NM_002775.4:c.1333G>A (p.Ala445Thr) is a missense variant in HTRA1 located within the peptidase S1 serine protease domain (residues 157–473), a well-established functional domain critical for HTRA1 protease activity. Loss-of-function missense variants in this domain are a known cause of cerebral small vessel disease including CARASIL and CADASIL2.

This variant is present at very low frequency in population databases: gnomAD v2.1 allele frequency is 0.012% (35/282,868 alleles, 0 homozygotes) and gnomAD v4.1 allele frequency is 0.010% (168/1,613,814 alleles, 0 homozygotes). The variant is absent from gnomAD-Canada. All frequencies fall well below the 0.1% PM2 threshold.

Multiple in silico predictors suggest a neutral effect: REVEL score is 0.133 (below pathogenic threshold), BayesDel score is −0.219 (negative, favoring benign), and SpliceAI predicts no splice alteration (max delta = 0.00). These orthogonal computational lines of evidence support a benign interpretation.

This variant has been reported in ClinVar (Variation ID 877269) as Uncertain significance by 8 clinical submitters with no expert panel review. No pathogenic or benign assertions have been made by a reputable source. All 16 associated PMIDs are policy or guideline documents unrelated to this specific variant.

No functional studies (PS3/BS3), case-control data (PS4), de novo observations (PS2/PM6), segregation data (PP1/BS4), or same-residue pathogenic comparators (PS5/PM5) were identified for this variant in the published literature or databases.

Applying generic ACMG/AMP 2015 combination rules: PM1_Supporting + PM2_Supporting versus BP4_Supporting results in two opposing supporting-level criteria. Since no criterion reaches moderate or higher strength on either side, and the evidence is balanced with low-confidence signals in both directions, the final classification defaults to Variant of Uncertain Significance (VUS).