Starting
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HTRA1
Final classification
VUS
HTRA1 c.1333G>A · p.Ala445Thr
HTRA1

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.

Gene
HTRA1
Transcript
NM_002775.4
HGVS · transcript:coding
NM_002775.4:c.1333G>A
Consequence
N/A
GRCh38
chr10:122514249 G>A
GRCh37
chr10:124273765 G>A
Basis gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PM1 supporting, PM2 supporting, BP4 supporting benign; combination = 2 supporting + 1 supporting benign, which maps to VUS because the evidence is conflicting.
gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PM1 supporting, PM2 supporting, BP4 supporting benign; combination = 2 supporting + 1 supporting benign, which maps to VUS because the evidence is conflicting.
Classification rationale
PM1PM2 BP4 VUS
HTRA1 c.1333G>A

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 CADASIL2.1 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.2 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.3 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.4 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).5

PM1 + PM2 + BP4 VUS
1 pvs1_gene_context
3 revelbayesdelspliceai ↗
Gene diagram · NM_002775.4 · variants mapped to exon structure
HTRA1 NM_002775.4
Fetching transcript structure from UCSC…
Applied criteria · 3 met · select any tile
Met
Not met
Not assessed
N/A
Strength very strong supporting
Pathogenic evidence
PVS
PS
PM
PP
Benign evidence
BA
BS
BP
Rationale
Select a criterion.
Sources
Evidence used
    Gaps remaining
      Rule
      Research & evidence
      Population frequency
      gnomAD v4.1 screenshot
      gnomAD v4.1
      gnomAD v2.1 screenshot
      gnomAD v2.1
      v4.1
      This variant is present in gnomAD v4.1 (AF= 0.000104101; MAF= 0.01041%, 168/1613814 alleles, homozygotes = 0) and has highest observed frequency in the Middle Eastern population (AF= 0.000829187; MAF= 0.08292%, 5/6030 alleles, homozygotes = 0); grpmax FAF= 0.00032642.
      v2.1
      This variant is present in gnomAD v2.1 (AF= 0.000123733; MAF= 0.01237%, 35/282868 alleles, homozygotes = 0) and has highest observed frequency in the Admixed American population (AF= 0.000282167; MAF= 0.02822%, 10/35440 alleles, homozygotes = 0); grpmax FAF= 0.00015644.
      🇨🇦 CA
      This variant is absent from gnomAD-Canada.
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      0.01% · 168 / 1,613,814
      0 hom · FAF 0.033%
      Middle Eastern
      5 / 6,030
      0.083%
      Remaining individuals
      21 / 62,492
      0.034%
      African/African American
      20 / 75,008
      0.027%
      Admixed American
      13 / 60,014
      0.022%
      European (non-Finnish)
      105 / 1,179,802
      0.0089%
      South Asian
      3 / 91,064
      0.0033%
      East Asian
      1 / 44,866
      0.0022%
      + 3 not observed (European (Finnish), Amish, Ashkenazi Jewish)
      gnomAD v2.1
      0.012% · 35 / 282,868
      0 hom · FAF 0.016%
      Admixed American
      10 / 35,440
      0.028%
      Remaining individuals
      2 / 7,224
      0.028%
      African/African American
      5 / 24,958
      0.02%
      European (non-Finnish)
      17 / 129,188
      0.013%
      South Asian
      1 / 30,616
      0.0033%
      + 3 not observed (Ashkenazi Jewish, East Asian, European (Finnish))
      gnomAD Canada 🇨🇦
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      ClinVar screenshot
      ClinVar
      This variant has been reported in ClinVar as Uncertain significance (7 clinical laboratories). (ClinVarID = 877269)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.133. BayesDel score = -0.219368.
      Functional No data
      No calibrated functional assay or RNA evidence was identified for this variant.
      OncoKB ↗
      COSMIC screenshot
      COSMIC
      Cancer hotspots screenshot
      Cancer hotspots
      Somatic evidence Not in COSMIC / hotspots
      COSMIC
      This variant does not lie in a statistically significant hotspot. This variant has previously been reported in somatic cancers (COSMIC; COSV64564366, n = 1 times).
      Hotspots
      This variant does not lie in a statistically significant hotspot.
      Literature · how each cited paper was used
      2papers cited
      Each card is an audit: what was searched, what was found, whether it names the variant, which criteria it fed, and why. 14 further PMIDs triaged but not cited — see Sources & References.
      PMID 28126975
      Found
      HTRA1 loss of protease activity via mutations in the protease domain causes CARASIL.
      Applied to
      PM1 supports · met
      PMID 40607620
      Found
      Heterozygous HTRA1 missense variants cause autosomal dominant CSVD (CADASIL2) all 15 variants were functionally validated in the protease domain.
      Applied to
      PM1 supports · met
      Sources & reference links
      7Sources
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots
      Triaged references · 14 PMIDs not cited in assessment
      23619275 ↗ ACMG position statement on prenatal/preconception expanded carrier screening. CLINVAR
      23652378 ↗ A framework to start the debate on neonatal screening policies in the EU: an Expert Opinion Document. CLINVAR
      25626707 ↗ Whole-genome sequencing in newborn screening? A statement on the continued importance of targeted approaches in newborn screening programmes. CLINVAR
      25730230 ↗ Expanded carrier screening in reproductive medicine-points to consider: a joint statement of the American College of Medical Genetics and Genomics, American College of Obstetricians and Gynecologists, National Society of Genetic Counselors, Perinatal Quality Foundation, and Society for Maternal-Fetal Medicine. CLINVAR
      25741868 ↗ Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. CLINVAR
      26467025 ↗ A Standardized DNA Variant Scoring System for Pathogenicity Assessments in Mendelian Disorders. CLINVAR
      20437615 ↗ PMID:20437615 CLINVAR
      23169492 ↗ The perspective from EASAC and FEAM on direct-to-consumer genetic testing for health-related purposes. CLINVAR
      22947299 ↗ Specific guidelines for assessing and improving the methodological quality of economic evaluations of newborn screening. CLINVAR
      23037933 ↗ Including the initial newborn screening bloodspot collection device serial number on birth certificates: basis and recommendations from the Secretary of Health and Human Services' Advisory Committee on Heritable Disorders in Newborns and Children. CLINVAR
      23881473 ↗ Newborn screening: education, consent, and the residual blood spot. The position of the national society of genetic counselors. CLINVAR
      24022298 ↗ Offering prenatal diagnostic tests: European guidelines for clinical practice [corrected]. CLINVAR
      24394680 ↗ Parental permission for pilot newborn screening research: guidelines from the NBSTRN. CLINVAR
      28492532 ↗ Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. CLINVAR