CAPN11

Chr 6

calpain 11

Also known as: calpain11

NCBI Gene: 11131ENSG00000137225UniProt: Q9UMQ6

Calpains constitute a family of intracellular calcium-dependent cysteine proteases. There are eight members in this superfamily. They consist of a variable 80 kDa subunit and an invariant 30 kDa subunit. This calpain protein appears to have protease activity and calcium-binding ability. A similar mouse protein may play a functional role in spermatogenesis and in the regulation of calcium-dependent signal transduction events during meiosis. [provided by RefSeq, Dec 2008]

114
ClinVar variants
9
Pathogenic / LP
0.00
pLI score
0
Active trials
Clinical Summary— CAPN11
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
9 Pathogenic / Likely Pathogenic· 95 VUS of 114 total submissions

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint?LOEUF (Loss-of-function Observed/Expected Upper bound Fraction) is the upper bound of the 90% CI for LoF OE — the preferred gnomAD v4 metric. Lower = more intolerant to LoF. LOEUF < 0.35 = highly constrained.
1.15LOEUF
pLI 0.000
Z-score 0.73
OE 0.88 (0.68–1.15)
Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?Missense Z-score: standard deviations fewer missense variants observed vs. expected. Z > 3.09 (p < 0.001) = gene does not tolerate missense variation. OE missense < 0.6 is also considered constrained.
0.23Z-score
OE missense 0.97 (0.89–1.05)
399 obs / 412.3 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios?Shaded band = 90% confidence interval. Vertical tick = point estimate. Grey threshold line = gnomAD constraint cutoff for that variant class.
LoF OE?Ratio of observed to expected LoF variants. Upper CI bound (LOEUF) ≤ 0.35 = strong LoF constraint signal.0.88 (0.68–1.15)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.0.97 (0.89–1.05)
0≤0.61.4
Synonymous OE?Control metric — synonymous variants are largely neutral and expected near OE = 1.0. Significant deviation may indicate annotation issues.1.00
0≤1.21.6
LoF obs/exp: 39 / 44.3Missense obs/exp: 399 / 412.3Syn Z: 0.02

ClinVar Variant Classifications

114 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic8
Likely Pathogenic1
VUS95
Likely Benign8
Benign2
8
Pathogenic
1
Likely Pathogenic
95
VUS
8
Likely Benign
2
Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
8
0
8
Likely Pathogenic
0
0
1
0
1
VUS
0
93
2
0
95
Likely Benign
0
6
2
0
8
Benign
0
0
0
2
2
Total099132114

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

View in ClinVar →

Protein Context — Lollipop Plot

CAPN11 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

OMIM — Genotype-Phenotype Relationships

1 OMIM entry

OMIM
CALPAIN 11; CAPN11
MIM #604822 · *
Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
Characterisation of capn1, capn2-like, capn3 and capn11 genes in Atlantic halibut (Hippoglossus hippoglossus L.): Transcriptional regulation across tissues and in skeletal muscle at distinct nutritional states.
Macqueen DJ et al.·Gene
2010
A genome-wide association study of obstructive heart defects among participants in the National Birth Defects Prevention Study.
Rashkin SR et al.·Am J Med Genet A
2022
Sex-Specific Whole-Transcriptome Analysis in the Cerebral Cortex of FAE Offspring.
Mishra NK et al.·Cells
2023
CAPN11: A calpain with high mRNA levels in testis and located on chromosome 6.
Dear TN et al.·Genomics
1999
Both the conserved and the unique gene structure of stomach-specific calpains reveal processes of calpain gene evolution.
Hata S et al.·J Mol Evol
2001
A newly classified vertebrate calpain protease, directly ancestral to CAPN1 and 2, episodically evolved a restricted physiological function in placental mammals.
Macqueen DJ et al.·Mol Biol Evol
2010
Characterization of the definitive classical calpain family of vertebrates using phylogenetic, evolutionary and expression analyses.
Macqueen DJ et al.·Open Biol
2014
Potential biomarkers of nonobstructive azoospermia identified in microarray gene expression analysis.
Malcher A et al.·Fertil Steril
2013
Calpain 11 is unique to mouse spermatogenic cells.
Ben-Aharon I et al.·Mol Reprod Dev
2006Functional
Proteomic analysis of ursolic acid-induced apoptosis in cervical carcinoma cells.
Yim EK et al.·Cancer Lett
2006
Top 10 resultsSearch PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →

External Resources

Links to major genomics databases and tools