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NM_002439.5(MSH3):c.115T>A (p.Ser39Thr) AND Familial adenomatous polyposis 4

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jan 9, 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:
RCV003153845.1

Allele description [Variation Report for NM_002439.5(MSH3):c.115T>A (p.Ser39Thr)]

NM_002439.5(MSH3):c.115T>A (p.Ser39Thr)

Genes:
DHFR:dihydrofolate reductase [Gene - OMIM - HGNC]
MSH3:mutS homolog 3 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
5q14.1
Genomic location:
Preferred name:
NM_002439.5(MSH3):c.115T>A (p.Ser39Thr)
HGVS:
  • NC_000005.10:g.80654842T>A
  • NG_016607.2:g.5368T>A
  • NG_023304.1:g.5140A>T
  • NG_105205.1:g.438T>A
  • NG_105205.2:g.465T>A
  • NM_000791.4:c.-353A>TMANE SELECT
  • NM_001290354.2:c.-459A>T
  • NM_001290357.2:c.-353A>T
  • NM_002439.5:c.115T>AMANE SELECT
  • NP_002430.3:p.Ser39Thr
  • NC_000005.9:g.79950661T>A
  • NM_002439.3:c.115T>A
  • NM_002439.4:c.115T>A
  • NR_110936.2:n.142A>T
Protein change:
S39T
Links:
dbSNP: rs1580538013
NCBI 1000 Genomes Browser:
rs1580538013
Molecular consequence:
  • NM_000791.4:c.-353A>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001290354.2:c.-459A>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001290357.2:c.-353A>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_002439.5:c.115T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NR_110936.2:n.142A>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:
Familial adenomatous polyposis 4 (FAP4)
Synonyms:
MSH3-related attenuated familial adenomatous polyposis
Identifiers:
MONDO: MONDO:0044300; MedGen: C4310719; Orphanet: 480536; OMIM: 617100

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV003842980St. Jude Molecular Pathology, St. Jude Children's Research Hospital
criteria provided, single submitter

(St. Jude Assertion Criteria 2020)		Uncertain significance
(Jan 9, 2023) 		germlineclinical testing

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From St. Jude Molecular Pathology, St. Jude Children's Research Hospital, SCV003842980.1

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

Description

The MSH3 c.115T>A (p.Ser39Thr) missense change is absent in gnomAD v2.1.1 (https://gnomad.broadinstitute.org/). The in silico tool REVEL predicts a benign effect of this variant on protein function, and to our knowledge functional studies have not been performed. To our knowledge, this variant has not been reported in individuals with MSH3-related attenuated familial adenomatous polyposis. In summary, the evidence currently available is insufficient to determine the clinical significance of this variant. It has therefore been classified as of uncertain significance.

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

Last Updated: Sep 29, 2024