NM_000111.3(SLC26A3):c.1652del (p.Phe551fs) AND Congenital secretory diarrhea, chloride type

Germline classification:: Likely pathogenic (2 submissions)
Last evaluated:: Jun 20, 2019
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:: RCV000991385.5

Allele description [Variation Report for NM_000111.3(SLC26A3):c.1652del (p.Phe551fs)]

NM_000111.3(SLC26A3):c.1652del (p.Phe551fs)

Gene:

SLC26A3:solute carrier family 26 member 3 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

7q22.3

Genomic location:

Preferred name:

NM_000111.3(SLC26A3):c.1652del (p.Phe551fs)

HGVS:

NC_000007.14:g.107776479del
NG_008046.1:g.31757del
NM_000111.3:c.1652delMANE SELECT
NP_000102.1:p.Phe551fs
LRG_683t1:c.1652del
LRG_683:g.31757del
NC_000007.13:g.107416924del
NM_000111.2:c.1652delT

Protein change:

F551fs

Links:

OMIM: 126650.0009; dbSNP: rs1584403556

NCBI 1000 Genomes Browser:

rs1584403556

Molecular consequence:

NM_000111.3:c.1652del - frameshift variant - [Sequence Ontology: SO:0001589]

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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001142779	Hadassah Hebrew University Medical Center	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Jun 20, 2019)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV001443782	OMIM	no assertion criteria provided	Pathogenic (May 2, 2022)	germline	literature only	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001142779

Hadassah Hebrew University Medical Center

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Jun 20, 2019)

germline

clinical testing

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

SCV001443782

OMIM

no assertion criteria provided

Pathogenic
(May 2, 2022)

germline

literature only

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	not provided	not provided	not provided	not provided	not provided	not provided	literature only

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee.

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

The utility of next generation sequencing in the correct diagnosis of congenital hypochloremic hypokalemic metabolic alkalosis.

Ben-David Y, Halevy R, Sakran W, Zehavi Y, Spiegel R.

Eur J Med Genet. 2019 Oct;62(10):103728. doi: 10.1016/j.ejmg.2019.103728. Epub 2019 Jul 17.

PubMed [citation]

PMID:: 31325522

Details of each submission

From Hadassah Hebrew University Medical Center, SCV001142779.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From OMIM, SCV001443782.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	literature only	PubMed (1)

Description

In a 10-year-old Arab girl, born to consanguineous parents, with congenital chloride diarrhea (DIAR1; 214700), Ben-David et al. (2019) identified homozygosity for a 1-bp deletion (c.1652delT, NM_000111.2) in the SLC26A3 gene, predicted to cause a frameshift and premature termination (Phe551fsTer25). The mutation was identified by whole-exome sequencing and confirmed by Sanger sequencing. The parents were confirmed to be carriers. Functional studies were not performed.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	not provided	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Dec 31, 2022

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