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NM_002439.5(MSH3):c.1148del (p.Lys383fs) AND Familial adenomatous polyposis 4

Germline classification:
Pathogenic (2 submissions)
Last evaluated:
Aug 29, 2023
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:
RCV000009277.18

Allele description [Variation Report for NM_002439.5(MSH3):c.1148del (p.Lys383fs)]

NM_002439.5(MSH3):c.1148del (p.Lys383fs)

Gene:
MSH3:mutS homolog 3 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
5q14.1
Genomic location:
Preferred name:
NM_002439.5(MSH3):c.1148del (p.Lys383fs)
HGVS:
  • NC_000005.10:g.80675103del
  • NC_000005.9:g.79970915del
  • NG_016607.2:g.25629del
  • NM_002439.5:c.1148delMANE SELECT
  • NP_002430.3:p.Lys383Argfs
  • NP_002430.3:p.Lys383fs
  • NC_000005.9:g.79970915del
  • NC_000005.9:g.79970922del
  • NC_000005.9:g.79970922delA
  • NG_016607.1:g.25629del
  • NM_002439.3:c.1148delA
  • NM_002439.4:c.1148del
  • NM_002439.4:c.1148delA
Note:
NCBI staff reviewed the sequence information reported in PubMed 8782829 Fig. 1 to determine the location of this allele on the current reference sequence.
Protein change:
K383fs
Links:
OMIM: 600887.0001; dbSNP: rs587776701
NCBI 1000 Genomes Browser:
rs587776701
Molecular consequence:
  • NM_002439.5:c.1148del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:
Familial adenomatous polyposis 4 (FAP4)
Identifiers:
MONDO: MONDO:0044300; MedGen: C4310719; OMIM: 617100

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000029495OMIM
no assertion criteria provided
Pathogenic
(Sep 1, 1996)
unknownliterature only

PubMed (2)
[See all records that cite these PMIDs]

SCV004189047Myriad Genetics, Inc.
criteria provided, single submitter

(Myriad Autosomal Dominant, Autosomal Recessive and X-Linked Classification Criteria (2023))
Pathogenic
(Aug 29, 2023)
unknownclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownnot providednot providednot providednot providednot providednot providedliterature only
not providedunknownunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Exome Sequencing Identifies Biallelic MSH3 Germline Mutations as a Recessive Subtype of Colorectal Adenomatous Polyposis.

Adam R, Spier I, Zhao B, Kloth M, Marquez J, Hinrichsen I, Kirfel J, Tafazzoli A, Horpaopan S, Uhlhaas S, Stienen D, Friedrichs N, Altmüller J, Laner A, Holzapfel S, Peters S, Kayser K, Thiele H, Holinski-Feder E, Marra G, Kristiansen G, Nöthen MM, et al.

Am J Hum Genet. 2016 Aug 4;99(2):337-51. doi: 10.1016/j.ajhg.2016.06.015. Epub 2016 Jul 28.

PubMed [citation]
PMID:
27476653
PMCID:
PMC4974087

Mutation of MSH3 in endometrial cancer and evidence for its functional role in heteroduplex repair.

Risinger JI, Umar A, Boyd J, Berchuck A, Kunkel TA, Barrett JC.

Nat Genet. 1996 Sep;14(1):102-5.

PubMed [citation]
PMID:
8782829

Details of each submission

From OMIM, SCV000029495.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (2)

Description

Familial Adenomatous Polyposis 4

In 2 sisters (family 1275) with autosomal recessive familial adenomatous polyposis-4 (FAP4; 617100), Adam et al. (2016) identified compound heterozygous mutations in the MSH3 gene: a 1-bp deletion (c.1148delA, NM_002439.4) in exon 7, resulting in a frameshift and premature termination (Lys383ArgfsTer32), and an A-to-C transversion in intron 21 (c.3001-2A-C; 600887.0002), resulting in aberrant splicing and premature termination (Val1001ArgfsTer16) that would alter the dimerization domain. The mutations, which were found by whole-exome sequencing and confirmed by Sanger sequencing, were filtered against the dbSNP, 1000 Genomes Project, Exome Variant Server, and ExAC databases, and an in-house database of 2,816 control exomes. The c.1148delA mutation was found at a low frequency (0.008%) in the ExAC database.

Endocrine Cancer, Somatic

In a primary endometrial cancer (608089) and in an endometrial carcinoma cell line, Risinger et al. (1996) found a somatic mutation in the MSH3 gene. The mutation resulted in a truncated product and consisted of a single nucleotide deletion, loss of an A/T basepair at position 1148. This change generated a premature nonsense codon and results in a protein 723 amino acids shorter than the wildtype gene product. No wildtype DNA sequence or gene product was evident in the cell line. Residual wildtype sequence in protein was present in the primary tumor sample, which may have resulted from contaminating normal cells. The mutation was absent in the DNA of normal cells from the patient.

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

From Myriad Genetics, Inc., SCV004189047.1

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

Description

This variant is considered pathogenic. This variant creates a frameshift predicted to result in premature protein truncation.

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

Last Updated: May 7, 2024