CAPN9 (calpain 9)

Gene

• Entrez ID: 10753
• Gene name: Calpain 9
• Gene symbol: CAPN9
• Synonyms (NCBI Gene): GC36, nCL-4
• Chromosome: 1
• Chromosome location: 1q42.2
• Summary: 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, an

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT029148	hsa-miR-26b-5p	Microarray	19088304
MIRT733909	hsa-miR-585-3p	qRT-PCR	34238324
MIRT733909	hsa-miR-585-3p	qRT-PCR	34238324
MIRT733909	hsa-miR-585-3p	Luciferase reporter assay, qRT-PCR, Western blotting	34238324
MIRT862130	hsa-miR-124	CLIP-seq
MIRT862131	hsa-miR-2682	CLIP-seq
MIRT862132	hsa-miR-3164	CLIP-seq
MIRT862133	hsa-miR-34a	CLIP-seq
MIRT862134	hsa-miR-34c-5p	CLIP-seq
MIRT862135	hsa-miR-3714	CLIP-seq
MIRT862136	hsa-miR-3910	CLIP-seq
MIRT862137	hsa-miR-449a	CLIP-seq
MIRT862138	hsa-miR-449b	CLIP-seq
MIRT862139	hsa-miR-449c	CLIP-seq
MIRT862140	hsa-miR-506	CLIP-seq
MIRT862141	hsa-miR-520d-5p	CLIP-seq
MIRT862142	hsa-miR-524-5p	CLIP-seq
MIRT1955772	hsa-miR-1298	CLIP-seq
MIRT1955773	hsa-miR-198	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0004198	Function	Calcium-dependent cysteine-type endopeptidase activity	IBA
GO:0004198	Function	Calcium-dependent cysteine-type endopeptidase activity	IEA
GO:0004198	Function	Calcium-dependent cysteine-type endopeptidase activity	TAS	9524069
GO:0005509	Function	Calcium ion binding	IEA
GO:0005509	Function	Calcium ion binding	TAS	9524069
GO:0005737	Component	Cytoplasm	IBA
GO:0006508	Process	Proteolysis	IBA
GO:0006508	Process	Proteolysis	IEA
GO:0007586	Process	Digestion	TAS	9524069
GO:0008233	Function	Peptidase activity	IEA
GO:0008234	Function	Cysteine-type peptidase activity	IEA
GO:0016787	Function	Hydrolase activity	IEA
GO:0046872	Function	Metal ion binding	IEA

Other IDs

• MIM: 606401
• HGNC: 1486
• e!Ensembl: ENSG00000135773

Protein

• UniProt ID: O14815
• Protein name: Calpain-9 (EC 3.4.22.-) (Digestive tract-specific calpain) (New calpain 4) (nCL-4) (Protein CG36)
• Protein function: Calcium-regulated non-lysosomal thiol-protease.
• PDB: 1ZIV, 2P0R
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF00648	Peptidase_C2	43 → 335	Calpain family cysteine protease	Family
  PF01067	Calpain_III	356 → 486	Calpain large subunit, domain III	Domain

• Tissue specificity: TISSUE SPECIFICITY: Expressed predominantly in stomach.
• Sequence:

  MPYLYRAPGPQAHPVPKDARITHSSGQSFEQMRQECLQRGTLFEDADFPASNSSLFYSER
  PQIPFVWKRPGEIVKNPEFILGGATRTDICQGELGDCWLLAAIASLTLNQKALARVIPQD
  QSFGPGYAGIFHFQFWQHSEWLDVVIDDRLPTFRDRLVFLHSADHNEFWSALLEKAYAKL
  NGSYEALKGGSAIEAMEDFTGGVAETFQTKEAPENFYEILEKALKRGSLLGCFIDTRSAA
  ESEARTPFGLIKGHAYSVTGIDQVSFRGQRIELIRIRNPWGQVEWNGSWSDSSPEWRSVG
  PAEQKRLCHTALDDGEFWMAFKDFKAHFDKVEICNLTPDALEEDAIHKWEVTVHQGSWVR
  GSTAGGCRNFLDTFWTNPQIKLSLTEKDEGQEECSFLVALMQKDRRKLKRFGANVLTIGY
  AIYECPDKDEHLNKDFFRYHASRARSKTFINLREVSDRFKLPPGEYILIPSTFEPHQEAD
  FCLRIFSEKKAITRDMDGNVDIDLPEPPKPTPPDQETEEEQRFRALFEQVAGEDMEVTAE
  ELEYVLNAVLQKKKDIKFKKLSLISCKNIISLMDTSGNGKLEFDEFKVFWDKLKQWINLF
  LRFDADKSGTMSTYELRTALKAAGFQLSSHLLQLIVLRYADEELQLDFDDFLNCLVRLEN
  ASRVFQALSTKNKEFIHLNINEFIHLTMNI

• Sequence length: 690

Pathways

Reactome:

Degradation of the extracellular matrix

Associated diseases

Evidence Score:

• ★☆☆☆☆  Gene-disease association found in Text Mining only
• ★★☆☆☆  Found in Text Mining and Unknown/Other Associations
• ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources
• ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants)
• ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
Chronic lymphocytic leukemia/small lymphocytic lymphoma	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Clear cell carcinoma of kidney	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
COLORECTAL CANCER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Gastric cancer	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant tumor of urinary bladder	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Melanoma	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Breast Neoplasms	Breast neoplasm	Pubtator	25539577	Associate	★☆☆☆☆ Found in Text Mining only
Congenital exomphalos	Congenital Exomphalos	BEFREE	30746724		★☆☆☆☆ Found in Text Mining only
Diabetes Mellitus, Non-Insulin-Dependent	Diabetes Mellitus	BEFREE	11516996		★☆☆☆☆ Found in Text Mining only
Endometrial Neoplasms	Endometrial neoplasm	Pubtator	22426144	Associate	★☆☆☆☆ Found in Text Mining only
Kidney Diseases	Kidney Disease	BEFREE	29945255		★☆☆☆☆ Found in Text Mining only
Ovarian Neoplasms	Ovarian neoplasm	Pubtator	34238324	Associate	★☆☆☆☆ Found in Text Mining only
Pulmonary Fibrosis	Pulmonary Fibrosis	BEFREE	31316008		★☆☆☆☆ Found in Text Mining only
Stomach Neoplasms	Stomach neoplasms	Pubtator	10835488	Inhibit	★☆☆☆☆ Found in Text Mining only