ClinVar Genomic variation as it relates to human health

Published in vitro functional studies demonstrate that the presence of the R262H variant causes reduced binding of kinesin and non-motor proteins and exhibits altered polymerization dynamics (Minoura et al., 2016).; Not observed at significant frequency in large population cohorts (gnomAD); Missense variants in this gene are often considered pathogenic (HGMD); This variant is associated with the following publications: (PMID: 27046833, 20074521, 27428177, 28840640, 31226147, 26582918, 26775887, 34652576, 27535533)

The TUBB3 c.785G>A (p.Arg262His) variant is a missense variant that has been reported in two studies, in which it is found in a de novo heterozygous state in three individuals with a severe form of congenital fibrosis of the extraocular muscles (CFEOM). Another variant at the same amino acid position has also been reported in 11 families with a milder form of CFEOM (Tischfield et al. 2010; MacKinnon et al. 2014). The p.Arg262His variant was absent from 1700 control chromosomes and is not found in the Genome Aggregation Database in a region of good sequence coverage, so the variant is presumed to be rare. Functional studies in yeast demonstrate that compared to wild-type microtubules, the p.Arg262His microtubules have prolonged growth events, longer astral microtubules, and an altered rate of polymerization and depolymerization. In vivo assays further demonstrate that p.Arg262His leads to significantly reduced kinesin interaction on microtubules and modifies the microtubule dynamics at both filament ends (Tischfield et al. 2010; Ti et al. 2016; Minoura et al. 2016). In vitro and in vivo transfection of variant TUBB3 resulted in reduced axon growth; this phenotype was rescued by co-transfection of a modified kinesin (Minoura et al. 2016). The p.Arg262His variant is predicted to abolish the hydrogen bond of the H8-S7 loop of b-tubulin and affect the tertiary protein structure and motor protein interactions with microtubules (Tischfield et al. 2010). Based on the collective evidence and application of the ACMG criteria, the p.Arg262His variant is classified as pathogenic for TUBB3-related tubulinopathy.

This variant was determined to be pathogenic according to ACMG Guidelines, 2015 [PMID:25741868].

This variant has been previously reported as a heterozygous change in patients with congenital fibrosis of extraocular muscles (CFEOM; PMID: 20074521, 34652576). A different amino acid change at the same residue (p.Arg262Cys) has been previously reported in individuals with CFEOM (PMID: 200774521, 27428177, 28832562, 29453417). Functional studies demonstrated that the c.785G>A (p.Arg262His) variant impairs both the motility and ATPase activity of kinesin and microtubule dynamics, which is required for normal axonal growth and brain development (PMID: 26775887, 27046833, 31226147). The c.785G>A (p.Arg262His) variant is absent from the gnomAD population database and thus is presumed to be rare. The c.785G>A (p.Arg262His) variant affects a highly conserved amino acid and 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.785G>A (p.Arg262His) variant is classified as Pathogenic.

This missense change has been observed in individual(s) with clinical features of congenital fibrosis of the extraocular muscles (PMID: 20074521, 24612975, 34652576). ClinVar contains an entry for this variant (Variation ID: 219256). 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 TUBB3 protein function. Experimental studies have shown that this missense change affects TUBB3 function (PMID: 20074521, 26775887, 27046833). This variant disrupts the p.Arg262 amino acid residue in TUBB3. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 20074521, 29453417). 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. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces arginine, which is basic and polar, with histidine, which is basic and polar, at codon 262 of the TUBB3 protein (p.Arg262His).