rs371443644

chr16-56865414-C-T

Variant summary

Our verdict is Pathogenic. Variant got 16 ACMG points: 16P and 0B. PM1 PM2 PP3_Strong PP5_Very_Strong

The NM_001126108.2(SLC12A3):c.179C>T(p.Thr60Met) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000316 in 1,614,094 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★★). Synonymous variant affecting the same amino acid position (i.e. T60T) has been classified as Likely benign.

• Frequency:
  • Genomes: 𝑓 0.000033 (0 hom., cov: 33)
  • Exomes 𝑓: 0.000031 (0 hom.)
• Consequence: SLC12A3 NM_001126108.2 missense
• Clinical Significance: Pathogenic criteria provided, multiple submitters, no conflicts P:13
• 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 16 ACMG points.

• PM1: In a hotspot region, there are 2 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 0 benign, 3 uncertain in NM_001126108.2
• PM2: Very rare variant in population databases, with high coverage
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.972
• PP5: Variant 16-56865414-C-T is Pathogenic according to our data. Variant chr16-56865414-C-T is described in ClinVar as [Pathogenic]. Clinvar id is 101514.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-56865414-C-T is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC12A3	NM_001126108.2	c.179C>T	p.Thr60Met	missense_variant	1/26	ENST00000563236.6
SLC12A3	NM_000339.3	c.179C>T	p.Thr60Met	missense_variant	1/26
SLC12A3	NM_001126107.2	c.179C>T	p.Thr60Met	missense_variant	1/26
SLC12A3	NM_001410896.1	c.179C>T	p.Thr60Met	missense_variant	1/26

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC12A3	ENST00000563236.6	c.179C>T	p.Thr60Met	missense_variant	1/26	1	NM_001126108.2	A1
SLC12A3	ENST00000438926.6	c.179C>T	p.Thr60Met	missense_variant	1/26	1		A1
SLC12A3	ENST00000566786.5	c.179C>T	p.Thr60Met	missense_variant	1/26	1		P4
SLC12A3	ENST00000262502.5	c.179C>T	p.Thr60Met	missense_variant	1/26	5		A1

Frequencies

GnomAD3 genomes AF: 0.0000328 AC: 5 AN: 152228 Hom.: 0 Cov.: 33

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000147

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.0000557 AC: 14 AN: 251452 Hom.: 0 AF XY: 0.0000662 AC XY: 9 AN XY: 135912

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.0000289

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.000598

Gnomad SAS exome AF: 0.0000327

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00000879

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.0000315 AC: 46 AN: 1461866 Hom.: 0 Cov.: 32 AF XY: 0.0000316 AC XY: 23 AN XY: 727242

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.0000447

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.000428

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000243

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0000328 AC: 5 AN: 152228 Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3 AN XY: 74376

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000770

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000147

Gnomad4 OTH AF: 0.00

Alfa AF: 0.0000956 Hom.: 0

Bravo AF: 0.0000264

ExAC AF: 0.0000741 AC: 9

Asia WGS AF: 0.000577 AC: 2 AN: 3478

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:13

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Familial hypokalemia-hypomagnesemia Pathogenic:10

Pathogenic, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Apr 27, 2017	The SLC12A3 c.179C>T (p.Thr60Met) missense variant is well described in the literature and noted to be one of the most common pathogenic variants associated with Gitelman syndrome in the Asian population (Shao et al. 2012). The p.Thr60Met variant is described in at least eight studies in which it is found in a total of 35 patients, including in ten individuals in a homozygous state, in 20 individuals in a compound heterozygous state, and in five in a heterozygous state (Maki et al. 2004; Shao et al. 2008; Qin et al. 2009; Miao et al. 2009; Jiang et al. 2014; Kim et al. 2016; Miao et al. 2016; Ma et al. 2016). The variant was detected in a heterozygous state in four out of 510 control individuals and is reported at a frequency of 0.00092 in the East Asian population of the Exome Aggregation Consortium. Functional studies in transgenic mice demonstrated that the p.Thr60Met variant resulted in reduced targeting to the apical membranes of distal convoluted tubule cells due to impaired phosphorylation of the Thr60 residue (Yang et al. 2013). Functional studies in Xenopus demonstrated that the variant showed the same pattern of complex glycosylation and similar cell surface expression as wild type but the intrinsic activity of the protein was abolished (Miao et al. 2009). Based on the collective evidence, the p.Thr60Met 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	Apr 09, 2020	Based on the classification scheme VCGS_Germline_v1.1.1, this variant is classified as 5-Pathogenic. Following criteria are met: 0102 - Loss-of-function is a known mechanism of disease for this gene. (N) 0106 - This gene is known to be associated with autosomal recessive disease. (N) 0200 - Variant is predicted to result in a missense amino acid change from a threonine to a methionine (exon 1). (N) 0251 - Variant is heterozygous. (N) 0304 - Variant is present in gnomAD <0.01 for a recessive condition (18 heterozygotes, 0 homozygotes). (P) 0501 - Missense variant consistently predicted to be damaging by multiple in silico tools and is highly conserved with a moderate amino acid change. (P) 0600 - Variant is located in an annotated domain or motif (AA permease N-terminal domain; PDB, DECIPHER). (N) 0801 - Strong previous evidence of pathogenicity in multiple unrelated individuals with Gitelman syndrome. (PMID: 22934535) (P) 0902 - Moderate evidence of variant segregating with disease in a family with 3 affected individuals (PMID: 18287808). (P) 1101 - Very strong and specific phenotype match. (P) 1201 - Heterozygous variant detected in trans with a second pathogenic heterozygous variant in a recessive disease (observed in IGV). (P) 1208 - Inheritance information for this variant is not currently available. (N) Legend: (P) - Pathogenic, (N) - Neutral, (B) - Benign -
Pathogenic, no assertion criteria provided	clinical testing	Department of Pediatrics, Taizhou Central Hospital, Taizhou University Hospital	Feb 01, 2024	- -
Pathogenic, no assertion criteria provided	literature only	OMIM	Oct 01, 2013	- -
Pathogenic, criteria provided, single submitter	clinical testing	Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center	Aug 25, 2023	PS3, PM2, PM3_Strong, PP3 -
Pathogenic, criteria provided, single submitter	clinical testing	Fulgent Genetics, Fulgent Genetics	Mar 26, 2022	- -
Pathogenic, criteria provided, single submitter	clinical testing	Genome-Nilou Lab	Jul 15, 2021	- -
Pathogenic, no assertion criteria provided	clinical testing	Natera, Inc.	Sep 16, 2020	- -
Pathogenic, criteria provided, single submitter	clinical testing	3billion	Oct 02, 2021	The variant has been reported to be in trans with a pathogenic variant as either compound heterozygous or homozygous in at least 4 similarly affected unrelated individuals (PMID:27454426, 27453715, 27173320, 24776766, 19451210, PM3_VS). It is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: 0.0000636, PM2). In silico tool predictions suggest damaging effect of the variant on gene or gene product (REVEL: 0.899, 3Cnet: 0.995, PP3). Patient's phenotype is considered compatible with Gitelman syndrome (3billion dataset, PP4). Therefore, this variant is classified as pathogenic according to the recommendation of ACMG/AMP guideline. -
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, PM2, PP3, PP5 -

not provided Pathogenic:3

Pathogenic, criteria provided, single submitter	clinical testing	Invitae	Jan 11, 2024	This sequence change replaces threonine, which is neutral and polar, with methionine, which is neutral and non-polar, at codon 60 of the SLC12A3 protein (p.Thr60Met). This variant is present in population databases (rs371443644, gnomAD 0.08%). This missense change has been observed in individual(s) with Gitelman syndrome (PMID: 19207868, 19451210, 24776766, 27453715). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. This variant is also known as c.185C>T (p.T60M). ClinVar contains an entry for this variant (Variation ID: 101514). 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: 19451210, 23833262). For these reasons, this variant has been classified as Pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Apr 27, 2022	Reported multiple times in the homozygous or compound heterozygous state in unrelated patients with Gitelman syndrome (Maki et al., 2004; Lin et al., 2004; Lin et al., 2005; Shao et al., 2008a; Shao et al. 2008b; Qin et al., 2009; Miao et al., 2009; Jiang et al., 2014; Yang et al., 2013); Published functional studies demonstrate p.(T60M) results in nearly complete loss of intrinsic transporter activity (Miao et al., 2009); 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: 23833262, 25990047, 19207868, 27173320, 29093260, 30596175, 24776766, 27453715, 26825084, 27216017, 27454426, 18580052, 30413979, 31672324, 31398183, 33024574, 32884933, 33163079, 34348722, 27535533, 33735743, 22627394, 19451210, 15069170) -
Pathogenic, criteria provided, single submitter	clinical testing	Athena Diagnostics	Mar 21, 2014	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.58
BayesDel_addAF	Pathogenic	0.24	D
BayesDel_noAF	Pathogenic	0.48
Cadd	Pathogenic	26
Dann	Uncertain	1.0
Eigen	Pathogenic	0.70
Eigen_PC	Uncertain	0.64
FATHMM_MKL	Uncertain	0.94	D
LIST_S2	Pathogenic	0.97	D;D;D;D
M_CAP	Pathogenic	0.41	D
MetaRNN	Pathogenic	0.97	D;D;D;D
MetaSVM	Pathogenic	1.1	D
MutationAssessor	Uncertain	2.5	M;M;M;.
MutationTaster	Benign	1.0	D;D;D;D
PrimateAI	Uncertain	0.68	T
PROVEAN	Pathogenic	-5.0	D;D;D;D
Sift	Pathogenic	0.0	D;D;D;D
Sift4G	Pathogenic	0.0010	D;D;D;D
Polyphen		1.0	D;D;D;.
Vest4		0.96
MutPred		0.90		Loss of phosphorylation at T60 (P = 0.0568);Loss of phosphorylation at T60 (P = 0.0568);Loss of phosphorylation at T60 (P = 0.0568);Loss of phosphorylation at T60 (P = 0.0568);
MVP		0.99
MPC		0.48
ClinPred		0.82	D
GERP RS		5.4
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.93
gMVP		0.83

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: rs371443644; hg19: chr16-56899326;