NM_000111.2(SLC26A3):c.392C>G (p.Pro131Arg) AND Congenital secretory diarrhea, chloride type

Clinical significance:Uncertain significance (Last evaluated: Apr 28, 2017)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
2 submissions [Details]
Record status:
current
Accession:
RCV000049408.2

Allele description [Variation Report for NM_000111.2(SLC26A3):c.392C>G (p.Pro131Arg)]

NM_000111.2(SLC26A3):c.392C>G (p.Pro131Arg)

Gene:
SLC26A3:solute carrier family 26 member 3 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
7q22.3
Genomic location:
Preferred name:
NM_000111.2(SLC26A3):c.392C>G (p.Pro131Arg)
HGVS:
  • NC_000007.14:g.107791226G>C
  • NG_008046.1:g.17008C>G
  • NM_000111.2:c.392C>G
  • NP_000102.1:p.Pro131Arg
  • LRG_683t1:c.392C>G
  • LRG_683:g.17008C>G
  • LRG_683p1:p.Pro131Arg
  • NC_000007.13:g.107431671G>C
  • P40879:p.Pro131Arg
Protein change:
P131R
Links:
UniProtKB: P40879#VAR_007430; dbSNP: rs386833481
NCBI 1000 Genomes Browser:
rs386833481
Molecular consequence:
  • NM_000111.2:c.392C>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Congenital secretory diarrhea, chloride type (DIAR1)
Synonyms:
Congenital chloride diarrhea; Diarrhea 1, secretory chloride, congenital; Chloridorrhea, congenital; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0008964; MedGen: C0267662; OMIM: 214700

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000081841Juha Muilu Group; Institute for Molecular Medicine Finland (FIMM)no assertion criteria providedprobable-pathogenicnot providednot provided

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

SCV000915195Illumina Clinical Services Laboratory,Illuminacriteria provided, single submitter
Uncertain significance
(Apr 28, 2017)
germlineclinical testing

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

Citation Link

Description

FinDis database variant: This variant was not found or characterized by our laboratory, data were collected from public sources: see reference

SCV000081841

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing
not providednot providednot providednot providednot providednot provided1not providedliterature only

Citations

PubMed

Proton pump inhibitor treatment for congenital chloride diarrhea.

Pieroni KP, Bass D.

Dig Dis Sci. 2011 Mar;56(3):673-6. doi: 10.1007/s10620-010-1491-z. Epub 2010 Dec 3. No abstract available.

PubMed [citation]
PMID:
21127979

Clustering of private mutations in the congenital chloride diarrhea/down-regulated in adenoma gene.

Höglund P, Haila S, Gustavson KH, Taipale M, Hannula K, Popinska K, Holmberg C, Socha J, de la Chapelle A, Kere J.

Hum Mutat. 1998;11(4):321-7.

PubMed [citation]
PMID:
9554749

Details of each submission

From Juha Muilu Group; Institute for Molecular Medicine Finland (FIMM), SCV000081841.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providednot provided PubMed (1)

Description

Converted during submission to Likely pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1not providednot provided1not providednot providednot providednot providednot providednot provided

From Illumina Clinical Services Laboratory,Illumina, SCV000915195.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)

Description

The SLC26A3 c.392C>G (p.Pro131Arg) variant is a missense variant that has been reported in two studies in a total of three unrelated individuals with familial chloride diarrhea, including one in a compound heterozygous state and two in a heterozygous state (Hoglund et al. 1998; Pieroni and Bass 2011). One of the individuals who was heterozygous for the variant was also heterozygous for a frameshift variant, although the phase of these variants is not reported. The p.Pro131Arg variant was absent from 104 control chromosomes and is reported at a frequency of 0.00002 in the European (non-Finnish) population of the Exome Aggregation Consortium. This frequency is based on one allele in an area of good coverage, so the variant is presumed to be rare. Based on the evidence, the p.Pro131Arg variant is classified as a variant of unknown significance but suspicious for pathogenicity for familial chloride diarrhea. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population.

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

Last Updated: Apr 17, 2020

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