ClinVar Genomic variation as it relates to human health

Published functional studies demonstrate a damaging effect as D801N is suggested to affect the activity of the Na+/K+ ATPase pump and the substitution of an Aspartic acid for an Asparagine at position 801 is predicted to prevent the normal binding of potassium ions (Heinzen et al., 2012); Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 25662428, 22850527, 28716275, 32339621, 30891744, 31130284, 24631656, 22842232, 23409136, 25523819, 26417536, 27634470, 27312461, 24842602, 29396171, 29895895, 31061839, 31959558, 32280259, 32653672, 32581362, 33996181, 32005694, 33880529, 32913013, 30755392, 33762331, 33126486, 33098801, 27535533)

This variant is interpreted as a Pathogenic, for Alternating hemiplegia of childhood-2, in Autosomal Dominant manner. The following ACMG Tag(s) were applied: PP3 => Multiple lines of computational evidence support a deleterious effect on the gene or gene product. PS3 => Well-established functional studies show a deleterious effect (PMID:22842232). PM2 => Absent from controls (or at extremely low frequency if recessive) in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium. PS4-Moderate => PS4 downgraded in strength to Moderate (PMID:23409136) (PMID:22842232). PS2 => De novo (paternity and maternity confirmed) (PMID:23409136) (PMID:22842232).

This variant has been previously reported as a de novo heterozygous change in multiple unrelated individuals with alternating hemiplegia of childhood (PMID: 22850527, 22842232, 23409136). Functional studies indicate that this variant exhibits reduced ATPase activity and phosphorylation in cell culture (PMID: 24631656) and manifests behavioral abnormalities, spontaneous recurrent seizures, and paroxysmal motor abnormalities in mouse models (PMID: 25523819). This variant has been reported in the ClinVar database (Variation ID: 37107). It is absent from the ExAC and gnomAD population databases and thus is presumed to be rare. The c.2440G>A (p.Asp814Asn) variant is predicted by multiple in silico tools to have a deleterious effect on protein function. Analysis of the parental samples was negative for the variant, indicating this variant likely occurred as a de novo event. Based on the available evidence, the c.2440G>A (p.Asp814Asn) variant is classified as Pathogenic.

This variant was classified as: Pathogenic. The following ACMG criteria were applied in classifying this variant: PS1,PM2,PM5,PP2,PP3.

The variant has been previously reported as de novo in a similarly affected individual (PMID: 24842602, PS2_S). Same nucleotide change resulting in same amino acid change has been previously reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000037107, PMID:22850527, PS1_S). The variant has been observed in multiple (>3) similarly affected unrelated individuals(PMID: 24842602, PS4_S). In silico tool predictions suggest damaging effect of the variant on gene or gene product (REVEL: 0.905, 3CNET: 0.987, PP3_P). A missense variant is a common mechanism associated with Alternating hemiplegia of childhood 2 (PP2_P). It is not observed in the gnomAD v2.1.1 dataset (PM2_M). A different missense change at the same codon has been reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000210383, PMID: 24100174, 32913013, 26410222, 29915382,15260953, PM5_M). Therefore, this variant is classified as pathogenic according to the recommendation of ACMG/AMP guideline.

This ATP1A3 missense variant at c.2440G>A (p.D814N) was discovered on exome through the Texome Project (R01HG011795). The variant was de novo in the patient (PS2). It has been previously reported in individuals with Alternating hemiplegia of childhood 2 (PMID: 22842232, 22850527, 23409136). It has not been observed in gnomAD (PM2) and is predicted to be deleterious by multiple computational models (CADD: 29.400)(PP3). The evolutionary conservation of this residue is high. We classify this variant as pathogenic.

The ATP1A3 c.2401G>A variant has been reported to be de novo in heterozygous state in multiple individuals affected with alternating hemiplegia of childhood 2 (Heinzen et. al., 2012; Ishii et. al., 2013). Experimental studies have shown that this missense change p.Asp801Asn causes reduced ATPase enzyme activity (Heinzen et. al., 2012), loss of potassium binding (Weigand et. al., 2014), reduced forward cycling and dominant negativity (Ishii et. al., 2013) and spontaneous recurrent seizures in mice (Hunanyan et. al., 2015). Multiple missense substitutions at this codon (p.D801E; p.D801V) have also been reported in patients with the same disorder (Hoei-Hansen CE et. al., 2014, Panagiotakaki et. al., 2015). This suggests that the aspartic acid residue is critical for ATP1A3 protein function. The p.Asp801Asn variant is novel (not in any individuals) in gnomAD Exomes and 1000 Genomes. This variant has been reported to the ClinVar database as Pathogenic. The amino acid Asp at position 801 is changed to a Asn changing protein sequence and it might alter its composition and physicochemical properties. The amino acid change p.Asp801Asn in ATP1A3 is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. For these reasons, this variant has been classified as Pathogenic.

This sequence change replaces aspartic acid, which is acidic and polar, with asparagine, which is neutral and polar, at codon 801 of the ATP1A3 protein (p.Asp801Asn). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with alternating hemiplegia of childhood (PMID: 22842232, 22850527, 23409136, 24431296, 24842602). In at least one individual the variant was observed to be de novo. ClinVar contains an entry for this variant (Variation ID: 37107). 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 ATP1A3 protein function with a positive predictive value of 95%. Experimental studies have shown that this missense change affects ATP1A3 function (PMID: 22842232, 24631656, 25523819, 25681536). This variant disrupts the p.D801 amino acid residue in ATP1A3. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 24100174, 26410222). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic.

Criteria applied: PS2_VSTR,PS4,PM5_STR,PS3_MOD,PM2,PP2,PP3

ATP1A3: PS2:Very Strong, PM1, PM2, PM5, PS4:Moderate, PP2, PP3, PS3:Supporting

ACMG classification criteria: PS3 supporting, PS4 moderate, PM2 moderate, PM5 supporting, PM6 strong, PP3 supporting

The ATP1A3 c.2440G>A variant is predicted to result in the amino acid substitution p.Asp814Asn. Also known as NM_152296.4:c.2401G (p.Asp801Asn), this variant has been reported to occur de novo in multiple individuals with ATP1A3 diseases including alternating hemiplegia of childhood (AHC) (see for examples at Rosewich et al. 2012 PubMed ID: 22850527; Dong et al. 2020. PubMed: 32005694). This variant has not been reported in a large population database, indicating this variant is rare. This variant is interpreted as pathogenic.