Across a selection of the available literature, the SLC12A3 c.2573T>A (p.Leu858His) variant, also known as c.2579T>A (p.Leu849His), has been reported in 10 studies and is found in a total of 13 patients with Gitelman syndrome, including two in a homozygous state, eight in a compound heterozygous state, and three in a heterozygous state where the second variant could not be identified (Monkawa et al. 2000; Fukuyama et al. 2003; Maki et al. 2004; Aoi et al. 2007; Tsutsui et al. 2011; Yagi et al. 2011; Imashuku et al. 2012; Ishimori et al. 2013; Miao et al. 2016; Mizokami et al. 2016). The p.Leu858His variant was absent from 400 control chromosomes in some studies (Monkawa et al. 2000; Fukuyama et al. 2003; Maki et al. 2004), however, the variant was detected in 47 out of 1852 healthy Japanese subjects in a heterozygous state (Tago et al. 2004) and is reported at a frequency of 0.01442 in the Japanese in Tokyo, Japan cohort of the 1000 Genomes Project. While this frequency is high, it is in alignment with the increased prevalence of Gitelman syndrome in Japan. In functional studies, sodium uptake of the p.Leu858His variant protein was found to be significantly reduced when expressed and evaluated in CHO cells, indicating that the p.Leu858His variant leads to loss of function (Naraba et al. 2005). Based on the evidence, the p.Leu858His 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.

Published functional studies demonstrate a damaging effect as p.(L858H) results in loss-of-function (Naraba et al., 2005); 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: 17873326, 33163079, 27173320, 26770037, 22802996, 23756661, 10616841, 15198479, 15069170, 21757836, 19489442, 31105122, 33328404, 21628937, 26041598, 33348466, 32884933, 30596175, 16471174)

Absent from controls (or at extremely low frequency if recessive) in Genome Aggregation Database, Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium.;For recessive disorders, detected in trans with a pathogenic variant.;Well-established in vitro or in vivo functional studies supportive of a damaging effect on the gene or gene product.;Multiple lines of computational evidence support a deleterious effect on the gene or gene product (conservation, evolutionary, splicing impact, etc).

This sequence change replaces leucine, which is neutral and non-polar, with histidine, which is basic and polar, at codon 858 of the SLC12A3 protein (p.Leu858His). This variant is present in population databases (rs185927948, gnomAD 0.09%). This missense change has been observed in individual(s) with SLC12A3-related conditions (PMID: 15069170, 21628937, 21757836, 26041598, 26770037). 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 p.Leu849His. ClinVar contains an entry for this variant (Variation ID: 225470). 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: 16471174). For these reasons, this variant has been classified as Pathogenic.

The c.2573T>A variant in SLC12A3 is a missense variant predicted to cause substitution of leucine to histidine at amino acid 858. This variant is rare in the general population with a frequency below the threshold expected for the associated phenotype(s). This variant has been observed in one or more individuals affected with the associated recessive disease, as either homozygous or compound heterozygous with a second variant (PMID: 21757836, 19508680). Computational prediction algorithms indicate this variant is likely to affect gene or protein function. Given the available evidence, this variant is classified as Pathogenic.

NM_001126108.2(SLC12A3):c.2546T>A (p.Leu849His) is a missense variant that results in the substitution of leucine with histidine. The affected residue or protein region has prior evidence supporting clinical relevance. This variant has been observed in affected individuals with related phenotype in a genotype context consistent with recessive disease (PMID: 12911530; PMID: 33328404; PMID: 30596175). This variant has been recurrently observed in individuals with related phenotype (PMID: 12911530; PMID: 33328404; PMID: 30596175). Multiple computational predictions support a deleterious effect on the gene or gene product. The variant is present at low frequency in population datasets. Based on the available data, this variant is classified as pathogenic.

The variant is observed at an extremely low frequency in the gnomAD v4.1.0 dataset (total allele frequency: 0.019%). Predicted Consequence/Location: Missense variant Functional studies provide strong evidence of the variant having a damaging effect on the gene or gene product (PMID: 16471174). In silico tool predictions suggest damaging effect of the variant on gene or gene product [REVEL: 0.78 (>=0.6, sensitivity 0.68 and specificity 0.92)]. The same nucleotide change resulting in the same amino acid change has been previously reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000225470 /PMID: 10616841 /3billion dataset). The variant has been reported to be in trans with a pathogenic variant as either compound heterozygous or homozygous in at least 2 similarly affected unrelated individuals (PMID: 15069170, 21628937, 26770037). The variant has been reported to co-segregate with the disease in at least one similarly affected relative/individual in the same family or similarly affected unrelated families (PMID: 15069170). Different missense changes at the same codon (p.Leu849Phe, p.Leu849Pro) have been reported to be associated with SLC12A3-related disorder (ClinVar ID: VCV002736354 /PMID: 22009145, 37702302). Therefore, this variant is classified as Pathogenic according to the recommendation of ACMG/AMP guideline.