CST1
Chr 20cystatin SN
Cystatin SN is a cysteine protease inhibitor found in saliva, tears, urine, and seminal fluid that inhibits enzymes including papain and dipeptidyl peptidase I. The gene shows very low constraint against loss-of-function variants (LOEUF 1.96), and no established disease associations with CST1 mutations have been reported in the literature. This gene encodes one of several related cystatin proteins that likely provide protective functions in human secretions.
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
69 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 | 37 | 2 | 0 | 39 |
Likely Benign | 0 | 5 | 1 | 2 | 8 |
Benign | 0 | 0 | 0 | 0 | 0 |
| Total | 0 | 42 | 23 | 2 | 67 |
LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly
View in ClinVar →Protein Context — Lollipop Plot
CST1 · 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