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NM_001126108.2(SLC12A3):c.2549T>C (p.Leu850Pro) AND SLC12A3-related disorder

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Dec 21, 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:
RCV003421914.4

Allele description [Variation Report for NM_001126108.2(SLC12A3):c.2549T>C (p.Leu850Pro)]

NM_001126108.2(SLC12A3):c.2549T>C (p.Leu850Pro)

Gene:
SLC12A3:solute carrier family 12 member 3 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
16q13
Genomic location:
Preferred name:
NM_001126108.2(SLC12A3):c.2549T>C (p.Leu850Pro)
HGVS:
  • NC_000016.10:g.56894558T>C
  • NG_009386.1:g.34352T>C
  • NM_000339.3:c.2576T>C
  • NM_001126107.2:c.2573T>C
  • NM_001126108.2:c.2549T>CMANE SELECT
  • NP_000330.3:p.Leu859Pro
  • NP_001119579.2:p.Leu858Pro
  • NP_001119580.2:p.Leu850Pro
  • NC_000016.9:g.56928470T>C
  • NM_000339.2:c.2576T>C
  • NM_001126108.1:c.2549T>C
  • NM_001126108.2:c.2549T>C
Protein change:
L850P; LEU850PRO
Links:
OMIM: 600968.0001; dbSNP: rs121909379
NCBI 1000 Genomes Browser:
rs121909379
Molecular consequence:
  • NM_000339.3:c.2576T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001126107.2:c.2573T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001126108.2:c.2549T>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
SLC12A3-related disorder
Synonyms:
SLC12A3-related condition
Identifiers:

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004116622PreventionGenetics, part of Exact Sciences
criteria provided, single submitter

(ACMG Guidelines, 2015)		Pathogenic
(Dec 21, 2022) 		germlineclinical testing

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

Help

Summary from all submissions

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

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

Details of each submission

From PreventionGenetics, part of Exact Sciences, SCV004116622.1

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

Description

The SLC12A3 c.2576T>C variant is predicted to result in the amino acid substitution p.Leu859Pro. This variant has been reported in the homozygous and compound heterozygous states in several individuals with Gitelman syndrome (reported as L850P in Simon et al. 1996. PubMed ID: 8528245; Supplemental tables in Vargas-Poussou et al. 2011. PubMed ID: 21415153; Berry et al. 2013. PubMed ID: 23328711). Functional studies in HEK293 cells indicated this variant results in significantly decreased NaCl cotransporter activity (Valdez-Flores et al. 2016. PubMed ID: 27582097). This variant is reported in 0.042% of alleles in individuals of Latino descent in gnomAD (http://gnomad.broadinstitute.org/variant/16-56928470-T-C). This variant is interpreted as pathogenic.

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

Last Updated: Sep 29, 2024