NM_001126108.2(SLC12A3):c.1388G>A (p.Gly463Glu) AND Familial hypokalemia-hypomagnesemia

Germline classification:: Likely pathogenic (2 submissions)
Last evaluated:: Apr 27, 2022
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV002243499.4

Allele description [Variation Report for NM_001126108.2(SLC12A3):c.1388G>A (p.Gly463Glu)]

NM_001126108.2(SLC12A3):c.1388G>A (p.Gly463Glu)

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.1388G>A (p.Gly463Glu)

HGVS:

NC_000016.10:g.56879594G>A
NG_009386.2:g.19388G>A
NM_000339.3:c.1388G>A
NM_001126107.2:c.1385G>A
NM_001126108.2:c.1388G>AMANE SELECT
NP_000330.3:p.Gly463Glu
NP_001119579.2:p.Gly462Glu
NP_001119580.2:p.Gly463Glu
NC_000016.9:g.56913506G>A
NG_009386.1:g.19388G>A
NM_000339.2:c.1388G>A

Protein change:

G462E

Links:

dbSNP: rs1375515522

NCBI 1000 Genomes Browser:

rs1375515522

Molecular consequence:

NM_000339.3:c.1388G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001126107.2:c.1385G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001126108.2:c.1388G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Familial hypokalemia-hypomagnesemia (GTLMNS)
Synonyms:: Potassium and magnesium depletion; Hypomagnesemia-hypokalemia, primary renotubular, with hypocalciuria
Identifiers:: MONDO: MONDO:0009904; MedGen: C0268450; Orphanet: 358; OMIM: 263800

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002513805	European Hospital Georges Pompidou Genetics Department, Assistance Publique - Hôpitaux de Paris AP-HP	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Apr 27, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002797163	Fulgent Genetics, Fulgent Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Mar 5, 2022)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002513805

European Hospital Georges Pompidou Genetics Department, Assistance Publique - Hôpitaux de Paris AP-HP

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Apr 27, 2022)

germline

clinical testing

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

SCV002797163

Fulgent Genetics, Fulgent Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Mar 5, 2022)

unknown

clinical testing

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	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical 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 European Hospital Georges Pompidou Genetics Department, Assistance Publique - Hôpitaux de Paris AP-HP, SCV002513805.1

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

Description

ACMG criteria used:PM1, PM2 PM5, PP3, PP5

#	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 Fulgent Genetics, Fulgent Genetics, SCV002797163.1

#	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	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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