Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Gene ontology Other IDs Protein Associated diseases
Entrez ID	8192
Gene name	Caseinolytic mitochondrial matrix peptidase proteolytic subunit
Gene symbol	CLPP
Synonyms (NCBI Gene)	DFNB81PRLTS3
Chromosome	19
Chromosome location	19p13.3
Summary	The protein encoded by this gene belongs to the peptidase family S14 and hydrolyzes proteins into small peptides in the presence of ATP and magnesium. The protein is transported into mitochondrial matrix and is associated with the inner mitochondrial memb

Show/Hide all (4)

SNP ID	Visualize variation	Clinical significance	Consequence
rs398123033	A>C,G	Pathogenic	Coding sequence variant, missense variant
rs398123034	G>A,C	Pathogenic	Coding sequence variant, missense variant
rs909909437	T>C	Pathogenic	Splice donor variant
rs1555719766	C>G	Pathogenic	Coding sequence variant, missense variant

Show/Hide all (50)

miRTarBase ID	miRNA	Experiments	Reference
MIRT022076	hsa-miR-128-3p	Microarray	17612493
MIRT039835	hsa-miR-615-3p	CLASH	23622248
MIRT039835	hsa-miR-615-3p	CLASH	23622248
MIRT549555	hsa-miR-5680	PAR-CLIP	21572407
MIRT549554	hsa-miR-6858-3p	PAR-CLIP	21572407
MIRT549553	hsa-miR-4676-5p	PAR-CLIP	21572407
MIRT549552	hsa-miR-575	PAR-CLIP	21572407
MIRT549551	hsa-miR-1265	PAR-CLIP	21572407
MIRT549550	hsa-miR-6890-5p	PAR-CLIP	21572407
MIRT549549	hsa-miR-4716-5p	PAR-CLIP	21572407
MIRT549548	hsa-miR-193b-5p	PAR-CLIP	21572407
MIRT549547	hsa-miR-4662a-5p	PAR-CLIP	21572407
MIRT549546	hsa-miR-197-3p	PAR-CLIP	21572407
MIRT549545	hsa-miR-3170	PAR-CLIP	21572407
MIRT549544	hsa-miR-6855-5p	PAR-CLIP	21572407
MIRT549543	hsa-miR-5096	PAR-CLIP	21572407
MIRT525175	hsa-miR-6768-5p	PAR-CLIP	22012620
MIRT525174	hsa-miR-4438	PAR-CLIP	22012620
MIRT525173	hsa-miR-3155a	PAR-CLIP	22012620
MIRT525172	hsa-miR-3155b	PAR-CLIP	22012620
MIRT525171	hsa-miR-484	PAR-CLIP	22012620
MIRT525170	hsa-miR-3690	PAR-CLIP	22012620
MIRT525168	hsa-miR-4638-3p	PAR-CLIP	22012620
MIRT525169	hsa-miR-1254	PAR-CLIP	22012620
MIRT525167	hsa-miR-3116	PAR-CLIP	22012620
MIRT525166	hsa-miR-661	PAR-CLIP	22012620
MIRT549555	hsa-miR-5680	PAR-CLIP	21572407
MIRT549554	hsa-miR-6858-3p	PAR-CLIP	21572407
MIRT549553	hsa-miR-4676-5p	PAR-CLIP	21572407
MIRT549552	hsa-miR-575	PAR-CLIP	21572407
MIRT549551	hsa-miR-1265	PAR-CLIP	21572407
MIRT549550	hsa-miR-6890-5p	PAR-CLIP	21572407
MIRT549549	hsa-miR-4716-5p	PAR-CLIP	21572407
MIRT549548	hsa-miR-193b-5p	PAR-CLIP	21572407
MIRT549547	hsa-miR-4662a-5p	PAR-CLIP	21572407
MIRT549546	hsa-miR-197-3p	PAR-CLIP	21572407
MIRT549545	hsa-miR-3170	PAR-CLIP	21572407
MIRT549544	hsa-miR-6855-5p	PAR-CLIP	21572407
MIRT549543	hsa-miR-5096	PAR-CLIP	21572407
MIRT525175	hsa-miR-6768-5p	PAR-CLIP	22012620
MIRT525174	hsa-miR-4438	PAR-CLIP	22012620
MIRT525173	hsa-miR-3155a	PAR-CLIP	22012620
MIRT525172	hsa-miR-3155b	PAR-CLIP	22012620
MIRT525171	hsa-miR-484	PAR-CLIP	22012620
MIRT525170	hsa-miR-3690	PAR-CLIP	22012620
MIRT525168	hsa-miR-4638-3p	PAR-CLIP	22012620
MIRT525169	hsa-miR-1254	PAR-CLIP	22012620
MIRT525167	hsa-miR-3116	PAR-CLIP	22012620
MIRT525166	hsa-miR-661	PAR-CLIP	22012620
MIRT1966206	hsa-miR-4326	CLIP-seq

Show/Hide all (30)

GO ID	Ontology	Definition	Evidence	Reference
GO:0004175	Function	Endopeptidase activity	IDA	22354088
GO:0004176	Function	ATP-dependent peptidase activity	IBA
GO:0004176	Function	ATP-dependent peptidase activity	IEA
GO:0004176	Function	ATP-dependent peptidase activity	TAS
GO:0004252	Function	Serine-type endopeptidase activity	IBA
GO:0004252	Function	Serine-type endopeptidase activity	IDA	11923310
GO:0004252	Function	Serine-type endopeptidase activity	IEA
GO:0005515	Function	Protein binding	IPI	11923310, 15522782, 16115876, 32296183, 32814053
GO:0005739	Component	Mitochondrion	HTP	34800366
GO:0005739	Component	Mitochondrion	IDA	22354088
GO:0005739	Component	Mitochondrion	IEA
GO:0005759	Component	Mitochondrial matrix	IDA	10525407
GO:0005759	Component	Mitochondrial matrix	IEA
GO:0005759	Component	Mitochondrial matrix	NAS	15522782
GO:0005759	Component	Mitochondrial matrix	TAS
GO:0006508	Process	Proteolysis	IDA	15522782
GO:0006508	Process	Proteolysis	IEA
GO:0006515	Process	Protein quality control for misfolded or incompletely synthesized proteins	IBA
GO:0008233	Function	Peptidase activity	IEA
GO:0008233	Function	Peptidase activity	TAS	8543061
GO:0008236	Function	Serine-type peptidase activity	IEA
GO:0009368	Component	Endopeptidase Clp complex	IBA
GO:0009368	Component	Endopeptidase Clp complex	IDA	11923310
GO:0009368	Component	Endopeptidase Clp complex	IPI	15522782
GO:0016787	Function	Hydrolase activity	IEA
GO:0033619	Process	Membrane protein proteolysis	IDA	22354088
GO:0035694	Process	Mitochondrial protein catabolic process	TAS
GO:0042802	Function	Identical protein binding	IEA
GO:0051117	Function	ATPase binding	IBA
GO:0051603	Process	Proteolysis involved in protein catabolic process	IDA	11923310

MIM	HGNC	e!Ensembl
601119	2084	ENSG00000125656

Q16740

Protein name

ATP-dependent Clp protease proteolytic subunit, mitochondrial (EC 3.4.21.92) (Caseinolytic mitochondrial matrix peptidase proteolytic subunit) (Endopeptidase Clp)

Protein function

Protease component of the ClpXP complex that cleaves peptides and various proteins in an ATP-dependent process. Has low peptidase activity in the absence of CLPX. The ClpXP complex can degrade CSN1S1, CSN2 and CSN3, as well as synthetic peptides

PDB

1TG6 , 6BBA , 6DL7 , 6H23 , 7UVM , 7UVN , 7UVR , 7UVU , 7UW0 , 7VP9 , 7WH5 , 8HGK , 8I7X , 8W7C , 8W7E , 8WUZ , 8YLB

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF00574	CLP_protease	67 → 248	Clp protease	Domain

Tissue specificity

TISSUE SPECIFICITY: Detected in liver (at protein level). Predominantly expressed in skeletal muscle. Intermediate levels in heart, liver and pancreas. Low in brain, placenta, lung and kidney. {ECO:0000269|PubMed:10525407, ECO:0000269|PubMed:8543061}.

Sequence

MWPGILVGGARVASCRYPALGPRLAAHFPAQRPPQRTLQNGLALQRCLHATATRALPLIP
IVVEQTGRGERAYDIYSRLLRERIVCVMGPIDDSVASLVIAQLLFLQSESNKKPIHMYIN
SPGGVVTAGLAIYDTMQYILNPICTWCVGQAASMGSLLLAAGTPGMRHSLPNSRIMIHQP
SGGARGQATDIAIQAEEIMKLKKQLYNIYAKHTKQSLQVIESAMERDRYMSPMEAQEFGI
LDKVLVHPPQDGEDEPTLVQKEPVEAAPAAEPVPAST

Sequence length

277

Interactions

View interactions

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)

Show/Hide Causal Diseases (4)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Autosomal recessive hearing impairment with normal menstrual cycles	Pathogenic	rs398123035	RCV000201253	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Perrault syndrome	Pathogenic	rs398123033, rs398123034, rs398123035	RCV002513675 RCV002513676 RCV002513677	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Perrault syndrome 1	Pathogenic	rs2512444496	RCV003328548	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Perrault syndrome 3	Likely pathogenic; Pathogenic	rs2145048931, rs756490492, rs780624187, rs1555719766, rs398123033, rs398123034, rs398123035, rs1599193093, rs2091852209	RCV001806386 RCV005051999 RCV003335958 RCV000656488 RCV000049282 View all (4 more)	★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)

Show/Hide Unknown Diseases (12)

Phenotype Name	Clinical Significance	Source	Evidence Score
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
ALZHEIMER DISEASE	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CLPP-related disorder	Benign; Likely benign; Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Familial cancer of breast	Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GONADAL DYSGENESIS XX TYPE DEAFNESS	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Melanoma	-	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Ovarian serous cystadenocarcinoma	Uncertain significance; Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PERIPHERAL ARTERIAL DISEASE	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PERRAULT SYNDROME 4	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PERRAULT SYNDROME TYPE 1	—	Disgenet, Orphanet Disgenet, Orphanet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PERRAULT SYNDROME TYPE 2	—	Orphanet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine carcinosarcoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
XX GONADAL DYSGENESIS-DEAFNESS SYNDROME-PROGRESSIVE NEUROLOGICAL MANIFESTATIONS	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Show/Hide Text Mining Associations (31)

Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Associations from Text Mining Disease associations identified through text mining
Amenorrhea	Amenorrhea	Pubtator	29240891	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Azoospermia	Azoospermia	Pubtator	29240891	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
CODAS syndrome	CODAS Syndrome	BEFREE	31547314		★★★★★ ★☆☆☆☆ Found in Text Mining only
Congenital sensorineural hearing loss	Congenital Sensorineural Hearing Loss	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Developmental Disabilities	Developmental disability	Pubtator	38454547	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Glioblastoma	Glioblastoma	Pubtator	35417530	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Glioma	Glioma	Pubtator	38386699	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Gonadal Dysgenesis	Gonadal dysgenesis	Pubtator	29240891	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Gonadal dysgenesis XX type deafness	Gonadal Dysgenesis	BEFREE	23541340, 25956234, 27087618, 27259978		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Gonadal dysgenesis XX type deafness	Gonadal Dysgenesis	GENOMICS_ENGLAND_DG	23541340		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Gonadal dysgenesis XX type deafness	Gonadal Dysgenesis	ORPHANET_DG	23541340		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Gonadal dysgenesis XX type deafness	Gonadal dysgenesis	Pubtator	23541340, 26657938, 27087618, 38454547	Associate	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Hearing Loss	Hearing loss	Pubtator	32842620, 33073672, 38454547	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Hearing Loss Sensorineural	Hearing loss	Pubtator	34943861	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Infertility	Infertility	Pubtator	33073672	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Liver Cirrhosis	Liver cirrhosis	Pubtator	30878663	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Metabolic Syndrome X	Metabolic Syndrome	BEFREE	29588285		★★★★★ ★☆☆☆☆ Found in Text Mining only
Mitochondrial cardiomyopathy	Mitochondrial Cardiomyopathy	BEFREE	27154400		★★★★★ ★☆☆☆☆ Found in Text Mining only
Mitochondrial Diseases	Mitochondrial disease	Pubtator	23541340	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Mitochondrial Diseases	Mitochondrial Diseases	BEFREE	27154400, 29588285		★★★★★ ★☆☆☆☆ Found in Text Mining only
Neuroblastoma	Neuroblastoma	Pubtator	36675163	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Perrault syndrome	Perrault Syndrome	Orphanet			★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
PERRAULT SYNDROME 3	Perrault Syndrome	CLINVAR_DG	23541340		★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
PERRAULT SYNDROME 3	Perrault Syndrome	CLINGEN_DG	23541340, 23851121, 25956234, 26970254, 27087618, 27650058, 27899912, 28604674		★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
PERRAULT SYNDROME 3	Perrault Syndrome	UNIPROT_DG	23541340, 25956234		★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
PERRAULT SYNDROME 3	Perrault Syndrome	BEFREE	30150665		★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
PERRAULT SYNDROME 3	Perrault Syndrome	GENOMICS_ENGLAND_DG	8543061		★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
PERRAULT SYNDROME 3	Perrault Syndrome	CTD_human_DG			★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Primary hypogonadism	Hypogonadism	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Primary physiologic amenorrhea	Physiologic Amenorrhea	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Sleep Deprivation	Sleep deprivation	Pubtator	29240891	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only

CLPP (caseinolytic mitochondrial matrix peptidase proteolytic subunit)