Overview #
The PP2 and BP1 criteria assess whether missense variants are a common or unlikely disease mechanism for a specific gene.
By analyzing gene-level tolerance to missense variation and the known mechanism of pathogenicity, these criteria provide valuable context for interpreting missense variants within disease-associated genes.
1. What Are PP2 and BP1? #
| Criterion | Definition | Evidence Direction |
| PP2 – Pathogenic Supporting 2 | “Missense variant in a gene that has a low rate of benign missense variation and in which missense variants are a common mechanism of disease.” | Supports pathogenicity when missense variation is known to cause disease in a gene that is intolerant to benign missense changes. |
| BP1 – Benign Supporting 1 | “Missense variant in a gene for which primarily truncating variants are known to cause disease.” | Supports benignity when disease-causing mechanisms for the gene are predominantly loss-of-function (LoF) and not missense-mediated. |
These criteria must always be interpreted within the gene-specific context — considering both the known pathogenic mechanism and population-level missense constraint.
2. SeqSMART’s Gene-Specific Evaluation Framework #
SeqSMART determines the applicability of PP2 and BP1 using a statistical and data-driven model that integrates curated information from ClinVar and gnomAD.
This model evaluates each gene’s pathogenic missense burden, pathogenic-to-benign ratio, and tolerance to missense variation.
3. PP2 – Missense Variants as a Common Pathogenic Mechanism #
For PP2 to apply, the gene must demonstrate clear evidence that missense variants commonly lead to disease.
SeqSMART considers PP2 met when two or more of the following three conditions are satisfied:
Condition 1: ClinVar Missense Burden #
- The gene contains ≥10 missense variants classified as Pathogenic (P) or Likely Pathogenic (LP) in ClinVar.
- This ensures that the gene has sufficient historical evidence linking missense variation to disease.
Condition 2: Pathogenic-to-Benign Ratio #
- SeqSMART calculates the ratio of pathogenic missense variants to benign missense variants for each gene.
- If the P/LP : B/LB ratio ≥ 3:1, the gene is considered to have a strong bias toward pathogenic missense events.
- This ratio filters out genes with frequent benign variation, focusing on those with selective missense intolerance.
Condition 3: Genomic Constraint (gnomAD Missense z-Score) #
- Using gnomAD v2/v3 constraint data, SeqSMART retrieves the missense z-score, a population-level measure of gene intolerance.
- If z-score > 3.09, the gene is highly constrained for missense variation — indicating that missense changes are rarely tolerated and likely pathogenic.
✅ If at least two of the three conditions are satisfied, PP2 is automatically applied to the missense variant.
4. BP1 – Missense Variants Unlikely to Be Pathogenic #
BP1 applies when a gene’s known disease mechanism involves loss-of-function (LoF) variants, and missense changes rarely cause disease.
SeqSMART applies BP1 when both of the following conditions are met:
Rule 1: Absence of Pathogenic Missense Variants #
- The gene contains no ClinVar missense variants classified as Pathogenic (P) or Likely Pathogenic (LP).
- This absence indicates that missense variants have not been implicated in disease causation.
Rule 2: Loss-of-Function Mechanism Dominance #
- The gene’s known pathogenic mechanism is LoF-based — typically involving nonsense, frameshift, or canonical splice-site variants.
- SeqSMART determines this using structured gene–disease mechanism databases and existing ClinVar annotations.
If both conditions hold true and the variant under review is a missense substitution, BP1 is marked as met (Supporting).
5. Data Sources and Quality Control #
SeqSMART relies on continuously updated and validated data sources to ensure accuracy and reproducibility:
| Source | Purpose |
| ClinVar | To identify and classify known pathogenic and benign missense variants per gene. |
| gnomAD v2/v3 | To derive missense constraint z-scores (population-level intolerance metrics). |
| SeqSMART internal models | To cross-check and flag genes with conflicting or uncertain variant interpretations. |
Genes with ambiguous data or conflicting ClinVar entries are excluded from automatic PP2/BP1 assignment to maintain high-confidence classifications.
6. Transparency and Manual Control #
SeqSMART ensures full visibility into how PP2 or BP1 were applied:
- Gene-Level Metrics: Users can view the number of known pathogenic and benign missense variants for each gene.
- Pathogenic-to-Benign Ratio: Displayed numerically with the applied threshold.
- gnomAD Constraint Score: Shown alongside reference version and percentile ranking.
- Manual Override: Users may accept, remove, or adjust PP2/BP1 manually if institutional data or literature provides stronger evidence.
Every action is logged in the case’s audit trail with author identity and timestamp, ensuring full traceability.
7. Important Considerations #
- PP2 and BP1 apply only to missense variants.
- PP2 requires at least moderate confidence in a gene’s established missense pathogenicity mechanism.
- BP1 should not be used in genes with both LoF and missense mechanisms contributing to disease (e.g., TP53, BRCA1).
- SeqSMART automatically avoids applying either rule to genes with mixed or uncertain molecular mechanisms.
Summary #
SeqSMART evaluates PP2 and BP1 through a quantitative, gene-specific framework that combines ClinVar variant distributions and gnomAD constraint metrics.
By integrating pathogenic burden, population intolerance, and mechanism-of-disease data, SeqSMART delivers a transparent, reliable, and context-aware application of these supporting ACMG criteria.
SeqSMART Gene Mechanism Principle:
Know the gene — understand the variant.