CST2
Chr 20cystatin SA
CST2 encodes a secreted thiol protease inhibitor found at high levels in saliva, tears, and seminal plasma. The gene is not constrained against loss-of-function variants (LOEUF 1.94), and no Mendelian diseases have been definitively associated with CST2 mutations in current databases. Clinical significance of variants in this gene remains uncertain.
Population Genetics & Constraint
gnomAD v4 — loss-of-function & missense intolerance
Highly tolerant — LoF variants common in population
Tolerant to missense variation
The highest-scoring mechanism for this gene is dominant-negative.
Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.
Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.
ClinVar Variant Classifications
77 submitted variants in ClinVar
Classification Summary
Curated Variants Distribution
Classified variants from ClinVar · 5 ACMG categories
| Classification | LoF | Missense + Inframe | Non-coding | Synonymous | Total |
|---|---|---|---|---|---|
Pathogenic | 0 | 0 | 17 | 0 | 17 |
Likely Pathogenic | 0 | 0 | 3 | 0 | 3 |
VUS | 0 | 41 | 2 | 0 | 43 |
Likely Benign | 0 | 5 | 3 | 0 | 8 |
Benign | 0 | 1 | 1 | 0 | 2 |
| Total | 0 | 47 | 26 | 0 | 73 |
LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly
View in ClinVar →Protein Context — Lollipop Plot
CST2 · protein map & ClinVar variants
Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.
External Resources
Links to major genomics databases and tools
Clinical Trials
Active and recruiting trials from ClinicalTrials.gov
No active trials found for this gene.
Search ClinicalTrials.gov →External Resources
Links to major genomics databases and tools