CST3
Chr 20ADcystatin C
Also known as: ADLDWA, ARMD11, HEL-S-2
The cystatin superfamily encompasses proteins that contain multiple cystatin-like sequences. Some of the members are active cysteine protease inhibitors, while others have lost or perhaps never acquired this inhibitory activity. There are three inhibitory families in the superfamily, including the type 1 cystatins (stefins), type 2 cystatins and the kininogens. The type 2 cystatin proteins are a class of cysteine proteinase inhibitors found in a variety of human fluids and secretions, where they appear to provide protective functions. The cystatin locus on chromosome 20 contains the majority of the type 2 cystatin genes and pseudogenes. This gene is located in the cystatin locus and encodes the most abundant extracellular inhibitor of cysteine proteases, which is found in high concentrations in biological fluids and is expressed in virtually all organs of the body. A mutation in this gene has been associated with amyloid angiopathy. Expression of this protein in vascular wall smooth muscle cells is severely reduced in both atherosclerotic and aneurysmal aortic lesions, establishing its role in vascular disease. In addition, this protein has been shown to have an antimicrobial function, inhibiting the replication of herpes simplex virus. Alternative splicing results in multiple transcript variants encoding a single protein. [provided by RefSeq, Nov 2014]
Limited evidence — not for standalone diagnostic reporting
2 total gene-disease associations curated
Population Genetics & Constraint
gnomAD v4 — loss-of-function & missense intolerance
Highly tolerant — LoF variants common in population
Tolerant to missense variation
This gene — mechanism propensity
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
74 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 | 1 | 1 | 0 | 2 |
Likely Pathogenic | 0 | 0 | 0 | 0 | 0 |
VUS | 4 | 33 | 0 | 0 | 37 |
Likely Benign | 0 | 3 | 3 | 10 | 16 |
Benign | 0 | 3 | 2 | 5 | 10 |
Conflicting | — | 2 | |||
| Total | 4 | 40 | 6 | 15 | 67 |
LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly
View in ClinVar →21 pathogenic / likely-pathogenic (of 23) ClinVar copy-number / structural variants overlap CST3 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →
Protein Context — Lollipop Plot
CST3 · 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
CALM-AF-AI: Counteracting Age-related Loss of Muscle With AAV-Follistatin Combined With Angiogenesis-Inducing VEGF Plasmid Gene Therapy
RECRUITINGSafety and Efficacy of Klotho and Follistatin Gene Therapy
RECRUITINGAcute Reno-Cardiac Action of Dapagliflozin In Advanced Heart Failure Patients on Heart Transplant Waiting List
RECRUITINGDietary Strategy to Tackle Cognitive and Locomotor Abilities in Early Elderly Subjects
RECRUITINGPathogenesis of Chronic Kidney Disease Associated With Metabolic Dysfunction- Associated Fatty Liver Disease (MAFLD) and Treatment Response of Oral Semaglutide.
NOT YET RECRUITINGSafety and Efficacy of Injectable Klotho Plasmid Gene Therapy in Humans
RECRUITINGEvaluate the Safety and Therapeutic Effects of a Single Intravenous Infusion (IV) of Autologous CD34+ Cells Enriched With Allogenic Placenta-derived Mitochondria in Patients With a Diagnosis of Pearson Syndrome (PS)
RECRUITINGSweet & Sour: Dietary Acid Load in Type 2 Diabetes and Kidney Disease Across Sex and Ethnic Groups
NOT YET RECRUITINGNatural History of Sphingosine Phosphate Lyase Insufficiency Syndrome (SPLIS)
RECRUITINGPhysical Exercise and Biomolecular Analysis to Reduce Uremic Toxins in Chronic Kidney Disease: An Exploratory Study
ENROLLING BY INVITATIONExploring Biomarkers in Hereditary Transthyretin Amyloidosis
RECRUITINGEffect of Inulin on Gut Microbiota and Gut Barrier in Chronic Kidney Disease
RECRUITINGExternal Resources
Links to major genomics databases and tools