chr16-56887967-G-A

Position:

• chr16-56887967-G-A

Variant summary

Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PM2 PP5_Very_Strong

The NM_001126108.2(SLC12A3):​c.2221G>A​(p.Gly741Arg) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000764 in 1,612,942 control chromosomes in the GnomAD database, with no homozygous occurrence. 12/21 in silico tools predict a damaging outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★).

• Frequency:
  • Genomes: 𝑓 0.00041 (0 hom., cov: 30)
  • Exomes 𝑓: 0.00080 (0 hom.)
• Consequence: SLC12A3 NM_001126108.2 missense
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:24
• Conservation: PhyloP100: 9.83

Genes affected

SLC12A3 (HGNC:10912): (solute carrier family 12 member 3) This gene encodes a renal thiazide-sensitive sodium-chloride cotransporter that is important for electrolyte homeostasis. This cotransporter mediates sodium and chloride reabsorption in the distal convoluted tubule. Mutations in this gene cause Gitelman syndrome, a disease similar to Bartter's syndrome, that is characterized by hypokalemic alkalosis combined with hypomagnesemia, low urinary calcium, and increased renin activity associated with normal blood pressure. This cotransporter is the target for thiazide diuretics that are used for treating high blood pressure. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Pathogenic. Variant got 10 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 16-56887967-G-A is Pathogenic according to our data. Variant chr16-56887967-G-A is described in ClinVar as [Likely_pathogenic]. Clinvar id is 208612.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-56887967-G-A is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC12A3	NM_001126108.2	c.2221G>A	p.Gly741Arg	missense_variant	18/26	ENST00000563236.6	NP_001119580.2
SLC12A3	NM_000339.3	c.2221G>A	p.Gly741Arg	missense_variant	18/26		NP_000330.3
SLC12A3	NM_001126107.2	c.2218G>A	p.Gly740Arg	missense_variant	18/26		NP_001119579.2
SLC12A3	NM_001410896.1	c.2218G>A	p.Gly740Arg	missense_variant	18/26		NP_001397825.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC12A3	ENST00000563236.6	c.2221G>A	p.Gly741Arg	missense_variant	18/26	1	NM_001126108.2	ENSP00000456149	A1
SLC12A3	ENST00000438926.6	c.2221G>A	p.Gly741Arg	missense_variant	18/26	1		ENSP00000402152	A1
SLC12A3	ENST00000566786.5	c.2218G>A	p.Gly740Arg	missense_variant	18/26	1		ENSP00000457552	P4
SLC12A3	ENST00000262502.5	c.2218G>A	p.Gly740Arg	missense_variant	18/26	5		ENSP00000262502	A1

Frequencies

GnomAD3 genomes AF: 0.000408 AC: 62 AN: 151816 Hom.: 0 Cov.: 30

Gnomad AFR AF: 0.000121

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000131

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000794

Gnomad OTH AF: 0.000479

GnomAD3 exomes AF: 0.000370 AC: 93 AN: 251298 Hom.: 0 AF XY: 0.000346 AC XY: 47 AN XY: 135884

Gnomad AFR exome AF: 0.000123

Gnomad AMR exome AF: 0.000202

Gnomad ASJ exome AF: 0.000199

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.0000327

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000695

Gnomad OTH exome AF: 0.000326

GnomAD4 exome AF: 0.000802 AC: 1171 AN: 1461010 Hom.: 0 Cov.: 31 AF XY: 0.000788 AC XY: 573 AN XY: 726842

Gnomad4 AFR exome AF: 0.000120

Gnomad4 AMR exome AF: 0.000313

Gnomad4 ASJ exome AF: 0.000383

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000232

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00101

Gnomad4 OTH exome AF: 0.000348

GnomAD4 genome AF: 0.000408 AC: 62 AN: 151932 Hom.: 0 Cov.: 30 AF XY: 0.000390 AC XY: 29 AN XY: 74276

Gnomad4 AFR AF: 0.000121

Gnomad4 AMR AF: 0.000131

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000795

Gnomad4 OTH AF: 0.000474

Alfa AF: 0.000634 Hom.: 0

Bravo AF: 0.000389

TwinsUK AF: 0.000539 AC: 2

ALSPAC AF: 0.000519 AC: 2

ESP6500AA AF: 0.00 AC: 0

ESP6500EA AF: 0.000581 AC: 5

ExAC AF: 0.000404 AC: 49

EpiCase AF: 0.000382

EpiControl AF: 0.000889

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:24

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Familial hypokalemia-hypomagnesemia Pathogenic:12

Pathogenic, criteria provided, single submitter	clinical testing	Victorian Clinical Genetics Services, Murdoch Childrens Research Institute	Jul 17, 2023	Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Pathogenic. Following criteria are met: 0102 - Loss of function is a known mechanism of disease in this gene and is associated with Gitelman syndrome (MIM#263800). (I) 0106 - This gene is associated with autosomal recessive disease. (I) 0200 - Variant is predicted to result in a missense amino acid change from glycine to arginine. (I) 0251 - This variant is heterozygous. (I) 0304 - Variant is present in gnomAD (v2) <0.01 for a recessive condition (104 heterozygotes, 0 homozygotes). (SP) 0501 - Missense variant consistently predicted to be damaging by multiple in silico tools and highly conserved with a major amino acid change. (SP) 0600 - Variant is located in the annotated SLC12 family domain (DECIPHER). (I) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals. This variant has been classified as pathogenic by at least fifteen clinical diagnostic laboratories and has been reported as one of the five most frequent pathogenic missense variants associated with Gitelman syndrome in Caucasians (ClinVar; PMID: 35591852). (SP) 1208 - Inheritance information for this variant is not currently available in this individual. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign -
Pathogenic, criteria provided, single submitter	clinical testing	Genome-Nilou Lab	Jul 15, 2021	- -
Pathogenic, criteria provided, single submitter	clinical testing	Genetics and Molecular Pathology, SA Pathology	Dec 20, 2022	The SLC12A3 c.2221G>A variant is classified as Pathogenic (PS3, PM3_strong2, PP3) The SLC12A3 c.2221G>A variant is a single nucleotide change in exon 18/26 of the SLC12A3 gene, which is predicted to change the amino acid glycine at position 741 in the protein to arginine. Functional studies show that the variant results in a non-functional protein (PMID:12039972)(PS3). This variant has been detected in trans with pathogenic variants for this recessive condition (PMID:17329572) (PM3_strong). Computational predictions support a deleterious effect on the gene or gene product (PP3). The variant has been reported in dbSNP (rs138977195), in population databases (gnomAD 62/151816, 0 homs, highest freq 0.079% non-Finnish European) and as disease causing in the HGMD database (CM961300). It has been reported as Conflicting interpretations of pathogenicity by other diagnostic laboratories (ClinVar Variation ID: 208612). The variant has been widely reported in the literature in patients with Gitelman syndrome and has been described as a hotspot mutation (PMID:8528245, 12039972, 17329572, 21415153, 22009145). -
Likely pathogenic, criteria provided, single submitter	clinical testing	DASA	Feb 05, 2022	The c.2221G>A;p.(Gly741Arg) missense variant has been observed in affected individual(s) and ClinVar contains an entry for this variant (ClinVar ID: 208612; PMID: 18391953; 17329572; 21415153; 22009145; 23328711; 8528245) - PS4. The variant is present at low allele frequencies population databases (rs138977195 – gnomAD 0.0004084%; ABraOM no frequency - http://abraom.ib.usp.br/) - PM2_supporting. The variant co-segregated with disease in multiple affected family members (PMID: 8528245) - PP1. In summary, the currently available evidence indicates that the variant is likely pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego	-	This variant has been previously reported as a compound heterozygous change in patients with Gitelman syndrome (PMID: 8528245, 17329572, 21415153, 22009145, 23328711, 32939031). Functional studies have shown that this change results in reduced sodium uptake (PMID: 12039972). The c.2221G>A (p.Gly741Arg) variant is present in the heterozygous state in the gnomAD population database at a frequency of 0.03685% (104/282254) and is absent in the homozygous state, thus it is presumed to be rare. The c.2221G>A (p.Gly741Arg) variant affects a highly conserved amino acid and is predicted by multiple in silico tools to have a deleterious effect on protein function. Based on the available evidence, the c.2221G>A (p.Gly741Arg) variant is classified as Pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Centogene AG - the Rare Disease Company	Dec 06, 2018	- -
Pathogenic, criteria provided, single submitter	clinical testing	European Hospital Georges Pompidou Genetics Department, Assistance Publique - Hôpitaux de Paris AP-HP	Apr 27, 2022	ACMG criteria used:PS3 PS4 PM1 PM2 PM3 PP3 PP5 -
Pathogenic, criteria provided, single submitter	clinical testing	Fulgent Genetics, Fulgent Genetics	Jun 30, 2021	- -
Pathogenic, criteria provided, single submitter	clinical testing	Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center	Mar 24, 2022	PS3, PM2, PM3_Strong, PP3 -
Pathogenic, criteria provided, single submitter	clinical testing	MGZ Medical Genetics Center	Oct 26, 2021	- -
Pathogenic, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Apr 28, 2017	Across a selection of the available literature, the SLC12A3 c.2221G>A (p.Gly741Arg) missense variant has been reported in four patients with Gitelman syndrome in a homozygous state and in 79 patients in a compound heterozygous state (Simon et al. 1996; Vargas-Poussou et al. 2011; Glaudemans et al. 2012; Berry et al. 2013; Dongilli et al. 2016). Control data are not available for this variant which is reported at a frequency of 0.00063 in the European (non-Finnish) population of the Exome Aggregation Consortium. Functional studies in Xenopus oocytes demonstrated that the p.Gly741Arg variant resulted in no sodium ion uptake activity, showed intracellular localization rather than plasma membrane localization compared to wild type, and was not glycosylated (De Jong et al. 2002). Based on the collective evidence, the p.Gly741Arg variant is classified as pathogenic for Gitelman syndrome. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population. -
Pathogenic, criteria provided, single submitter	clinical testing	Revvity Omics, Revvity	Feb 12, 2021	- -

not provided Pathogenic:8

Pathogenic, no assertion criteria provided	clinical testing	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Jun 01, 2019	- -
Pathogenic, no assertion criteria provided	clinical testing	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	Athena Diagnostics	Apr 23, 2021	The frequency of this variant in the general population is consistent with pathogenicity (http://gnomad.broadinstitute.org). Assessment of experimental evidence suggests this variant results in abnormal protein function. An in vitro study shows the variant protein is retained intracellulary and leads to loss of cotransporter function (PMID: 12039972). In multiple individuals, this variant has been seen with a single recessive pathogenic variant in the same gene, suggesting this variant may also be pathogenic. -
Pathogenic, no assertion criteria provided	research	Gharavi Laboratory, Columbia University	Sep 16, 2018	- -
Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Jan 06, 2022	In vitro functional analysis demonstrated significantly diminished metolazone-sensitive sodium uptake levels in cells harboring this variant; immunocytochemical analysis revealed that the altered protein was predominantly localized to the cytoplasm rather than the plasma membrane as observed with the wild-type protein (De Jong et al., 2002); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 8528245, 18391953, 10988270, 9734597, 30201548, 23328711, 17329572, 21415153, 22009145, 26921350, 30596175, 31916727, 31980526, 30136149, 32939031, 31672324, 12039972, 27535533) -
Pathogenic, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 31, 2024	This sequence change replaces glycine, which is neutral and non-polar, with arginine, which is basic and polar, at codon 741 of the SLC12A3 protein (p.Gly741Arg). This variant is present in population databases (rs138977195, gnomAD 0.07%). This missense change has been observed in individual(s) with Gitelman syndrome (PMID: 8528245, 17329572, 18391953, 21415153, 22009145, 23328711). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 208612). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt SLC12A3 protein function with a positive predictive value of 95%. Experimental studies have shown that this missense change affects SLC12A3 function (PMID: 12039972). For these reasons, this variant has been classified as Pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Clinical Genetics Laboratory, Skane University Hospital Lund	May 15, 2023	- -

Bartter syndrome;C0268450:Familial hypokalemia-hypomagnesemia Pathogenic:1

Pathogenic, no assertion criteria provided

clinical testing

Sydney Genome Diagnostics, Children's Hospital Westmead

Apr 05, 2018

This individual is heterozygous for the c.2221G>A variant in the SLC12A3 gene. This variant has been widely reported in numerous patients with Gitelman syndrome in the literature (Vargas-Poussou et al 2011 J Am Soc Nephrol 22:693-703. This variant is considered to be pathogenic according to the ACMG guidelines. -

Inherited renal tubular disease Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Sep 07, 2017

proposed classification - variant undergoing re-assessment, contact laboratory -

SLC12A3-related disorder Pathogenic:1

Pathogenic, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Feb 22, 2024

The SLC12A3 c.2221G>A variant is predicted to result in the amino acid substitution p.Gly741Arg. This variant has been reported in many unrelated individuals to be pathogenic for Gitelman syndrome (Simon et al. 1996. PubMed ID: 8528245; De Jong et al. 2002. PubMed ID: 12039972; Supp. Table 1 in Fujimura et al. 2018. PubMed ID: 30596175; Supp. Table S1 in Hureaux et al. 2019. PubMed ID: 31672324; Zacchia et al. 2021. PubMed ID: 33964006). Functional studies indicate that the p.Gly741Arg change impacts protein function (De Jong et al. 2002. PubMed ID: 12039972). This variant is reported in 0.068% of alleles in individuals of European (non-Finnish) descent in gnomAD. This variant is interpreted as pathogenic. -

Hypokalemia;C0151786:Muscle weakness;C0231528:Myalgia;C1522135:Hypermagnesemia Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Centre for Mendelian Genomics, University Medical Centre Ljubljana

Jan 01, 2017

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.97
BayesDel_addAF	Pathogenic	0.29	D
BayesDel_noAF	Pathogenic	0.55
CADD	Pathogenic	30
DANN	Pathogenic	1.0
DEOGEN2	Pathogenic	0.89	.;.;D;D
Eigen	Pathogenic	0.71
Eigen_PC	Uncertain	0.55
FATHMM_MKL	Pathogenic	1.0	D
LIST_S2	Pathogenic	1.0	D;D;D;D
M_CAP	Pathogenic	0.31	D
MetaRNN	Uncertain	0.70	D;D;D;D
MetaSVM	Uncertain	0.33	D
MutationAssessor	Pathogenic	3.5	.;H;H;.
MutationTaster	Benign	1.0	D;D;D;D
PrimateAI	Pathogenic	0.80	T
PROVEAN	Pathogenic	-7.4	D;D;D;D
REVEL	Pathogenic	0.85
Sift	Pathogenic	0.0	D;D;D;D
Sift4G	Pathogenic	0.0	D;D;D;D
Polyphen		1.0	D;D;D;.
Vest4		0.99
MutPred		0.89		.;Gain of MoRF binding (P = 0.0166);Gain of MoRF binding (P = 0.0166);.;
MVP		0.96
MPC		0.52
ClinPred		0.37	T
GERP RS		3.7
Varity_R		0.94
gMVP		0.94

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.10		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs138977195; hg19: chr16-56921879;