CAPN7

gene
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Also known as PalBH

Summary

CAPN7 (calpain 7, HGNC:1484) is a protein-coding gene on chromosome 3p25.1, encoding Calpain-7 (Q9Y6W3). Calcium-regulated non-lysosomal thiol-protease.

Calpains are ubiquitous, well-conserved family of calcium-dependent, cysteine proteases. The calpain proteins are heterodimers consisting of an invariant small subunit and variable large subunits. The large subunit possesses a cysteine protease domain, and both subunits possess calcium-binding domains. Calpains have been implicated in neurodegenerative processes, as their activation can be triggered by calcium influx and oxidative stress. The function of the protein encoded by this gene is not known. An orthologue has been found in mouse but it seems to diverge from other family members. The mouse orthologue is thought to be calcium independent with protease activity.

Source: NCBI Gene 23473 — RefSeq curated summary.

At a glance

  • GWAS associations: 1
  • Clinical variants (ClinVar): 116 total
  • MANE Select transcript: NM_014296

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:1484
Approved symbolCAPN7
Namecalpain 7
Location3p25.1
Locus typegene with protein product
StatusApproved
AliasesPalBH
Ensembl geneENSG00000131375
Ensembl biotypeprotein_coding
OMIM606400
Entrez23473

Gene structure

Transcript identifiers

Ensembl transcripts: 14 — 9 protein_coding, 3 nonsense_mediated_decay, 2 retained_intron

ENST00000253693, ENST00000415565, ENST00000418994, ENST00000443567, ENST00000457023, ENST00000463417, ENST00000472400, ENST00000901140, ENST00000901141, ENST00000901142, ENST00000901143, ENST00000901144, ENST00000928381, ENST00000965910

RefSeq mRNA: 7 — MANE Select: NM_014296 NM_001376086, NM_001376087, NM_001376089, NM_001376090, NM_001376091, NM_001376093, NM_014296

CCDS: CCDS2624

Canonical transcript exons

ENST00000253693 — 21 exons

ExonStartEnd
ENSE000009013051520624615206597
ENSE000009013191524145315241588
ENSE000011495071522078115220981
ENSE000012414331525111615252916
ENSE000016403611524075415240853
ENSE000016531021523251915232665
ENSE000016653891523044215230535
ENSE000017004211522783915227965
ENSE000017136311522347515223561
ENSE000017310201523502515235145
ENSE000017766001523386715233973
ENSE000017808971524047315240617
ENSE000018036951522897415229059
ENSE000034718751524552615245671
ENSE000035539361521742515217582
ENSE000035831691521847315218540
ENSE000035904941524732715247457
ENSE000035931991524217815242253
ENSE000035952441525093115251023
ENSE000036594741524673215246794
ENSE000036903931521210415212212

Expression profiles

Bgee: expression breadth ubiquitous, 291 present calls, max score 98.13.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 12.1236 / max 89.6429, expressed in 1783 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
3549511.82091781
354940.3027139

Top tissues by expression

298 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
secondary oocyteCL:000065598.13gold quality
oocyteCL:000002395.57gold quality
calcaneal tendonUBERON:000370195.16gold quality
adrenal tissueUBERON:001830393.90gold quality
left ovaryUBERON:000211992.65gold quality
tibiaUBERON:000097992.58gold quality
mucosa of stomachUBERON:000119992.28gold quality
popliteal arteryUBERON:000225091.74gold quality
tibial arteryUBERON:000761091.74gold quality
gastrocnemiusUBERON:000138891.65gold quality
endocervixUBERON:000045891.62gold quality
arteryUBERON:000163791.31gold quality
right ovaryUBERON:000211891.24gold quality
body of uterusUBERON:000985391.19gold quality
ovaryUBERON:000099291.05gold quality
muscle of legUBERON:000138390.96gold quality
aortaUBERON:000094790.93gold quality
tibial nerveUBERON:000132390.82gold quality
muscle layer of sigmoid colonUBERON:003580590.79gold quality
esophagogastric junction muscularis propriaUBERON:003584190.76gold quality
hindlimb stylopod muscleUBERON:000425290.67gold quality
cerebellar hemisphereUBERON:000224590.66gold quality
cerebellar cortexUBERON:000212990.60gold quality
left lobe of thyroid glandUBERON:000112090.55gold quality
right uterine tubeUBERON:000130290.55gold quality
lower esophagus muscularis layerUBERON:003583390.53gold quality
lower esophagusUBERON:001347390.51gold quality
right hemisphere of cerebellumUBERON:001489090.51gold quality
ventricular zoneUBERON:000305390.41gold quality
thyroid glandUBERON:000204690.35gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes8.96

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

132 targeting CAPN7, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-340-5P100.0072.504437
HSA-MIR-3064-3P100.0070.091254
HSA-MIR-4668-3P100.0068.742635
HSA-MIR-3924100.0072.092394
HSA-MIR-30A-5P100.0076.313233
HSA-MIR-30B-5P100.0076.293248
HSA-MIR-30C-5P100.0076.293248
HSA-MIR-30D-5P100.0076.323233
HSA-MIR-30E-5P100.0076.323242
HSA-LET-7A-3P100.0074.033932
HSA-LET-7B-3P100.0074.083913
HSA-LET-7F-1-3P100.0074.023928
HSA-MIR-98-3P100.0074.083907
HSA-MIR-6740-5P100.0065.64932
HSA-MIR-4789-5P99.9870.762721
HSA-MIR-1213699.9872.815713
HSA-MIR-548N99.9871.944170
HSA-MIR-485-3P99.9870.681585
HSA-MIR-539-3P99.9870.741616
HSA-MIR-1468-3P99.9672.743797
HSA-MIR-590-3P99.9674.346478
HSA-MIR-548AJ-3P99.9673.385345
HSA-MIR-548X-3P99.9673.385345
HSA-MIR-55999.9572.283609
HSA-MIR-548AB99.9571.313488
HSA-MIR-128-3P99.9571.172484
HSA-MIR-216A-3P99.9571.192505
HSA-MIR-548A-5P99.9471.273482
HSA-MIR-548AD-5P99.9471.233502
HSA-MIR-548AE-5P99.9471.233502

Literature-anchored findings (GeneRIF, showing 6)

  • Results demonstrate that human calpain 7 is proteolytically active, and imply that calpain 7 is activated by ESCRT-III-related protein IST1. (PMID:20849418)
  • The detected enhancement of autolysis of mGFP-fused calpain-7 by coexpression with CHMP1B and observed further activation by additional coexpression of IST1 in HEK293T cells. (PMID:21616915)
  • Mutational analysis of calpain-7 reveals the importance of not only the N-terminal microtubule-interacting and trafficking domains but also the C-terminal C2 domain-like domains for proteolytic activity. (PMID:23497113)
  • Data indicate that CAPN 7 promotes endometrial stromal cell (hESC) migration and invasion by increasing the activity of MMP-2 via an increased ratio of MMP-2 to TIMP-2. (PMID:23855590)
  • The proteolytic activity of CAPN7 is important for the acceleration of EGFR degradation via the endosomal sorting pathway. (PMID:24953135)
  • Calpain7 negatively regulates human endometrial stromal cell decidualization in EMs by promoting FoxO1 nuclear exclusion via hydrolyzing AKT1. (PMID:35191464)

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
danio_reriocapn7ENSDARG00000102987
mus_musculusCapn7ENSMUSG00000021893
rattus_norvegicusCapn7ENSRNOG00000019273
caenorhabditis_elegansWBGENE00000543

Paralogs (20): CAPN1 (ENSG00000014216), SRI (ENSG00000075142), CAPN6 (ENSG00000077274), CAPN3 (ENSG00000092529), CAPN15 (ENSG00000103326), GCA (ENSG00000115271), ADGB (ENSG00000118492), CAPNS1 (ENSG00000126247), CAPN9 (ENSG00000135773), CAPN11 (ENSG00000137225), CAPN10 (ENSG00000142330), CAPN5 (ENSG00000149260), PEF1 (ENSG00000162517), CAPN2 (ENSG00000162909), CAPN13 (ENSG00000162949), CAPN12 (ENSG00000182472), CAPN8 (ENSG00000203697), CAPN14 (ENSG00000214711), PDCD6 (ENSG00000249915), CAPNS2 (ENSG00000256812)

Protein

Protein identifiers

Calpain-7Q9Y6W3 (reviewed: Q9Y6W3)

Alternative names: PalB homolog

All UniProt accessions (5): F8WCZ1, F8WDQ3, H7C0F1, H7C1B7, Q9Y6W3

UniProt curated annotations — full annotation on UniProt →

Function. Calcium-regulated non-lysosomal thiol-protease.

Subcellular location. Nucleus.

Tissue specificity. Ubiquitous.

Similarity. Belongs to the peptidase C2 family.

RefSeq proteins (7): NP_001363015, NP_001363016, NP_001363018, NP_001363019, NP_001363020, NP_001363022, NP_055111* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001300Peptidase_C2_calpain_catDomain
IPR007330MIT_domDomain
IPR022682Calpain_domain_IIIDomain
IPR022683Calpain_IIIDomain
IPR022684Calpain_cysteine_proteaseFamily
IPR036181MIT_dom_sfHomologous_superfamily
IPR036213Calpain_III_sfHomologous_superfamily
IPR038765Papain-like_cys_pep_sfHomologous_superfamily
IPR051297PalB/RIM13Family

Pfam: PF00648, PF01067, PF04212

Enzyme classification (BRENDA):

  • EC 3.4.22.B27 — (BRENDA: organisms, substrates, inhibitors, Km, kcat entries)

UniProt features (27 total): strand 9, helix 8, active site 3, region of interest 2, modified residue 2, chain 1, domain 1, turn 1

Structure

Experimental structures (PDB)

2 structures.

PDBMethodResolution (Å)
2QFEX-RAY DIFFRACTION1.45
8UC6X-RAY DIFFRACTION2.7

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9Y6W3-F188.880.71

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Catalytic / active sites (3): 290; 458; 478

Post-translational modifications (2): 1, 95

Function

Pathways and Gene Ontology

Reactome pathways

2 pathways

IDPathway
R-HSA-1474228Degradation of the extracellular matrix
R-HSA-1474244Extracellular matrix organization

MSigDB gene sets: 131 (showing top): TGGTGCT_MIR29A_MIR29B_MIR29C, BORCZUK_MALIGNANT_MESOTHELIOMA_UP, KAAB_FAILED_HEART_ATRIUM_DN, GOBP_REGULATION_OF_EPITHELIAL_CELL_MIGRATION, GOBP_AMEBOIDAL_TYPE_CELL_MIGRATION, GOBP_TISSUE_MIGRATION, GOMF_CYSTEINE_TYPE_PEPTIDASE_ACTIVITY, LASTOWSKA_NEUROBLASTOMA_COPY_NUMBER_DN, GOBP_POSITIVE_REGULATION_OF_EPITHELIAL_CELL_MIGRATION, ACTTTAT_MIR1425P, JOSEPH_RESPONSE_TO_SODIUM_BUTYRATE_DN, BURTON_ADIPOGENESIS_12, SPIELMAN_LYMPHOBLAST_EUROPEAN_VS_ASIAN_DN, PARENT_MTOR_SIGNALING_UP, TAATTA_CHX10_01

GO Biological Process (3): proteolysis (GO:0006508), positive regulation of epithelial cell migration (GO:0010634), self proteolysis (GO:0097264)

GO Molecular Function (8): endopeptidase activity (GO:0004175), cysteine-type endopeptidase activity (GO:0004197), calcium-dependent cysteine-type endopeptidase activity (GO:0004198), MIT domain binding (GO:0090541), protein binding (GO:0005515), peptidase activity (GO:0008233), cysteine-type peptidase activity (GO:0008234), hydrolase activity (GO:0016787)

GO Cellular Component (4): nucleus (GO:0005634), centrosome (GO:0005813), cytosol (GO:0005829), extracellular exosome (GO:0070062)

Reactome top-level categories

Rollup of top-1 pathways:

CategoryPathways
Extracellular matrix organization1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
peptidase activity2
protein metabolic process1
epithelial cell migration1
regulation of epithelial cell migration1
positive regulation of cell migration1
proteolysis1
endopeptidase activity1
cysteine-type peptidase activity1
cysteine-type endopeptidase activity1
protein domain specific binding1
binding1
hydrolase activity1
catalytic activity, acting on a protein1
catalytic activity1
intracellular membrane-bounded organelle1
centriole1
microtubule organizing center1
cytoplasm1
cellular anatomical structure1
extracellular vesicle1

Protein interactions and networks

STRING

1449 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
CAPN7OXNAD1Q96HP4891
CAPN7XIRP1Q702N8832
CAPN7TTRP02766637
CAPN7CASTP20810590
CAPN7CAPNS1P04632567
CAPN7CAV3P56539553
CAPN7CAPNS2Q96L46543
CAPN7TFAP2AP05549514
CAPN7CHMP1BQ7LBR1474
CAPN7IST1P53990432
CAPN7TMEM132EQ6IEE7400
CAPN7RIBC1Q8N443394
CAPN7MTURNQ8N3F0380
CAPN7TOPAZ1Q8N9V7377
CAPN7MROH7Q68CQ1375

IntAct

64 interactions, top by confidence:

ABTypeScore
CAPN7IST1psi-mi:“MI:0915”(physical association)0.680
IST1CAPN7psi-mi:“MI:0407”(direct interaction)0.680
IST1CAPN7psi-mi:“MI:0915”(physical association)0.680
CAPN7ZNF655psi-mi:“MI:0915”(physical association)0.560
TNFAIP1CAPN7psi-mi:“MI:0915”(physical association)0.560
IFT88CAPN7psi-mi:“MI:0915”(physical association)0.560
PPP1R13BCAPN7psi-mi:“MI:0915”(physical association)0.560
PRPSAP1CAPN7psi-mi:“MI:0915”(physical association)0.560
CEP63CAPN7psi-mi:“MI:0915”(physical association)0.560
GOLGA2CAPN7psi-mi:“MI:0915”(physical association)0.560
TRIM27CAPN7psi-mi:“MI:0915”(physical association)0.560
MAGED1CAPN7psi-mi:“MI:0915”(physical association)0.560
CTBP2CAPN7psi-mi:“MI:0915”(physical association)0.560
MAD1L1CAPN7psi-mi:“MI:0915”(physical association)0.560
AXIN2CAPN7psi-mi:“MI:0915”(physical association)0.560
ARNT2CAPN7psi-mi:“MI:0915”(physical association)0.560
ZNF655CAPN7psi-mi:“MI:0915”(physical association)0.560
VHLEGLN3psi-mi:“MI:0915”(physical association)0.370
CAPN7psi-mi:“MI:0915”(physical association)0.370
Spastpsi-mi:“MI:0914”(association)0.350
Ptpn23UMAD1psi-mi:“MI:0914”(association)0.350
Vps4bCNOT1psi-mi:“MI:0914”(association)0.350
CHMP4BELOCpsi-mi:“MI:0914”(association)0.350
HTRA2VWA8psi-mi:“MI:0914”(association)0.350
IMMP1LEIF1AYpsi-mi:“MI:0914”(association)0.350
CFAP184TARS3psi-mi:“MI:0914”(association)0.350
PTGES3SBNO1psi-mi:“MI:0914”(association)0.350

BioGRID (47): CAPN7 (Two-hybrid), CAPN7 (Two-hybrid), CAPN7 (Two-hybrid), ZFYVE19 (Two-hybrid), UBL7 (Two-hybrid), ZBTB9 (Two-hybrid), CAPN7 (Affinity Capture-MS), CAPN7 (Affinity Capture-MS), CAPN7 (Affinity Capture-MS), CAPN7 (Affinity Capture-MS), CAPN7 (Affinity Capture-MS), CAPN7 (Affinity Capture-MS), CAPN7 (Affinity Capture-MS), CAPN7 (Proximity Label-MS), CAPN7 (Two-hybrid)

ESM2 similar proteins: A0A0G2QC33, A0FKG7, A6H7H7, F1N9S8, O95453, P0C0T1, P42694, P50747, P69341, Q0IIH8, Q0VGM9, Q13572, Q28559, Q4R528, Q5BJZ6, Q5F480, Q5R699, Q5RC51, Q5ZIA0, Q5ZIW7, Q640G7, Q6DDJ3, Q6DFV5, Q6DG88, Q6DJB3, Q6GR37, Q6NYU2, Q6PZ02, Q6PZ03, Q6PZ05, Q7T0P6, Q80UY1, Q80YV4, Q811C2, Q8BGE6, Q8BYN3, Q8C9S8, Q8N4J0, Q8VDG3, Q8WYN0

Diamond homologs: A0FKG7, G3UZ78, P27398, Q00204, Q55FS2, Q78EJ9, Q8RVL1, Q9R1S8, Q9Y6W3, Q9Y6Z8, A6NHC0, A8MX76, O08529, O08688, O14815, O15484, O35350, O35920, O75808, P00789, P06814, P07384, P17655, P20807, P27730, P35750, P97571, Q07009, Q11002, Q27970, Q27971, Q4V8Q1, Q5NVS7, Q6J756, Q6ZFZ4, Q6ZSI9, Q8IAA9, Q8R4C0, Q8RVL2, Q91VA3

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

116 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance88
Likely benign7
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

3042 predictions. Top by Δscore:

VariantEffectΔscore
3:15206593:ACAAG:Adonor_loss1.0000
3:15206594:CAAG:Cdonor_loss1.0000
3:15206595:AAGGT:Adonor_loss1.0000
3:15206596:AGG:Adonor_loss1.0000
3:15206597:GGTAG:Gdonor_loss1.0000
3:15206599:T:Gdonor_loss1.0000
3:15211060:G:GTdonor_gain1.0000
3:15211091:A:AGdonor_gain1.0000
3:15212097:T:Gacceptor_gain1.0000
3:15212208:AGCAG:Adonor_loss1.0000
3:15212209:GCAG:Gdonor_gain1.0000
3:15212209:GCAGG:Gdonor_loss1.0000
3:15212210:CAGG:Cdonor_loss1.0000
3:15212212:GGTT:Gdonor_loss1.0000
3:15212213:G:Adonor_loss1.0000
3:15217419:T:Gacceptor_gain1.0000
3:15217422:TA:Tacceptor_loss1.0000
3:15217423:A:AGacceptor_gain1.0000
3:15217424:G:GAacceptor_gain1.0000
3:15217424:GTT:Gacceptor_gain1.0000
3:15217424:GTTC:Gacceptor_gain1.0000
3:15217424:GTTCA:Gacceptor_gain1.0000
3:15217560:C:Gdonor_gain1.0000
3:15217579:AACA:Adonor_gain1.0000
3:15217580:ACA:Adonor_gain1.0000
3:15217581:CA:Cdonor_gain1.0000
3:15217583:GT:Gdonor_gain1.0000
3:15217600:T:Gdonor_gain1.0000
3:15217609:A:Gdonor_gain1.0000
3:15218468:TTAAG:Tacceptor_loss1.0000

AlphaMissense

5351 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
3:15212107:G:CA36P1.000
3:15217481:G:CA90P1.000
3:15217491:T:CL93P1.000
3:15217550:T:GY113D1.000
3:15217559:G:CA116P1.000
3:15218530:G:CA143P1.000
3:15227894:T:AW261R1.000
3:15227894:T:CW261R1.000
3:15227965:G:CQ284H1.000
3:15227965:G:TQ284H1.000
3:15228989:T:CC290R1.000
3:15228990:G:AC290Y1.000
3:15228991:C:GC290W1.000
3:15229008:T:CL296P1.000
3:15229010:G:CA297P1.000
3:15229019:G:CA300P1.000
3:15230484:T:AN327K1.000
3:15230484:T:GN327K1.000
3:15230497:T:GY332D1.000
3:15230520:T:AN339K1.000
3:15230520:T:GN339K1.000
3:15230531:G:CR343T1.000
3:15230532:A:CR343S1.000
3:15230532:A:TR343S1.000
3:15232597:T:AW371R1.000
3:15232597:T:CW371R1.000
3:15232614:A:CE376D1.000
3:15232614:A:TE376D1.000
3:15232648:T:CF388L1.000
3:15232650:T:AF388L1.000

dbSNP variants (sampled 300 via entrez): RS1000067855 (3:15223995 G>A), RS1000080514 (3:15219706 T>C), RS1000120044 (3:15223779 G>A), RS1000237992 (3:15237698 C>T), RS1000290101 (3:15231474 A>G), RS1000296083 (3:15244137 A>G), RS1000401019 (3:15212692 G>A), RS1000555634 (3:15219414 A>G,T), RS1000563974 (3:15237385 A>G), RS1000740815 (3:15204585 G>A), RS1000753477 (3:15210269 A>T), RS1000764969 (3:15214170 A>G), RS1000808085 (3:15250428 G>C), RS1000854131 (3:15251993 A>G), RS1000937745 (3:15247681 A>G)

Disease associations

OMIM: gene MIM:606400 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

1 associations (top):

StudyTraitp-value
GCST009391_250Metabolite levels2.000000e-06

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0010495guanosine monophosphate measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

32 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
Valproic Acidincreases expression, decreases expression2
dicrotophosdecreases expression1
2,4,6-tribromophenoldecreases expression1
methylmercuric chloridedecreases expression1
triphenyl phosphateaffects expression1
pirinixic acidaffects binding, increases activity, increases expression1
bisphenol Adecreases expression1
tetrabromobisphenol Adecreases expression1
MDL 201053decreases expression, decreases reaction, increases degradation1
di-n-butylphosphoric acidaffects expression1
glycidamideincreases expression1
CGP 52608affects binding, increases reaction1
aloxistatindecreases expression, decreases reaction, increases degradation1
2,2’,4,4’-tetrabromodiphenyl etherdecreases expression1
hexabrominated diphenyl ether 153decreases expression1
jinfukangdecreases expression1
Sunitinibincreases expression1
Calcitriolincreases expression1
Doxorubicindecreases expression1
Ethyl Methanesulfonateincreases expression1
Formaldehydeincreases expression1
Methyl Methanesulfonateincreases expression1
Piroxicamdecreases expression1
Seleniumdecreases expression1
Tobacco Smoke Pollutionaffects expression1
Vitamin Edecreases expression1
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxidedecreases expression1
Cyclosporineincreases expression1
Asbestos, Crocidolitedecreases expression1
Antirheumatic Agentsincreases expression1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.