ClinVar Genomic variation as it relates to human health

Published functional studies suggest the E288K variant may affect protein processing (Oegema et al., 2015); The majority of missense variants in this gene are considered pathogenic (HGMD); Not observed in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 28503613, 29261186, 31269740, 26130693, 28677066, 30667171, 32570172, 32901917)

Same nucleotide change resulting in same amino acid change has been previously reported as pathogenic/likely pathogeic with strong evidence and some affected individual has been obsered as de novoo (ClinVar ID: VCV000384329.4, PMID:32570172, PS1 and PS2). It is not observed in the gnomAD v2.1.1 dataset (PM2). A different missense change at the same codon (p.Glu288Ala) has been reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000931842.2, PM5). The variant was observed as assumed (i.e. paternity and maternity not confirmed) de novoo (3billion dataset, PM6). In silico tool predictions suggest damaging effect of the variant on gene or gene product (REVEL: 0.873, 3Cnet: 0.987, PP3). Patient's phenotype is considered compatible with Cortical dysplasia, complex, with other brain malformations 1 (3billion dataset, PP4). Therefore, this variant is classified as likely pathogenic according to the recommendation of ACMG/AMP guideline.

Variant summary: TUBB3 c.862G>A (p.Glu288Lys) results in a conservative amino acid change located in the Tubulin/FtsZ, 2-layer sandwich domain (IPR018316) of the encoded protein sequence. Three of five in-silico tools predict a damaging effect of the variant on protein function. The variant was absent in 250300 control chromosomes (gnomAD). c.862G>A has been reported in the literature in multiple individuals affected with Cortical Dysplasia, Complex, With Other Brain Malformations 1, including de novo occurrences (Oegema_2015, Romaniello_2017, Boissel_2017, Accogli_2020, Seo_2020). These data indicate that the variant is very likely to be associated with disease. At least one functional study reports experimental evidence evaluating an impact on protein function and this variant did not incorporate into microtubules (Oegema_2015). Three ClinVar submitters (evaluation after 2014) cite this variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic.

For these reasons, this variant has been classified as Pathogenic. Experimental studies have shown that this missense change affects TUBB3 function (PMID: 26130693). 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. ClinVar contains an entry for this variant (Variation ID: 384329). This missense change has been observed in individual(s) with cortical malformations (PMID: 26130693, 29261186). In at least one individual the variant was observed to be de novo. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces glutamic acid, which is acidic and polar, with lysine, which is basic and polar, at codon 288 of the TUBB3 protein (p.Glu288Lys).

Based on the classification scheme VCGS_Germline_v1.3.5, this variant is classified as Pathogenic. Following criteria are met: 0104 - Dominant negative is a known mechanism of disease in this gene and is associated with cortical dysplasia, complex, with other brain malformations 1 (MIM#614039) and fibrosis of extraocular muscles, congenital, 3A (MIM#600638) (PMID: 31219644). (I) 0107 - This gene is associated with autosomal dominant disease. (I) 0200 - Variant is predicted to result in a missense amino acid change from glutamic acid to lysine. (I) 0251 - This variant is heterozygous. (I) 0301 - Variant is absent from gnomAD (v2, v3 and v4). (SP) 0502 - Missense variant with conflicting in silico predictions and uninformative conservation. (I) 0600 - Variant is located in the annotated tubulin C-terminal domain (DECIPHER). (I) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals. It has been reported in multiple affected individuals, including multiple de novo occurences (PMIDs: 32570172, 29261186, 26130693; DECIPHER). In addition, it has been classified as pathogenic and likely pathogenic by multiple clinical laboratories (ClinVar). (SP) 1203 - This variant has been shown to be de novo in the proband (parental status confirmed by trio analysis). (SP) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign