16-56886366-C-T

Position:

• chr16-56886366-C-T

Variant summary

Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PM2 PP3 PP5_Very_Strong

The NM_001126108.2(SLC12A3):​c.1928C>T​(p.Pro643Leu) variant causes a missense, splice region change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000128 in 1,612,442 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 12/21 in silico tools predict a damaging outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely pathogenic (★★). Synonymous variant affecting the same amino acid position (i.e. P643P) has been classified as Likely benign.

• Frequency:
  • Genomes: 𝑓 0.00014 (0 hom., cov: 32)
  • Exomes 𝑓: 0.00013 (0 hom.)
• Consequence: SLC12A3 NM_001126108.2 missense, splice_region
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:17
• Conservation: PhyloP100: 7.86

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 11 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.812
• PP5: Variant 16-56886366-C-T is Pathogenic according to our data. Variant chr16-56886366-C-T is described in ClinVar as [Likely_pathogenic]. Clinvar id is 417863.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-56886366-C-T is described in Lovd as [Pathogenic]. Variant chr16-56886366-C-T is described in Lovd as [Likely_pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC12A3	NM_001126108.2	c.1928C>T	p.Pro643Leu	missense_variant, splice_region_variant	16/26	ENST00000563236.6
SLC12A3	NM_000339.3	c.1928C>T	p.Pro643Leu	missense_variant, splice_region_variant	16/26
SLC12A3	NM_001126107.2	c.1925C>T	p.Pro642Leu	missense_variant, splice_region_variant	16/26
SLC12A3	NM_001410896.1	c.1925C>T	p.Pro642Leu	missense_variant, splice_region_variant	16/26

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC12A3	ENST00000563236.6	c.1928C>T	p.Pro643Leu	missense_variant, splice_region_variant	16/26	1	NM_001126108.2	A1
SLC12A3	ENST00000438926.6	c.1928C>T	p.Pro643Leu	missense_variant, splice_region_variant	16/26	1		A1
SLC12A3	ENST00000566786.5	c.1925C>T	p.Pro642Leu	missense_variant, splice_region_variant	16/26	1		P4
SLC12A3	ENST00000262502.5	c.1925C>T	p.Pro642Leu	missense_variant, splice_region_variant	16/26	5		A1

Frequencies

GnomAD3 genomes AF: 0.000138 AC: 21 AN: 152240 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.0000241

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000785

Gnomad ASJ AF: 0.00173

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000294

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.000164 AC: 41 AN: 250040 Hom.: 0 AF XY: 0.000163 AC XY: 22 AN XY: 135344

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.000260

Gnomad ASJ exome AF: 0.00159

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.0000653

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000800

Gnomad OTH exome AF: 0.000816

GnomAD4 exome AF: 0.000127 AC: 185 AN: 1460084 Hom.: 0 Cov.: 31 AF XY: 0.000131 AC XY: 95 AN XY: 726500

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.000313

Gnomad4 ASJ exome AF: 0.00218

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000464

Gnomad4 FIN exome AF: 0.0000188

Gnomad4 NFE exome AF: 0.0000855

Gnomad4 OTH exome AF: 0.000216

GnomAD4 genome AF: 0.000138 AC: 21 AN: 152358 Hom.: 0 Cov.: 32 AF XY: 0.000134 AC XY: 10 AN XY: 74500

Gnomad4 AFR AF: 0.0000240

Gnomad4 AMR AF: 0.000784

Gnomad4 ASJ AF: 0.00173

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000294

Gnomad4 OTH AF: 0.00

Alfa AF: 0.000226 Hom.: 0

Bravo AF: 0.000185

ESP6500AA AF: 0.00 AC: 0

ESP6500EA AF: 0.000465 AC: 4

ExAC AF: 0.000181 AC: 22

EpiCase AF: 0.0000545

EpiControl AF: 0.000178

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:17

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Familial hypokalemia-hypomagnesemia Pathogenic:9

Pathogenic, criteria provided, single submitter	clinical testing	Fulgent Genetics, Fulgent Genetics	Mar 26, 2022	- -
Pathogenic, no assertion criteria provided	research	Division of Human Genetics, Children's Hospital of Philadelphia	Sep 23, 2015	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Genome-Nilou Lab	Jul 15, 2021	- -
Likely 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:PS4, PM1, PM2, PM3, PP3, PP5 -
Pathogenic, criteria provided, single submitter	clinical testing	Laboratory of Medical Genetics, National & Kapodistrian University of Athens	Oct 05, 2021	PM2, PP2, PP3, PP5 -
Pathogenic, criteria provided, single submitter	clinical testing	Center of Genomic medicine, Geneva, University Hospital of Geneva	May 30, 2018	- -
Pathogenic, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Apr 08, 2019	Across a selection of the available literature, the SLC12A3 c.1928C>T (p.Pro643Leu) missense variant has been reported in at least 20 unrelated individuals affected with Gitelman syndrome, including in a homozygous state in three and in a compound heterozygous state in 17 (Cruz et al. 2001; Pantanetti et al. 2002; Talaulikar and Falk 2005; Vargas-Poussou et al. 2011; Balavoine et al. 2011; Glaudemans et al. 2012; Nakhoul et al. 2012; Zahed et al. 2017). Control data are unavailable for this variant, which is reported at a frequency of 0.001774 in the Ashkenazi Jewish population of the Genome Aggregation Database. Based on the collective evidence, the p.Pro643Leu 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	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 proline to leucine. (I) 0251 - This variant is heterozygous. (I) 0304 - Variant is present in gnomAD (v2) <0.01 for a recessive condition (43 heterozygote(s), 0 homozygotes). (SP) 0309 - An alternative amino acid change at the same position has been observed in gnomAD (v2) (1 heterozygote, 0 homozygotes). (I) 0501 - Missense variant consistently predicted to be damaging by multiple in silico tools or highly conserved with a major amino acid change. (SP) 0602 - Variant is located in a hotspot region or cluster of pathogenic variants at the end of the amino acid permease domain (DECIPHER). (SP) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals. This variant has been classified as pathogenic and likely pathogenic by multiple clinical laboratories in ClinVar and has been observed as both homozygous and compound heterozygous in individuals with Gitelman syndrome (PMID: 33585337). This variant has also been previously reported along with two other SLC12A3 variants, p.(Arg955Gln) and p.(Ser28Argfs*19), in one individual with Gitelman syndrome (PMID: 21415153). (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	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Nov 13, 2023	The p.Pro643Leu variant in SLC12A3 has been reported in the homozygous or compound heterozygous state in at least 20 individuals (3 homozygotes; 17 compound heterozygotes) with clinical features of or a diagnosis of Gitelman syndrome and segregated with disease in 1 affected individual from 1 family (Cruz 2001 PMID: 11168953, Pantanetti 2002 PMID: 11940055, Talaulikar 2005 PMID: 15976513, Fava 2007 PMID: 17654016, Balavoine 2011 PMID: 21753071, Vargas-Poussou 2011 PMID: 21415153, Glaudemans 2012 PMID: 22009145, Zahed 2017 PMID: 28947054). This variant has also been reported by other clinical laboratories in ClinVar (Variation ID 417863) and has been identified in 0.17% (6/3472) of Ashkenazi Jewish and 0.079% (12/15286) of Latino chromosomes by gnomAD (http://gnomad.broadinstitute.org, v.3.1.2). This frequency is low enough to be consistent with the frequency of Gitelman syndrome in the general population. Computational prediction tools and conservation analyses are consistent with pathogenicity. In summary, this variant meets criteria to be classified as pathogenic for autosomal recessive Gitelman syndrome. ACMG/AMP Criteria applied: PM3_VeryStrong, PM2_supporting, PP3. -

not provided Pathogenic:6

Pathogenic, no assertion criteria provided	research	Gharavi Laboratory, Columbia University	Sep 16, 2018	- -
Likely pathogenic, no assertion criteria provided	clinical testing	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	-	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Invitae	Jan 31, 2024	This sequence change replaces proline, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 643 of the SLC12A3 protein (p.Pro643Leu). This variant is present in population databases (rs140012781, gnomAD 0.2%). This missense change has been observed in individuals with Gitelman syndrome (PMID: 11168953, 11940055, 17654016, 21753071, 22169961). ClinVar contains an entry for this variant (Variation ID: 417863). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. -
Likely pathogenic, criteria provided, single submitter	clinical testing	GeneDx	May 31, 2023	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: 22169961, 11940055, 17654016, 19349556, 11168953, 15976513, 21753071, 22009145, 28947054, 21415153, 33585337, 31672324, 32129221, 34426522, 35753512, 35327948, 25990047, 37078890) -
Pathogenic, criteria provided, single submitter	clinical testing	Athena Diagnostics	Dec 22, 2020	This variant is statistically more frequent in affected individuals than in the general population and/or healthy controls and therefore is consistent with pathogenicity (http://gnomad.broadinstitute.org). 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. Computational tools predict that this variant is damaging. -
Pathogenic, no assertion criteria provided	clinical testing	Genome Diagnostics Laboratory, University Medical Center Utrecht	-	- -

Inborn genetic diseases Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Nov 05, 2020

The c.1928C>T (p.P643L) alteration is located in exon 16 (coding exon 16) of the SLC12A3 gene. This alteration results from a C to T substitution at nucleotide position 1928, causing the proline (P) at amino acid position 643 to be replaced by a leucine (L). Based on data from the Genome Aggregation Database (gnomAD) database, the SLC12A3 c.1928C>T alteration was observed in 0.02% (43/281436) of total alleles studied, with a frequency of 0.17% (18/10354) in the Ashkenazi Jewish subpopulation. This alteration has been reported in multiple patients with Gitelman syndrome in both the homozygous and compound heterozygous states (Cruz, 2001; Pantanetti, 2002; Fava, 2007; Roser, 2009; Balavoine, 2011; Glaudemans, 2012; Zahed, 2017). This amino acid position is highly conserved in available vertebrate species. The p.P643L alteration is predicted to be deleterious by in silico analysis. Based on the available evidence, this alteration is classified as pathogenic. -

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

Likely pathogenic, no assertion criteria provided

clinical testing

Sydney Genome Diagnostics, Children's Hospital Westmead

Oct 24, 2018

This patient is heterozygous for a likely pathogenic variant, c.1928C>T p.(Pro643Leu), in the SLC12A3 gene. This variant (dbSNP: rs140012787) has been reported in the ExAC database (http://exac.broadinstitute.org/) with a very low allele frequency of 0.018% (22 out of 119660 alleles). This variant has been previously reported in trans with other SLC12A3 variants in patients with Gitelman syndrome in the literature (Vargas-Poussou et al 2011 J Am Soc Nephrol 22:693-703). In addition, this variant has been reported in cis with SLC12A3 p.(Pro548Leu), and in trans with SLC12A3 p.(Gly439Ser), in a patient with remarkably severe Gitelman syndrome (Roser et al 2009 Hypertension 53:893-897) -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.84
BayesDel_addAF	Pathogenic	0.36	D
BayesDel_noAF	Pathogenic	0.58
CADD	Pathogenic	32
DANN	Pathogenic	1.0
DEOGEN2	Pathogenic	0.99	.;.;D;D
Eigen	Pathogenic	0.95
Eigen_PC	Pathogenic	0.86
FATHMM_MKL	Uncertain	0.95	D
LIST_S2	Pathogenic	0.99	D;D;D;D
M_CAP	Pathogenic	0.34	D
MetaRNN	Pathogenic	0.81	D;D;D;D
MetaSVM	Uncertain	0.53	D
MutationAssessor	Pathogenic	3.7	.;H;H;.
MutationTaster	Benign	1.0	D;D;D;D
PrimateAI	Uncertain	0.78	T
PROVEAN	Pathogenic	-9.6	D;D;D;D
REVEL	Pathogenic	0.85
Sift	Pathogenic	0.0	D;D;D;D
Sift4G	Pathogenic	0.0010	D;D;D;D
Polyphen		1.0	D;D;D;.
Vest4		0.98
MVP		0.98
MPC		0.48
ClinPred		0.99	D
GERP RS		5.1
Varity_R		0.85
gMVP		0.97

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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: rs140012781; hg19: chr16-56920278;