NM_002775.4:c.1333G>A

HTRA1 · NP_002766.1:p.(Ala445Thr) · NM_002775.4

GRCh37: chr10:124273765 G>A · GRCh38: chr10:122514249 G>A

Gene: HTRA1 Transcript: NM_002775.4

Final call

VUS

PM1 supporting PM2 supporting BP4 supporting benign

Variant details

Gene

HTRA1

Transcript

NM_002775.4

Protein

NP_002766.1:p.(Ala445Thr)

gnomAD AF

0.00010410121612527838 (v4.1)

ClinVar

Uncertain significance

OncoKB

Classification rationale

Interpretation summary

Generated evidence synthesis

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).

Final determination: Generic ACMG/AMP 2015 fallback rules identified both pathogenic and benign evidence, so the overall classification remains Variant of Uncertain Significance because the evidence is conflicting.

Criteria assessment

ACMG/AMP criteria review

Criteria shown when status is available

All criteria require review: For research and educational purposes only.

Criterion	Status	Rationale	Evidence used
PVS1	N/A	PVS1 is reserved for null variants (nonsense, frameshift, canonical ±1,2 splice sites). NM_002775.4:c.1333G>A is a missense substitution (p.Ala445Thr) and does not fall into any PVS1 null-variant bucket. The generic PVS1 framework (PMC6185798) confirms ineligibility.	pvs1_generic_framework pvs1_variant_assessment
PS1	Not assessed	PS1 requires the same amino acid change (p.Ala445Thr) to have been reported as pathogenic via a different nucleotide change (e.g., c.1333G>C). No such variant was identified in ClinVar or the literature. This criterion cannot be assessed without a validated same-residue comparator.
PS2	Not met	No confirmed de novo occurrence of NM_002775.4:c.1333G>A with established maternity and paternity was identified in the literature or databases. PS2 requires a proven de novo event in a patient with the disease and no family history.
PS3	Not met	No well-established in vitro or in vivo functional studies specifically assessing the damaging effect of p.Ala445Thr on HTRA1 protease activity were identified. The ClinVar-associated PMIDs (25741868, 26467025) are methodological guidelines, not variant-specific functional studies.
PS4	Not met	No case-control study or statistical enrichment analysis has been performed for this variant in HTRA1-associated disease. ClinVar lists the variant as Uncertain significance from clinical laboratories, but without validated cohort data or quantified prevalence in affected individuals, PS4 cannot be applied.	clinvar
PS5	Not assessed	PS5 requires a different pathogenic missense change at the same amino acid residue (p.Ala445). No such pathogenic variant at residue 445 was identified in ClinVar, COSMIC, or the literature. PM5 candidate search also returned no comparators.
PM1	Met	The variant p.Ala445Thr is located within the peptidase S1 (trypsin-like serine protease) domain (residues 157–473), a well-established critical functional domain. Loss of HTRA1 protease activity through missense variants in this domain is the established mechanism for cerebral small vessel disease (CARASIL/CADASIL2). Published literature confirms that missense variants clustering in the protease domain are a common cause of monogenic CSVD.	pvs1_gene_context
PM2	Met	This variant is present at very low frequency in population databases. gnomAD v2.1 reports an allele frequency of 0.01237% (35/282,868 alleles, 0 homozygotes) and gnomAD v4.1 reports 0.01041% (168/1,613,814 alleles, 0 homozygotes). Both are well below the 0.1% threshold for PM2. The variant is absent from gnomAD-Canada v1.0. The highest subpopulation frequency is 0.028% (Admixed American, v2.1) and 0.083% (Middle Eastern, v4.1), both below 0.1%.	gnomad_v2 gnomad_v4
PM5	Not met	PM5 requires a different pathogenic missense change at the same amino acid residue. The systematic PM5 candidate search identified no same-residue pathogenic comparators for residue Ala445 in HTRA1.	pm5_candidates
PM6	Not met	No assumed de novo occurrence (without confirmation of parentage) has been reported for this variant. Exploratory evidence recovery found no such observations.
PP1	Not met	No co-segregation data for this variant in multiple affected family members were identified. PP1 requires the variant to co-segregate with disease in a family; no such published pedigree includes c.1333G>A.
PP2	Not met	PP2 requires a missense variant in a gene with a low rate of benign missense variation where missense is a common disease mechanism. While HTRA1 missense variants are a known mechanism for CSVD, no formal constraint metric (e.g., missense Z-score, gnomAD constraint) was evaluated to demonstrate a low rate of benign missense variation for this gene. The evidence is insufficient to apply PP2.
PP3	Not met	Multiple in silico predictors do not support a deleterious effect. REVEL score is 0.133 (well below the pathogenic threshold of 0.5). BayesDel score is -0.219368 (negative, indicating a benign prediction). SpliceAI predicts no splice impact (max delta score = 0.00). No in silico evidence supports pathogenicity.	revel bayesdel spliceai
PP4	Not met	No detailed patient phenotype or family history data specific to this variant were available. PP4 requires the variant to be observed in a patient whose phenotype or family history is highly specific for the disease. Insufficient clinical information was available.
PP5	Not met	No reputable source has classified this variant as pathogenic. ClinVar records 8 submissions, all reporting Uncertain significance. No expert panel or clinical laboratory has asserted a pathogenic or likely pathogenic classification. All associated PMIDs are policy/guideline documents that do not discuss this specific variant.	clinvar
BA1	Not met	BA1 requires an allele frequency >1% in any population database. gnomAD v2.1 total AF is 0.01237% and v4.1 total AF is 0.01041%. The highest subpopulation frequency is 0.083% (Middle Eastern, v4.1). All observed frequencies are well below 1%.	gnomad_v2 gnomad_v4
BS1	Not met	BS1 requires an allele frequency >0.3% in population databases. gnomAD v2.1 total AF is 0.01237% and v4.1 total AF is 0.01041%. The grpmax FAF is 0.0156% (v2.1) and 0.0326% (v4.1), both well below 0.3%. The highest subpopulation frequency is 0.083% (Middle Eastern, v4.1).	gnomad_v2 gnomad_v4
BS2	Not met	No observation of this variant in a healthy adult individual has been reported for a disorder assumed to be fully penetrant. BS2 requires documented presence in a healthy adult for a dominant disorder, which has not been established for c.1333G>A.
BS3	Not met	No well-established functional studies demonstrating a neutral effect of p.Ala445Thr on HTRA1 protease activity were identified. The ClinVar-associated PMIDs assigned to BS3 (25741868, 26467025) are ACMG/AMP and Sherloc methodological guidelines, not variant-specific functional studies.
BS4	Not met	No evidence of non-segregation with disease in affected members of a family was identified. BS4 requires the variant to be absent in an affected family member or present in unaffected family members, thereby reducing pathogenicity likelihood.
BP1	Not met	BP1 applies to a missense variant in a gene for which primarily truncating variants are known to cause disease. HTRA1-associated cerebral small vessel disease is caused by both missense and truncating variants; published cohorts (PMID:40607620, PMID:28126975) demonstrate that missense variants in the protease domain are a common pathogenic mechanism. Therefore, BP1 is not applicable.
BP2	Not met	No observation of this variant in trans with a dominant pathogenic variant or in cis with a recessive pathogenic HTRA1 variant was identified. Exploratory evidence recovery found no such phased observations.
BP4	Met	Multiple lines of computational evidence suggest no impact on the gene product. REVEL score is 0.133 (well below pathogenic threshold of 0.5). BayesDel score is -0.219368 (negative, consistent with a benign prediction). SpliceAI predicts no splice alteration (max delta = 0.00). These three independent in silico predictors converge on a neutral/benign interpretation.	revel bayesdel spliceai
BP5	Not met	No case was identified in which this variant co-occurs with an alternate molecular basis for the observed disease phenotype. BP5 requires observation in a patient with an alternative definitive genetic cause.
BP6	Not met	No reputable source has classified this variant as benign. BP6 requires classification as benign or likely benign by a reputable source (e.g., clinical laboratory with established methodology). All ClinVar submissions for Variation ID 877269 classify this variant as Uncertain significance.	clinvar
BP7	N/A	BP7 applies exclusively to synonymous (silent) variants. NM_002775.4:c.1333G>A is a missense variant resulting in p.Ala445Thr and is not eligible for BP7 assessment.

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