28110_28113delAGAA
  • NM_000179.2:c.3699_3702delAGAA
  • NP_000170.1:p.Lys1233Asnfs
  • LRG_219t1:c.3699_3702delAGAA
  • LRG_219:g.28110_28113delAGAA
  • LRG_219p1:p.Lys1233Asnfs
  • NC_000002.11:g.48033395_48033398delAGAA
  • NM_000179.2:c.3699_3702del
  • p.K1233NFS*6
  • p.Lys1233AsnfsX6
Links:
dbSNP: rs193922343
NCBI 1000 Genomes Browser:
rs193922343
Molecular consequence:
  • NM_000179.2:c.3699_3702delAGAA - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Identifiers:
MedGen: CN221809

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000257273Mayo Clinic Genetic Testing Laboratories,Mayo Clinic
no assertion criteria provided
Pathogenicunknownresearch

SCV000279110GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))		Pathogenic
(Mar 8, 2016) 		germlineclinical testing

Citation Link

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Summary from all submissions

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

Details of each submission

From Mayo Clinic Genetic Testing Laboratories,Mayo Clinic, SCV000257273.1

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

From GeneDx, SCV000279110.1

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

Description

This deletion of 4 nucleotides in MSH6 is denoted c.3699_3702delAGAA at the cDNA level and p.Lys1233AsnfsX6 (K1233NfsX6) at the protein level. The normal sequence, with the bases that are deleted in braces, is TTAA{AGAA}CTTG. The deletion causes a frameshift, which changes a Lysine to an Asparagine at codon 1233, and creates a premature stop codon at position 6 of the new reading frame. This variant is predicted to cause loss of normal protein function through either protein truncation or nonsense-mediated mRNA decay. MSH6 c.3699_3702delAGAA has been reported in association with Lynch syndrome (Bonadona 2011, Goldberg 2014). We consider this variant to be pathogenic.

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

Last Updated: Oct 3, 2016