ClinVar Genomic variation as it relates to human health

Variant summary: Variant summary: The ATP7B c.2906G>A (p.Arg969Gln) variant involves the alteration of a highly conserved nucleotide. The variant is located within the putative ATP binding site of the conserved P-type_ATPase_Cu-like domain and 3/5 in silico tools predict a damaging outcome for this variant. These predictions were confirmed by the functional studies, where R969Q was shown to markedly affect copper transport and lead to hyperphosphorylation (Huster, 2012). This variant was found in 10/277242 control chromosomes at a frequency of 0.000036, which does not exceed the estimated maximal expected allele frequency of a pathogenic ATP7B variant (0.0054006). The variant was identified in multiple affected individuals with clinically and biochemically confirmed Wilsons disease (WD). In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as pathogenic. Taken together, this variant is classified as Pathogenic.

This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 969 of the ATP7B protein (p.Arg969Gln). This variant is present in population databases (rs121907996, gnomAD 0.01%). This missense change has been observed in individual(s) with Wilson disease (PMID: 8533760, 9801873, 17325640, 20517649, 22308153, 26819605). This variant is also known as p.Arg970Gln. ClinVar contains an entry for this variant (Variation ID: 3860). 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 ATP7B protein function with a negative predictive value of 80%. Experimental studies are conflicting or provide insufficient evidence to determine the effect of this variant on ATP7B function (PMID: 22240481, 22692182). For these reasons, this variant has been classified as Pathogenic.

The p.Arg969Gln variant in ATP7B has been reported in >20 probands with Wilson disease, including at least 13 homozygotes and 14 compound heterozygotes (Ferenci 2014), and has been reported in ClinVar (Variation ID 3860). It has also been identified in 3/30600 South Asian chromosomes by gnomAD (http://gnomad.broadinstitute.org). However, this frequency is low enough to be consistent with a recessive carrier frequency. Computational prediction tools and conservation analysis suggest that this variant may impact the protein, though this information is not predictive enough to determine pathogenicity. In vitro functional studies provide some evidence that this variant impacts protein function (Huster 2012). In summary, this variant meets criteria to be classified as pathogenic for autosomal recessive Wilson Disease. ACMG/AMP Criteria applied: PM3_VeryStrong, PM2, PS3_Supporting, PP3.

Criteria applied: PS3, PM5, PM3_VSTR,PM2_SUP,PP3,PP4

ATP7B: PM3:Very Strong, PM2, PM5, PP4, PS3:Supporting

The R969Q pathogenic variant in the ATP7B gene has been reported previously, using alternate nomenclature A970Q, in association with Wilson disease when present in the homozygous state or when in trans with another disease-causing variant (Figus et al., 1995). The R969Q variant was not observed in approximately 6,200 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. The R969Q variant is a semi-conservative amino acid substitution, which may impact secondary protein structure as these residues differ in some properties. This substitution occurs at a position that is conserved across species. Functional studies show R969Q had a significant decrease in copper uptake compared to wild type (Huster et al., 2012). Missense variants in the same and nearby residues (R969W, A971V, T974M) have been reported in the Human Gene Mutation Database in association with Wilson disease (Stenson et al., 2014), supporting the functional importance of this region of the protein. We interpret R969Q as a pathogenic variant.

PS3, PS4_moderate, PM2, PP3, PP4

The ATP7B c.2906G>A variant is predicted to result in the amino acid substitution p.Arg969Gln. This variant has been reported in the homozygous state and in the heterzogyous state with a second pathogenic variant in multiple individuals with Wilson disease (see for example, Figus et al. 1995. PubMed ID: 8533760; Panagiotakaki et al. 2004. PubMed ID: 15523622; Zhang et al. 2022. PubMed ID: 35220961). Although one in vitro study found the p.Arg969Gln variant had copper transport activity similar to wild type (Schushan et al. 2012. PubMed ID: 22692182), two other studies have reported moderate to complete loss of transport function (Huster et al. 2012. PubMed ID: 22240481; Das et al. 2022. PubMed ID: 35762218). Furthermore, ATP7A protein with the p.Arg969Gln variant has been shown to have reduced expression relative to wild type and improper cellular localization to the endoplasmic reticulum (Das et al. 2022. PubMed ID: 35762218). This variant is reported in 0.0098% of alleles in individuals of South Asian descent in gnomAD. Of note, a different missense variant at the same amino acid position (p.Arg969Trp) has also been reported in an individual with Wilson disease (Lepori et al. 2007. PubMed ID: 17949296). Taken together, this variant is interpreted as pathogenic.

The specific mutation is seen to affect the ATP7B in certain populations and in turn lowering ceruloplasmin levels https://www.nature.com/articles/s41598-021-87000-9