rs147901432

Positions:

• chr16-56885364-G-A

Variant summary

Our verdict is Pathogenic. Variant got 16 ACMG points: 16P and 0B. PM2 PM5 PP3_Strong PP5_Very_Strong

The NM_001126108.2(SLC12A3):​c.1925G>A​(p.Arg642His) variant causes a missense, splice region change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000285 in 1,543,980 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 14/25 in silico tools predict a damaging outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Pathogenic (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R642C) has been classified as Pathogenic.

• Frequency:
  • Genomes: 𝑓 0.000033 (0 hom., cov: 32)
  • Exomes 𝑓: 0.000028 (0 hom.)
• Consequence: SLC12A3 NM_001126108.2 missense, splice_region
• Scores: Splicing: ADA: 1.000
• Clinical Significance: Pathogenic criteria provided, multiple submitters, no conflicts P:8
• Conservation: PhyloP100: 9.94

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.

• PM2: Very rare variant in population databases, with high coverage
• PM5: Other missense variant is known to change same aminoacid residue: Variant chr16-56885363-C-T is described in ClinVar as [Pathogenic]. Clinvar id is 944812.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• PP3: Splicing scoreres supports a deletorius effect: Scorers claiming Pathogenic: dbscSNV1_ADA, dbscSNV1_RF, max_spliceai. No scorers claiming Uncertain. No scorers claiming Benign.
• PP5: Variant 16-56885364-G-A is Pathogenic according to our data. Variant chr16-56885364-G-A is described in ClinVar as [Pathogenic]. Clinvar id is 319909.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC12A3	NM_001126108.2	c.1925G>A	p.Arg642His	missense_variant, splice_region_variant	15/26	ENST00000563236.6
SLC12A3	NM_000339.3	c.1925G>A	p.Arg642His	missense_variant, splice_region_variant	15/26
SLC12A3	NM_001126107.2	c.1922G>A	p.Arg641His	missense_variant, splice_region_variant	15/26
SLC12A3	NM_001410896.1	c.1922G>A	p.Arg641His	missense_variant, splice_region_variant	15/26

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC12A3	ENST00000563236.6	c.1925G>A	p.Arg642His	missense_variant, splice_region_variant	15/26	1	NM_001126108.2	A1
SLC12A3	ENST00000438926.6	c.1925G>A	p.Arg642His	missense_variant, splice_region_variant	15/26	1		A1
SLC12A3	ENST00000566786.5	c.1922G>A	p.Arg641His	missense_variant, splice_region_variant	15/26	1		P4
SLC12A3	ENST00000262502.5	c.1922G>A	p.Arg641His	missense_variant, splice_region_variant	15/26	5		A1

Frequencies

GnomAD3 genomes AF: 0.0000329 AC: 5 AN: 152156 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.0000483

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.0000941

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0000147

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.0000280 AC: 39 AN: 1391706 Hom.: 0 Cov.: 28 AF XY: 0.0000247 AC XY: 17 AN XY: 687290

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.0000279

Gnomad4 SAS exome AF: 0.0000126

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000336

Gnomad4 OTH exome AF: 0.0000173

GnomAD4 genome AF: 0.0000328 AC: 5 AN: 152274 Hom.: 0 Cov.: 32 AF XY: 0.0000537 AC XY: 4 AN XY: 74450

Gnomad4 AFR AF: 0.0000481

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.0000941

Gnomad4 NFE AF: 0.0000147

Gnomad4 OTH AF: 0.00

Alfa AF: 0.0000475 Hom.: 0

Bravo AF: 0.0000151

ESP6500AA AF: 0.00 AC: 0

ESP6500EA AF: 0.000118 AC: 1

ExAC AF: 0.0000392 AC: 4

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:8

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Familial hypokalemia-hypomagnesemia Pathogenic:6

Pathogenic, criteria provided, single submitter	clinical testing	Revvity Omics, Revvity	Feb 20, 2021	- -
Pathogenic, no assertion criteria provided	clinical testing	Natera, Inc.	Sep 16, 2020	- -
Pathogenic, criteria provided, single submitter	clinical testing	Genome-Nilou Lab	Jul 15, 2021	- -
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, PM5,PP3, PP5 -
Pathogenic, criteria provided, single submitter	clinical testing	Fulgent Genetics, Fulgent Genetics	May 06, 2022	- -
Pathogenic, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Apr 27, 2017	Across a selection of the available literature, the SLC12A3 c.1925G>A (p.Arg642His) missense variant has been identified in a homozygous state in three patients with Gitelman syndrome from two families, in a compound heterozygous state in eight patients, and in a heterozygous state in at least one patient (Lemmink et al. 1998; Calò et al. 2001; Syren et al. 2002; Colussi et al. 2007; Riveira-Munoz et al. 2007; Ji et al. 2008; Coto et al. 2009; Balavoine et al. 2011; Vigano et al. 2013; Davis et al. 2013; Makino et al. 2014). The variant has also been reported in a heterozygous state in at least three unaffected family members (Coto et al. 2009; Makino et al. 2014). The variant was absent from 3150 control individuals, 3125 of whom were participants in the Framingham Heart Study (Lemmink et al. 1998; Ji et al. 2008), and is reported at a frequency of 0.00012 in the European American population of the Exome Sequencing Project. This frequency is based on one allele only, in a region of poor sequencing coverage. The p.Arg642His variant is located in a conserved residue in an apparent mutation hotspot where two other missense variants have also been identified resulting in substitution of the Arg642 residue. Analysis of cDNA performed by two independent groups demonstrated that the variant caused aberrant splicing, producing a correctly spliced transcript and a second transcript containing an inserted intronic sequence which resulted in a frameshift, present at 32% of the normal transcript (Riveira-Munoz et al. 2007; Coto et al. 2009). Based on the collective evidence, the p.Arg643His 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. -

not provided Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Athena Diagnostics	Aug 15, 2019	Not found in the gnomAD data set. Found in at least one symptomatic patient. Predicted to have a damaging effect on the protein. Predicted to negatively affect a known splice site. Statistically enriched in patients compared to ethnically matched controls. Occurs in three or more cases with a recessive pathogenic variant in the same gene. Moderate co-segregation with disease, and data include affected and unaffected individuals from a single family. -
Pathogenic, criteria provided, single submitter	clinical testing	Invitae	Jan 11, 2024	This sequence change replaces arginine, which is basic and polar, with histidine, which is basic and polar, at codon 642 of the SLC12A3 protein (p.Arg642His). This variant also falls at the last nucleotide of exon 15, which is part of the consensus splice site for this exon. This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with Gitelman's syndrome (PMID: 9734597, 17699451, 30413979). 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. This variant is also known as 1950G>A. ClinVar contains an entry for this variant (Variation ID: 319909). 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. Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.67
BayesDel_addAF	Pathogenic	0.57	D
BayesDel_noAF	Pathogenic	0.58
CADD	Pathogenic	36
DANN	Pathogenic	1.0
DEOGEN2	Pathogenic	0.96	.;.;D;D
Eigen	Pathogenic	1.0
Eigen_PC	Pathogenic	0.95
FATHMM_MKL	Pathogenic	0.98	D
LIST_S2	Pathogenic	0.99	D;D;D;D
M_CAP	Uncertain	0.26	D
MetaRNN	Pathogenic	0.89	D;D;D;D
MetaSVM	Uncertain	0.31	D
MutationAssessor	Pathogenic	3.6	.;H;H;.
MutationTaster	Benign	1.0	D;D;D;D
PrimateAI	Uncertain	0.73	T
PROVEAN	Pathogenic	-4.8	D;D;D;D
REVEL	Pathogenic	0.70
Sift	Pathogenic	0.0	D;D;D;D
Sift4G	Uncertain	0.041	D;D;D;D
Polyphen		1.0	D;D;D;.
Vest4		0.86
MVP		0.99
MPC		0.53
ClinPred		1.0	D
GERP RS		5.4
Varity_R		0.85
gMVP		0.95

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	1.0
SpliceAI score (max)		0.51		Details are displayed if max score is > 0.2
DS_DL_spliceai		0.51		Position offset: 0

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

Publications

LitVar

Other links and lift over

dbSNP: rs147901432; hg19: chr16-56919276;