NM_001126108.2(SLC12A3):c.2615_2633dup (p.Ile879fs) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Dec 31, 2022
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:: RCV003681007.2

Allele description [Variation Report for NM_001126108.2(SLC12A3):c.2615_2633dup (p.Ile879fs)]

NM_001126108.2(SLC12A3):c.2615_2633dup (p.Ile879fs)

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.2615_2633dup (p.Ile879fs)

HGVS:

NC_000016.10:g.56894624_56894642dup
NG_009386.2:g.34418_34436dup
NM_000339.3:c.2642_2660dup
NM_001126107.2:c.2639_2657dup
NM_001126108.2:c.2615_2633dupMANE SELECT
NM_001410896.1:c.2612_2630dup
NP_000330.3:p.Ile888fs
NP_001119579.2:p.Ile887fs
NP_001119580.2:p.Ile879fs
NP_001397825.1:p.Ile878fs
NC_000016.9:g.56928535_56928536insTGGACCAGGAGAGAAAGGC
NC_000016.9:g.56928536_56928554dup

Protein change:

I878fs

Molecular consequence:

NM_000339.3:c.2642_2660dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001126107.2:c.2639_2657dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001126108.2:c.2615_2633dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001410896.1:c.2612_2630dup - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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CCCH-type zinc fingerfamily protein with RNA-binding domain-containing protein [...
CCCH-type zinc fingerfamily protein with RNA-binding domain-containing protein [Arabidopsis thaliana]
gi|240256278|ref|NP_568277.5|

Protein
hypothetical protein L914_20124 [Phytophthora nicotianae]
hypothetical protein L914_20124 [Phytophthora nicotianae]
gi|568034790|gb|ETM32455.1||gnl|WGS |L914_20124T0

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004427718	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Dec 31, 2022)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 20848653, 22009145, 25841442, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004427718

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Dec 31, 2022)

germline

clinical testing

PubMed (4)
[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 (4)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004427718.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

Description

For these reasons, this variant has been classified as Pathogenic. This variant has not been reported in the literature in individuals affected with SLC12A3-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Ile888Glyfs*20) 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).

#	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: Sep 29, 2024

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