CST3

Chr 20AD

cystatin 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]

OMIMResearchGenerating clinical summary…
DNmechanismADLOEUF 1.603 OMIM phenotypes
Clinical SummaryCST3
🧬
Gene-Disease Validity (ClinGen)
leukodystrophy, adult-onset, autosomal dominant, without amyloid angiopathy · ADLimited

Limited evidence — not for standalone diagnostic reporting

2 total gene-disease associations curated

Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
2 unique Pathogenic / Likely Pathogenic· 37 VUS of 74 total submissions
💊
Clinical Trials
12 active or recruiting trials — potential therapeutic options may be available

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

Tolerant — LoF & missense variants common in population
LoF Constraint?
1.60LOEUF
pLI 0.004
Z-score 0.58
OE 0.73 (0.361.60)
Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?
-0.50Z-score
OE missense 1.17 (0.971.41)
81 obs / 69.4 exp
Tolerant

Tolerant to missense variation

Observed / Expected Ratios?
LoF OE?0.73 (0.361.60)
00.351.4
Missense OE?1.17 (0.971.41)
00.61.4
Synonymous OE?1.12
01.21.6
LoF obs/exp: 4 / 5.5Missense obs/exp: 81 / 69.4Syn Z: -0.52

This gene — mechanism propensity

DN
0.76top 25%
GOF
0.5660th %ile
LOF
0.2678th %ile

The highest-scoring mechanism for this gene is dominant-negative.

DNprediction above median

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

Pathogenic2
VUS37
Likely Benign16
Benign10
Conflicting2
2
Pathogenic
37
VUS
16
Likely Benign
10
Benign
2
Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
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
Total44061567

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.

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

Age-related Muscle Decline

CALM-AF-AI: Counteracting Age-related Loss of Muscle With AAV-Follistatin Combined With Angiogenesis-Inducing VEGF Plasmid Gene Therapy

RECRUITING
NCT07443826Phase PHASE1, PHASE2Unlimited Biotechnology LLCStarted 2026-03-31
AAV9-Follistatin gene therapyVEGF Plasmid
Healthy Adults

Safety and Efficacy of Klotho and Follistatin Gene Therapy

RECRUITING
NCT07285629Phase EARLY_PHASE1MinicircleStarted 2025-12-16
Follistatin and klotho gene therapy
Heart Failure

Acute Reno-Cardiac Action of Dapagliflozin In Advanced Heart Failure Patients on Heart Transplant Waiting List

RECRUITING
NCT06868797Phase NACentral Hospital, Nancy, FranceStarted 2025-08-29
Biological sample for the measurement of suPAR levels.
Cognitive DisordersMuscular Disorders, Atrophic

Dietary Strategy to Tackle Cognitive and Locomotor Abilities in Early Elderly Subjects

RECRUITING
NCT06871384Phase NAUniversity Rovira i VirgiliStarted 2025-03-26
Nonalcoholic red wine group (Intervention group)Drinking water group (Control group)
Chronic Kidney DiseasesMAFLD

Pathogenesis of Chronic Kidney Disease Associated With Metabolic Dysfunction- Associated Fatty Liver Disease (MAFLD) and Treatment Response of Oral Semaglutide.

NOT YET RECRUITING
NCT07391267Phase NAInstitute of Liver and Biliary Sciences, IndiaStarted 2026-02-01
Semaglutide Oral TabletPlaceboStandard medical treatment
Healthy Adults

Safety and Efficacy of Injectable Klotho Plasmid Gene Therapy in Humans

RECRUITING
NCT07216781Phase PHASE1MinicircleStarted 2025-10-06
Injectable Plasmid Klotho Gene Therapy
Mitochondrial DiseasesPearson Syndrome

Evaluate 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)

RECRUITING
NCT06017869Phase PHASE2Minovia Therapeutics Ltd.Started 2023-07-31
MNV-201
Type 2 DiabetesChronic Kidney Disease

Sweet & Sour: Dietary Acid Load in Type 2 Diabetes and Kidney Disease Across Sex and Ethnic Groups

NOT YET RECRUITING
NCT07587918Phase NAErasmus Medical CenterStarted 2026-06-01
Low Dietary Acid Load
Sphingosine Phosphate Lyase Insufficiency Syndrome (SPLIS)

Natural History of Sphingosine Phosphate Lyase Insufficiency Syndrome (SPLIS)

RECRUITING
NCT06669949University of California, San FranciscoStarted 2025-04-22
no intervention
Kidney Disease, ChronicKidney Failure Chronic

Physical Exercise and Biomolecular Analysis to Reduce Uremic Toxins in Chronic Kidney Disease: An Exploratory Study

ENROLLING BY INVITATION
NCT06910475Phase NACatholic University of BrasíliaStarted 2025-04-01
Resistance trainingEndurance trainingConcurrent training
Hereditary Transthyretin Amyloidosis

Exploring Biomarkers in Hereditary Transthyretin Amyloidosis

RECRUITING
NCT05929209Phase NAFondazione Policlinico Universitario Agostino Gemelli IRCCSStarted 2023-05-01
Assessment of disease biomarkers
Chronic Kidney Disease 5D

Effect of Inulin on Gut Microbiota and Gut Barrier in Chronic Kidney Disease

RECRUITING
NCT05071131Phase NACharite University, Berlin, GermanyStarted 2022-02-01
InulinPlacebo