ClinVar Genomic variation as it relates to human health

Same nucleotide change resulting in same amino acid change has been previously reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000006964, PMID:20074521). The variant has been observed in at least two similarly affected unrelated individuals (PMID: 20074521). Functional assays showed that the variant had moderate level of impact on gene/protein function (PMID: 20074521). In silico tool predictions suggest damaging effect of the variant on gene or gene product (REVEL: 0.867>=0.6). A missense variant is a common mechanism. It is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency:0.000004). Different pathogenic/likely pathogenic amino acid change has been reported with supporting evidence at the same codon (ClinVar ID: VCV000030275, PMID:20829227). Therefore, this variant is classified as pathogenic according to the recommendation of ACMG/AMP guideline.

For these reasons, this variant has been classified as Pathogenic. Experimental studies have shown that this missense change affects TUBB3 function (PMID: 20074521, 29382549, 31226147). Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be disruptive. ClinVar contains an entry for this variant (Variation ID: 6964). This missense change has been observed in individual(s) with TUBB3-related conditions (PMID: 20074521). In at least one individual the variant was observed to be de novo. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This sequence change replaces alanine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 302 of the TUBB3 protein (p.Ala302Thr).

The A302T pathogenic variant in the TUBB3 gene has been reported previously in three unrelated families with congenital fibrosis of the extraocular muscles type 3 (CFEOM3) (Tischfield et al., 2010). In vitro functional studies of A302T-TUBB3 showed disrupted tubulin heterdimer formation and altered microtubule dynamics compared to wild-type TUBB3 (Tischfield et al., 2010). The A302T variant was not observed in approximately 6500 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 A302T variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. This substitution occurs at a position that is conserved across species. A missense variant in the same residue (A302V) has been reported in a family with brain malformations, nystagmus and strabismus, thus supporting the functional importance of this residue (Poirier et al., 2010). We interpret A302T as a pathogenic variant.