16-56867150-G-C

Position:

• chr16-56867150-G-C

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM1 BP4_Moderate BS2

The ENST00000563236.6(SLC12A3):​c.363G>C​(p.Glu121Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00152 in 1,614,098 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

• Frequency:
  • Genomes: 𝑓 0.0010 (0 hom., cov: 33)
  • Exomes 𝑓: 0.0016 (2 hom.)
• Consequence: SLC12A3 ENST00000563236.6 missense
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:4 U:7 B:2
• Conservation: PhyloP100: 0.782

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 Likely_benign. Variant got -4 ACMG points.

• PM1: In a topological_domain Cytoplasmic (size 134) in uniprot entity S12A3_HUMAN there are 22 pathogenic changes around while only 6 benign (79%) in ENST00000563236.6
• BP4: Computational evidence support a benign effect (MetaRNN=0.07202932).
• BS2: High Homozygotes in GnomAdExome4 at 2 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC12A3	NM_001126108.2	c.363G>C	p.Glu121Asp	missense_variant	2/26	ENST00000563236.6	NP_001119580.2
SLC12A3	NM_000339.3	c.363G>C	p.Glu121Asp	missense_variant	2/26		NP_000330.3
SLC12A3	NM_001126107.2	c.360G>C	p.Glu120Asp	missense_variant	2/26		NP_001119579.2
SLC12A3	NM_001410896.1	c.360G>C	p.Glu120Asp	missense_variant	2/26		NP_001397825.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC12A3	ENST00000563236.6	c.363G>C	p.Glu121Asp	missense_variant	2/26	1	NM_001126108.2	ENSP00000456149	A1
SLC12A3	ENST00000438926.6	c.363G>C	p.Glu121Asp	missense_variant	2/26	1		ENSP00000402152	A1
SLC12A3	ENST00000566786.5	c.360G>C	p.Glu120Asp	missense_variant	2/26	1		ENSP00000457552	P4
SLC12A3	ENST00000262502.5	c.360G>C	p.Glu120Asp	missense_variant	2/26	5		ENSP00000262502	A1

Frequencies

GnomAD3 genomes AF: 0.000999 AC: 152 AN: 152210 Hom.: 0 Cov.: 33

Gnomad AFR AF: 0.000362

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00150

Gnomad ASJ AF: 0.000576

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.00162

Gnomad OTH AF: 0.000478

GnomAD3 exomes AF: 0.000927 AC: 232 AN: 250226 Hom.: 1 AF XY: 0.000982 AC XY: 133 AN XY: 135466

Gnomad AFR exome AF: 0.000248

Gnomad AMR exome AF: 0.000898

Gnomad ASJ exome AF: 0.000399

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.0000464

Gnomad NFE exome AF: 0.00167

Gnomad OTH exome AF: 0.000491

GnomAD4 exome AF: 0.00157 AC: 2302 AN: 1461770 Hom.: 2 Cov.: 32 AF XY: 0.00148 AC XY: 1074 AN XY: 727172

Gnomad4 AFR exome AF: 0.000269

Gnomad4 AMR exome AF: 0.000895

Gnomad4 ASJ exome AF: 0.000498

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000696

Gnomad4 FIN exome AF: 0.0000375

Gnomad4 NFE exome AF: 0.00195

Gnomad4 OTH exome AF: 0.00104

GnomAD4 genome AF: 0.000998 AC: 152 AN: 152328 Hom.: 0 Cov.: 33 AF XY: 0.000859 AC XY: 64 AN XY: 74486

Gnomad4 AFR AF: 0.000361

Gnomad4 AMR AF: 0.00150

Gnomad4 ASJ AF: 0.000576

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00162

Gnomad4 OTH AF: 0.000473

Alfa AF: 0.00169 Hom.: 0

Bravo AF: 0.00122

TwinsUK AF: 0.00162 AC: 6

ALSPAC AF: 0.00208 AC: 8

ESP6500AA AF: 0.000455 AC: 2

ESP6500EA AF: 0.00116 AC: 10

ExAC AF: 0.000758 AC: 92

Asia WGS AF: 0.000289 AC: 1 AN: 3478

EpiCase AF: 0.00147

EpiControl AF: 0.00148

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:4 Uncertain:7 Benign:2

Revision: criteria provided, conflicting classifications

Submissions by phenotype

Familial hypokalemia-hypomagnesemia Pathogenic:3 Uncertain:1

Likely pathogenic, criteria provided, single submitter	clinical testing	Fulgent Genetics, Fulgent Genetics	Jun 30, 2021	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Genome-Nilou Lab	Jul 15, 2021	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Jan 09, 2019	The SLC12A3 c.363G>C (p.Glu121Asp) variant has been reported in two studies and is found in a total of three probands with Gitelman syndrome in a compound heterozygous state (Glaudemans et al. 2012; Berry et al. 2013). Control data are unavailable for this variant, which is reported at a frequency of 0.00132 in the European (non-Finnish) population of the Exome Aggregation Consortium. Functional studies in Xenopus oocytes demonstrated proper localization but sodium uptake was significantly reduced compared to wild type (Glaudemans et al. 2012). Based on the evidence, the p.Glu121Asp variant is classified as likely pathogenic for Gitelman syndrome. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population. -
Uncertain significance, no assertion criteria provided	clinical testing	Natera, Inc.	Sep 16, 2020	- -

not provided Pathogenic:1 Uncertain:2 Benign:1

Uncertain significance, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Sep 19, 2022	This sequence change replaces glutamic acid, which is acidic and polar, with aspartic acid, which is acidic and polar, at codon 121 of the SLC12A3 protein (p.Glu121Asp). This variant is present in population databases (rs146632606, gnomAD 0.2%), and has an allele count higher than expected for a pathogenic variant. This missense change has been observed in individual(s) with Gitelman syndrome (PMID: 22009145, 23328711, 31672324). ClinVar contains an entry for this variant (Variation ID: 505768). 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 not expected to disrupt SLC12A3 protein function. Experimental studies have shown that this missense change affects SLC12A3 function (PMID: 22009145). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Uncertain significance, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Jan 29, 2024	The p.Glu121Asp variant in SLC12A3 has been reported in the compound heterozygous state in 6 individuals with symptoms or a diagnosis of Gitelman syndrome or urinary stone disease, at least 4 of whom carried a second disease-causing SLC12A3 variant (Glaudemans 2012 PMID: 22009145, Berry 2013 PMID: 23328711, Groopman 2019 PMID: 30586318, Hureaux PMID: 31672324, Cogal 2021 PMID: 34805638). In at least one of these individuals, the reported levels of urinary calcium were normal. This variant has also been identified in 0.16% (110/68042) of European chromosomes by the Genome Aggregation Database (gnomAD v.3.1.2, http://gnomad.broadinstitute.org). This variant has also been reported in ClinVar (Variation ID 505768). Computational prediction tools and conservation analyses do not provide strong support for or against an impact to the protein. In vitro functional studies provide some evidence that the p.Glu121Asp variant may impact protein function (Glaudemans 2012 PMID: 22009145); however, these types of assays may not accurately represent biological function. In summary, while there is some suspicion for a pathogenic role, the clinical significance of the p.Glu121Asp variant is uncertain. ACMG/AMP Criteria applied: PM3_Strong, PS3_Supporting. -
Likely benign, flagged submission	clinical testing	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	-	- -
Likely pathogenic, no assertion criteria provided	research	Gharavi Laboratory, Columbia University	Sep 16, 2018	- -

not specified Uncertain:2 Benign:1

Uncertain significance, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Sep 07, 2022	Variant summary: SLC12A3 c.363G>C (p.Glu121Asp) results in a conservative amino acid change in the encoded protein sequence. Five of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 0.00093 in 250226 control chromosomes in the gnomAD database, including 1 homozygote. This frequency does not allow conclusions about variant significance. c.363G>C has been reported in the literature in individuals with Gitelman syndrome, at-least one of whom reported normal levels of urinary calcium (examples: Glaudemans_2012, and Berry 2013) and chronic kidney disease/urinary stone disease (example: Groopman_2019, Cogal_2021). These reports do not provide unequivocal conclusions about association of the variant with Familial Hypokalemia-Hypomagnesemia (Gitelman syndrome). At least one publication reports experimental evidence evaluating an impact on protein function in the Xenopus laevis oocyte system (example: Glaudemans_ 2012). The most pronounced variant effect results in approximately 30% of normal thiazide-sensitive NaCl cotransporter (NCC) activity and normal localization to the plasma membrane. Six clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 and classified the variant as VUS (n=2) and likely pathogenic (n=4). Based on the evidence outlined above, the variant was classified as VUS-possibly pathogenic. -
Benign, flagged submission	clinical testing	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	-	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital	Aug 15, 2023	- -

Inborn genetic diseases Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Jul 27, 2021

The c.363G>C (p.E121D) alteration is located in exon 2 (coding exon 2) of the SLC12A3 gene. This alteration results from a G to C substitution at nucleotide position 363, causing the glutamic acid (E) at amino acid position 121 to be replaced by an aspartic acid (D). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

SLC12A3-related disorder Uncertain:1

Uncertain significance, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Jun 21, 2024

The SLC12A3 c.363G>C variant is predicted to result in the amino acid substitution p.Glu121Asp. This variant has been reported with a second SLC12A3 variant in at least 6 individuals with presumed Gitelman Syndrome (Glaudemans et al. 2012. PubMed ID: 22009145; Berry et al. 2013. PubMed ID: 23328711; Hureaux et al. 2019. PubMed ID: 31672324, supplementary data; Groopman et al. 2019. PubMed ID: 30586318, supplementary data). One individual with suspected urinary stone disease also harbored this variant in the heterozygous state along with a SLC34A1 variant (PHN133, Cogal et al. 2021. PubMed ID: 34805638). Functional studies indicate that this variant affects the thiazide-sensitive NaCl cotransporter (NCC) activities through reducing the sodium uptake (Glaudemans et al. 2012. PubMed ID: 22009145). This amino acid position is moderately conserved and Asp is located at this position in Tetraodon (Alamut Visual Plus v1.6.1). This variant is reported in 0.16% of alleles in individuals of European (non-Finnish) descent in gnomAD V2. In the more recent gnomAD V4 data, this variant is observed in 2454/1,614,098 (0.15%) alleles and in 2 homozygotes, which may be too common to be a primary cause of disease (https://gnomad.broadinstitute.org/variant/16-56867150-G-C?dataset=gnomad_r4). Although we suspect this variant could possibly contribute to SLC12A3-related disorders, given the conflicting evidence, the clinical significance of this variant is uncertain. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.075
BayesDel_addAF	Benign	-0.19	T
BayesDel_noAF	Uncertain	-0.050
CADD	Benign	15
DANN	Uncertain	0.99
DEOGEN2	Benign	0.15	.;.;T;T
Eigen	Benign	-0.14
Eigen_PC	Benign	0.037
FATHMM_MKL	Uncertain	0.92	D
LIST_S2	Benign	0.76	T;T;T;T
M_CAP	Benign	0.014	T
MetaRNN	Benign	0.072	T;T;T;T
MetaSVM	Benign	-1.1	T
MutationAssessor	Benign	1.1	.;L;L;.
MutationTaster	Benign	1.0	N;N;N;N
PrimateAI	Benign	0.40	T
PROVEAN	Benign	-0.25	N;N;N;N
REVEL	Benign	0.22
Sift	Benign	0.19	T;T;T;T
Sift4G	Benign	0.36	T;T;T;T
Polyphen		0.0	B;B;B;.
Vest4		0.67
MutPred		0.17		.;Gain of catalytic residue at G123 (P = 0.1393);Gain of catalytic residue at G123 (P = 0.1393);.;
MVP		0.86
MPC		0.081
ClinPred		0.013	T
GERP RS		4.7
Varity_R		0.10
gMVP		0.60

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.050		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: rs146632606; hg19: chr16-56901062;