ClinVar Genomic variation as it relates to human health

Variant summary: HTRA1 c.854C>T (p.Pro285Leu) results in a non-conservative amino acid change in the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 4e-06 in 251248 control chromosomes (gnomAD). c.854C>T has been reported in the literature in the homozygous state in an individual affected with HTRA1-Related Cerebral Small Vessel Disease, with a brother who was similarly affected but was not available for genetic testing, and whose parents were heterozygous for the variant, the father reportedly having moderate symptoms (Chen_2013). The variant has also been reported in the heterozygous state in multiple individuals with a clinical diagnosis and/or features of HTRA1-Related Cerebral Small Vessel Disease, primarily with an adult onset of over 45 years of age (e.g. Nozaki_2016, Fokstuen_2016, Zhang_2022, Uemura_2023, He_2023). In one report the variant was found in several family members, including two siblings who both both presented with more severe symptoms such as gait disturbances, with white matter hyperintensities and lacunar infarcts at the ages of 59 and 64, whereas of the three younger relatives with the variant, one had alopecia and memory loss at age 30 and the other two (aged 28 and 14) did not manifest symptoms (He_2023). Altogether, these data indicate that the variant is very likely to be associated with disease. At least two publications report experimental evidence evaluating an impact on protein function (e.g. Nozaki_2016, Zhang_2022). The most pronounced variant effect results in 10%-<30% protease activity compared to the wild type protein. The following publications have been ascertained in the context of this evaluation (PMID: 23963851, 27353043, 36253578, 27164673, 36261288, 36047879, 36380532). Three submitters have cited clinical-significance assessments for this variant to ClinVar after 2014. Two submitters classified the variant as pathogenic/likely pathogenic and one classified it as uncertain significance. Based on the evidence outlined above, the variant was classified as pathogenic.

In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. This variant disrupts the p.Pro285 amino acid residue in HTRA1. Other variant(s) that disrupt this residue have been observed in individuals with HTRA1-related conditions (PMID: 26063658), which suggests that this may be a clinically significant amino acid residue. Experimental studies have shown that this missense change affects HTRA1 function (PMID: 27164673). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C15"). ClinVar contains an entry for this variant (Variation ID: 156100). This missense change has been observed in individuals with clinical features of HTRA1-related conditions (PMID: 23963851, 27164673, 27353043; Invitae). This variant is present in population databases (rs587776446, gnomAD 0.006%). This sequence change replaces proline, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 285 of the HTRA1 protein (p.Pro285Leu).