NM_001126108.2(SLC12A3):c.237_238dup (p.Arg80fs) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jan 19, 2024
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:: RCV000809020.4

Allele description [Variation Report for NM_001126108.2(SLC12A3):c.237_238dup (p.Arg80fs)]

NM_001126108.2(SLC12A3):c.237_238dup (p.Arg80fs)

Gene:

SLC12A3:solute carrier family 12 member 3 [Gene - OMIM - HGNC]

Variant type:

Duplication

Cytogenetic location:

16q13

Genomic location:

Preferred name:

NM_001126108.2(SLC12A3):c.237_238dup (p.Arg80fs)

HGVS:

NC_000016.10:g.56865472_56865473dup
NG_009386.1:g.5266_5267dup
NM_000339.3:c.237_238dup
NM_001126107.2:c.237_238dup
NM_001126108.2:c.237_238dupMANE SELECT
NP_000330.3:p.Arg80fs
NP_001119579.2:p.Arg80fs
NP_001119580.2:p.Arg80fs
NC_000016.9:g.56899381_56899382insCC
NC_000016.9:g.56899384_56899385dup
NM_000339.2:c.237_238dup
NM_000339.2:c.237_238dupCC
NM_000339.3:c.237_238dupCC

Protein change:

R80fs

Links:

dbSNP: rs780299444

NCBI 1000 Genomes Browser:

rs780299444

Molecular consequence:

NM_000339.3:c.237_238dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001126107.2:c.237_238dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001126108.2:c.237_238dup - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Sus scrofa chromosome 1 genomic scaffold
Sus scrofa chromosome 1 genomic scaffold
gi|328549805|gnl|WGS:AEMK01|chr1_69 6|gb|GL878658.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000949156	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jan 19, 2024)	germline	clinical testing	PubMed (5) [See all records that cite these PMIDs] 20848653, 22009145, 25841442, 8900229, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000949156

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jan 19, 2024)

germline

clinical testing

PubMed (5)
[See all records that cite these PMIDs]

Help

Summary from all submissions

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

Citations

PubMed

Generation and analysis of the thiazide-sensitive Na+ -Cl- cotransporter (Ncc/Slc12a3) Ser707X knockin mouse as a model of Gitelman syndrome.

Yang SS, Lo YF, Yu IS, Lin SW, Chang TH, Hsu YJ, Chao TK, Sytwu HK, Uchida S, Sasaki S, Lin SH.

Hum Mutat. 2010 Dec;31(12):1304-15. doi: 10.1002/humu.21364. Epub 2010 Oct 14.

PubMed [citation]

PMID:: 20848653

Novel NCC mutants and functional analysis in a new cohort of patients with Gitelman syndrome.

Glaudemans B, Yntema HG, San-Cristobal P, Schoots J, Pfundt R, Kamsteeg EJ, Bindels RJ, Knoers NV, Hoenderop JG, Hoefsloot LH.

Eur J Hum Genet. 2012 Mar;20(3):263-70. doi: 10.1038/ejhg.2011.189. Epub 2011 Oct 19.

PubMed [citation]

PMID:: 22009145
PMCID:: PMC3283182

See all PubMed Citations (5)

Details of each submission

From Invitae, SCV000949156.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (5)

Description

This sequence change creates a premature translational stop signal (p.Arg80Profs*35) in the SLC12A3 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in SLC12A3 are known to be pathogenic (PMID: 20848653, 22009145, 25841442). This variant is present in population databases (rs780299444, gnomAD 0.006%). This premature translational stop signal has been observed in individual(s) with Gitelman syndrome (PMID: 8900229). This variant is also known as c.237_238dupCC. ClinVar contains an entry for this variant (Variation ID: 653276). For these reasons, this variant has been classified as Pathogenic.

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

Last Updated: Aug 4, 2024

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