CST11

Chr 20

cystatin 11

Also known as: CST8L, CTES2, SC13, dJ322G13.6

NCBI Gene: 140880ENSG00000125831UniProt: Q9H112

CST11 encodes a type 2 cystatin protein that functions as a cysteine protease inhibitor with antimicrobial activity against gram-negative bacteria and may contribute to sperm maturation and fertilization. The gene is highly tolerant to loss-of-function variants (pLI 0.0001, LOEUF 1.8), and no established disease associations have been reported in the provided data. This epididymal-specific protein appears to have specialized reproductive functions rather than essential developmental roles.

Summary from RefSeq, UniProt
Research Assistant →
0
Active trials
0
Pubs (1 yr)
21
P/LP submissions
0%
P/LP missense
1.81
LOEUF
DN
Mechanism· predicted
Clinical Summary— CST11
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
21 unique Pathogenic / Likely Pathogenic· 22 VUS of 47 total submissions
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Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint
1.81LOEUF
pLI 0.000
Z-score -0.10
OE 1.05 (0.56–1.81)
Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint
-0.39Z-score
OE missense 1.13 (0.94–1.36)
80 obs / 70.7 exp
Tolerant

Tolerant to missense variation

Observed / Expected Ratios
LoF OE1.05 (0.56–1.81)
0≤0.351.4
Missense OE1.13 (0.94–1.36)
0≤0.61.4
Synonymous OE1.09
0≤1.21.6
LoF obs/exp: 6 / 5.7Missense obs/exp: 80 / 70.7Syn Z: -0.38
DN
0.75top 25%
GOF
0.4974th %ile
LOF
0.1994th %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

47 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic18
Likely Pathogenic3
VUS22
Likely Benign4
18
Pathogenic
3
Likely Pathogenic
22
VUS
4
Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
18
0
18
Likely Pathogenic
0
0
3
0
3
VUS
0
21
1
0
22
Likely Benign
0
3
1
0
4
Benign
0
0
0
0
0
Total02423047

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

CST11 · 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

ClinicalTrials.gov

No active trials found for this gene.

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Clinical Literature
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Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Top 5 full-text resultsSearch PubTator3 ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC

No open access results found

Top 5 resultsSearch Europe PMC ↗

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients