PPIB (peptidylprolyl isomerase B)

Gene

• Entrez ID: 5479
• Gene name: Peptidylprolyl isomerase B
• Gene symbol: PPIB
• Synonyms (NCBI Gene): CYP-S1, CYPB, HEL-S-39, OI9, SCYLP
• Chromosome: 15
• Chromosome location: 15q22.31
• Summary: The protein encoded by this gene is a cyclosporine-binding protein and is mainly located within the endoplasmic reticulum. It is associated with the secretory pathway and released in biological fluids. This protein can bind to cells derived from T- and B-

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs137853864	A>C,G,T	Not-provided, pathogenic	Missense variant, coding sequence variant
rs137853865	G>-	Not-provided, pathogenic	Coding sequence variant, frameshift variant
rs137853866	C>T	Not-provided, pathogenic	Missense variant, coding sequence variant
rs137853867	C>T	Pathogenic	Splice donor variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT001347	hsa-miR-1-3p	pSILAC	18668040
MIRT001347	hsa-miR-1-3p	Proteomics;Other	18668040
MIRT049173	hsa-miR-92a-3p	CLASH	23622248
MIRT049173	hsa-miR-92a-3p	CLASH	23622248
MIRT044215	hsa-miR-301a-3p	CLASH	23622248
MIRT513165	hsa-miR-4655-5p	PAR-CLIP	23446348
MIRT513164	hsa-miR-181d-3p	PAR-CLIP	23446348
MIRT513163	hsa-miR-3065-3p	PAR-CLIP	23446348
MIRT513162	hsa-miR-6784-5p	PAR-CLIP	23446348
MIRT513160	hsa-miR-3194-5p	PAR-CLIP	23446348
MIRT513161	hsa-miR-572	PAR-CLIP	23446348
MIRT513159	hsa-miR-1202	PAR-CLIP	23446348
MIRT513158	hsa-miR-3972	PAR-CLIP	23446348
MIRT001347	hsa-miR-1-3p	PAR-CLIP	26701625
MIRT001347	hsa-miR-1-3p	PAR-CLIP	26701625
MIRT513161	hsa-miR-572	PAR-CLIP	26701625
MIRT513161	hsa-miR-572	PAR-CLIP	26701625
MIRT513165	hsa-miR-4655-5p	PAR-CLIP	23446348
MIRT513164	hsa-miR-181d-3p	PAR-CLIP	23446348
MIRT513163	hsa-miR-3065-3p	PAR-CLIP	23446348
MIRT513162	hsa-miR-6784-5p	PAR-CLIP	23446348
MIRT513160	hsa-miR-3194-5p	PAR-CLIP	23446348
MIRT513161	hsa-miR-572	PAR-CLIP	23446348
MIRT513159	hsa-miR-1202	PAR-CLIP	23446348
MIRT513158	hsa-miR-3972	PAR-CLIP	23446348
MIRT1252826	hsa-miR-1	CLIP-seq
MIRT1252827	hsa-miR-1301	CLIP-seq
MIRT1252828	hsa-miR-148a	CLIP-seq
MIRT1252829	hsa-miR-148b	CLIP-seq
MIRT1252830	hsa-miR-152	CLIP-seq
MIRT1252831	hsa-miR-1825	CLIP-seq
MIRT1252832	hsa-miR-2964a-5p	CLIP-seq
MIRT1252833	hsa-miR-3184	CLIP-seq
MIRT1252834	hsa-miR-3190	CLIP-seq
MIRT1252835	hsa-miR-3673	CLIP-seq
MIRT1252836	hsa-miR-3918	CLIP-seq
MIRT1252837	hsa-miR-3944-5p	CLIP-seq
MIRT1252838	hsa-miR-4302	CLIP-seq
MIRT1252839	hsa-miR-4512	CLIP-seq
MIRT1252840	hsa-miR-4640-5p	CLIP-seq
MIRT1252841	hsa-miR-4660	CLIP-seq
MIRT1252842	hsa-miR-4697-3p	CLIP-seq
MIRT1252843	hsa-miR-4726-5p	CLIP-seq
MIRT1252844	hsa-miR-4730	CLIP-seq
MIRT1252845	hsa-miR-5047	CLIP-seq
MIRT1252846	hsa-miR-668	CLIP-seq
MIRT1252847	hsa-miR-888	CLIP-seq
MIRT2074462	hsa-miR-1233	CLIP-seq
MIRT2074463	hsa-miR-146b-3p	CLIP-seq
MIRT1252836	hsa-miR-3918	CLIP-seq
MIRT1252838	hsa-miR-4302	CLIP-seq
MIRT1252839	hsa-miR-4512	CLIP-seq
MIRT1252842	hsa-miR-4697-3p	CLIP-seq
MIRT1252844	hsa-miR-4730	CLIP-seq
MIRT1252846	hsa-miR-668	CLIP-seq
MIRT1252847	hsa-miR-888	CLIP-seq
MIRT1252826	hsa-miR-1	CLIP-seq
MIRT1252833	hsa-miR-3184	CLIP-seq
MIRT1252835	hsa-miR-3673	CLIP-seq
MIRT2598177	hsa-miR-1914	CLIP-seq
MIRT1252832	hsa-miR-2964a-5p	CLIP-seq
MIRT2598178	hsa-miR-339-5p	CLIP-seq
MIRT1252846	hsa-miR-668	CLIP-seq
MIRT1252847	hsa-miR-888	CLIP-seq
MIRT2598177	hsa-miR-1914	CLIP-seq
MIRT1252832	hsa-miR-2964a-5p	CLIP-seq
MIRT2598178	hsa-miR-339-5p	CLIP-seq
MIRT1252846	hsa-miR-668	CLIP-seq
MIRT1252847	hsa-miR-888	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0003723	Function	RNA binding	HDA	22658674, 22681889
GO:0003755	Function	Peptidyl-prolyl cis-trans isomerase activity	IBA
GO:0003755	Function	Peptidyl-prolyl cis-trans isomerase activity	IDA	20676357
GO:0003755	Function	Peptidyl-prolyl cis-trans isomerase activity	IEA
GO:0003755	Function	Peptidyl-prolyl cis-trans isomerase activity	ISS
GO:0003755	Function	Peptidyl-prolyl cis-trans isomerase activity	NAS	2000394
GO:0005515	Function	Protein binding	IPI	15095401, 15989969, 20147391, 21280149, 21516116, 22665516, 25416956, 30021884, 32296183, 32814053
GO:0005515	Function	Protein binding	ISS
GO:0005518	Function	Collagen binding	ISS
GO:0005634	Component	Nucleus	HDA	21630459
GO:0005654	Component	Nucleoplasm	IDA
GO:0005737	Component	Cytoplasm	IBA
GO:0005783	Component	Endoplasmic reticulum	IDA	20089953
GO:0005783	Component	Endoplasmic reticulum	IEA
GO:0005783	Component	Endoplasmic reticulum	TAS	2000394
GO:0005788	Component	Endoplasmic reticulum lumen	IEA
GO:0005788	Component	Endoplasmic reticulum lumen	NAS	1530944
GO:0005788	Component	Endoplasmic reticulum lumen	TAS
GO:0005790	Component	Smooth endoplasmic reticulum	IEA
GO:0005829	Component	Cytosol	TAS
GO:0005925	Component	Focal adhesion	HDA	21423176
GO:0006457	Process	Protein folding	IBA
GO:0006457	Process	Protein folding	IDA	22665516
GO:0006457	Process	Protein folding	IMP	20089953
GO:0016018	Function	Cyclosporin A binding	IBA
GO:0016020	Component	Membrane	HDA	19946888
GO:0016853	Function	Isomerase activity	IEA
GO:0030593	Process	Neutrophil chemotaxis	IDA	11688976
GO:0032991	Component	Protein-containing complex	ISS
GO:0034663	Component	Endoplasmic reticulum chaperone complex	IEA
GO:0040018	Process	Positive regulation of multicellular organism growth	IMP	20089953
GO:0042470	Component	Melanosome	IEA
GO:0043231	Component	Intracellular membrane-bounded organelle	IBA
GO:0044794	Process	Host-mediated activation of viral process	IMP	15989969
GO:0044829	Process	Host-mediated activation of viral genome replication	IMP	15989969
GO:0048471	Component	Perinuclear region of cytoplasm	IDA	15989969
GO:0050821	Process	Protein stabilization	IMP	20089953
GO:0051082	Function	Unfolded protein binding	TAS	2000394
GO:0060348	Process	Bone development	IMP	20089953
GO:0070062	Component	Extracellular exosome	HDA	19056867, 19199708, 20458337, 23533145
GO:0070063	Function	RNA polymerase binding	IPI	15989969
GO:1901873	Process	Regulation of post-translational protein modification	IMP	20089953

Other IDs

• MIM: 123841
• HGNC: 9255
• e!Ensembl: ENSG00000166794

Protein

• UniProt ID: P23284
• Protein name: Peptidyl-prolyl cis-trans isomerase B (PPIase B) (EC 5.2.1.8) (CYP-S1) (Cyclophilin B) (Rotamase B) (S-cyclophilin) (SCYLP)
• Protein function: PPIase that catalyzes the cis-trans isomerization of proline imidic peptide bonds in oligopeptides and may therefore assist protein folding.
• PDB: 1CYN, 3ICH, 3ICI, 8K0F, 8K0I, 8K0M, 8K17, 8KC9
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF00160	Pro_isomerase	47 → 204	Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD	Domain

• Sequence:

  MLRLSERNMKVLLAAALIAGSVFFLLLPGPSAADEKKKGPKVTVKVYFDLRIGDEDVGRV
  IFGLFGKTVPKTVDNFVALATGEKGFGYKNSKFHRVIKDFMIQGGDFTRGDGTGGKSIYG
  ERFPDENFKLKHYGPGWVSMANAGKDTNGSQFFITTVKTAWLDGKHVVFGKVLEGMEVVR
  KVESTKTDSRDKPLKDVIIADCGKIEVEKPFAIAKE

• Sequence length: 216

Pathways

Reactome:

Collagen biosynthesis and modifying enzymes

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)

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Clear cell carcinoma of kidney	Likely pathogenic	rs748284900	RCV005910853	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Osteogenesis imperfecta	Likely pathogenic; Pathogenic	rs1228817029, rs137853869, rs137853866	RCV002271935 RCV002307366 RCV003114203	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Osteogenesis imperfecta type 9	Likely pathogenic; Pathogenic	rs1211592084, rs137853869, rs121434559, rs137853865, rs137853866, rs398122834	RCV001849895 RCV000018433 RCV000018434 RCV000202411 RCV000202406 RCV000034321	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
Adrenocortical carcinoma, hereditary	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
BONE FRAGILITY WITH CONTRACTURES, ARTERIAL RUPTURE, AND DEAFNESS	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cervical cancer	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cholangiocarcinoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Colon adenocarcinoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Colorectal cancer	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DESBUQUOIS SYNDROME	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
EBV-positive nodal T- and NK-cell lymphoma	Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Lung cancer	Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Lymphoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant tumor of esophagus	Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Melanoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Nonpapillary renal cell carcinoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OSTEOGENESIS IMPERFECTA TYPE 2	—	Disgenet, Orphanet Disgenet, Orphanet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OSTEOGENESIS IMPERFECTA TYPE 3	—	Disgenet, Orphanet Disgenet, Orphanet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OSTEOGENESIS IMPERFECTA TYPE 4	—	Disgenet, Orphanet Disgenet, Orphanet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OSTEOGENESIS IMPERFECTA TYPE III	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OSTEOGENESIS IMPERFECTA TYPE IV	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OSTEOGENESIS IMPERFECTA, DOMINANT PERINATAL LETHAL	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Osteogenesis Imperfecta, Recessive	Benign; Likely benign; Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OSTEOGENESIS IMPERFECTA, TYPE IX	—	CTD, Disgenet, HPO CTD, Disgenet, HPO CTD, Disgenet, HPO	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OSTEOPOROSIS-PSEUDOGLIOMA SYNDROME	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PPIB-related disorder	Uncertain significance; Likely benign; Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Sarcoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Thymoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Thyroid cancer, nonmedullary, 1	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine corpus endometrial carcinoma	Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uveal melanoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Asthma	Asthma	Pubtator	21999750	Stimulate	★☆☆☆☆ Found in Text Mining only
Bone Diseases, Developmental	Bone Disease	BEFREE	24968150		★☆☆☆☆ Found in Text Mining only
Breast Carcinoma	Breast Carcinoma	BEFREE	19056847, 20237142		★☆☆☆☆ Found in Text Mining only
Breast Neoplasms	Breast neoplasm	Pubtator	19056847	Stimulate	★☆☆☆☆ Found in Text Mining only
Breast Neoplasms	Breast neoplasm	Pubtator	20237142	Associate	★☆☆☆☆ Found in Text Mining only
Carcinoma Hepatocellular	Hepatocellular carcinoma	Pubtator	33111654	Associate	★☆☆☆☆ Found in Text Mining only
Cartilage Diseases	Cartilage disease	Pubtator	19781681	Associate	★☆☆☆☆ Found in Text Mining only
Colon Carcinoma	Colon Carcinoma	BEFREE	11473727, 21748762		★☆☆☆☆ Found in Text Mining only
Colorectal Carcinoma	Colorectal Cancer	BEFREE	29876924		★☆☆☆☆ Found in Text Mining only
Congenital pectus carinatum	Congenital Pectus Carinatum	HPO_DG			★☆☆☆☆ Found in Text Mining only
Congenital pectus excavatum	Congenital Pectus Excavatum	HPO_DG			★☆☆☆☆ Found in Text Mining only
Dentinogenesis Imperfecta	Dentinogenesis Imperfecta	HPO_DG			★☆☆☆☆ Found in Text Mining only
Endometrial adenocarcinoma	Endometrial Adenocarcinoma	BEFREE	31783195		★☆☆☆☆ Found in Text Mining only
Endometrial Neoplasms	Endometrial neoplasm	Pubtator	34187415	Stimulate	★☆☆☆☆ Found in Text Mining only
Glioblastoma	Glioblastoma	BEFREE	24272483		★☆☆☆☆ Found in Text Mining only
Glioblastoma Multiforme	Glioblastoma	BEFREE	24272483		★☆☆☆☆ Found in Text Mining only
Hypertensive disease	Hypertension	BEFREE	29312150		★☆☆☆☆ Found in Text Mining only
leukemia	Leukemia	BEFREE	10528204		★☆☆☆☆ Found in Text Mining only
Liver carcinoma	Liver carcinoma	BEFREE	21748762, 22555451		★☆☆☆☆ Found in Text Mining only
Liver neoplasms	Liver neoplasms	BEFREE	22555451		★☆☆☆☆ Found in Text Mining only
Malignant Glioma	Glioma	BEFREE	24272483		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of breast	Breast Cancer	BEFREE	19056847, 20237142		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of pancreas	Pancreatic cancer	BEFREE	31043353		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of skin	Skin cancer	BEFREE	28789363		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of stomach	Stomach Neoplasms	BEFREE	26125731		★☆☆☆☆ Found in Text Mining only
Malignant Neoplasms	Malignant Neoplasm	BEFREE	11473727, 22555451		★☆☆☆☆ Found in Text Mining only
Malignant tumor of colon	Colonic Neoplasms	BEFREE	11473727, 21748762		★☆☆☆☆ Found in Text Mining only
Mammary Neoplasms	Mammary Neoplasms	BEFREE	15470903		★☆☆☆☆ Found in Text Mining only
Metabolic Syndrome X	Metabolic Syndrome	BEFREE	29312150		★☆☆☆☆ Found in Text Mining only
Nasopharyngeal Carcinoma	Nasopharyngeal carcinoma	Pubtator	31040200	Associate	★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	10528204, 11473727		★☆☆☆☆ Found in Text Mining only
Non-Small Cell Lung Carcinoma	Lung carcinoma	BEFREE	31043353		★☆☆☆☆ Found in Text Mining only
Obesity	Obesity	BEFREE	29312150		★☆☆☆☆ Found in Text Mining only
Osteogenesis Imperfecta	Osteogenesis Imperfecta	BEFREE	19781681, 20089953, 20485499, 20855225, 20946018, 21282188, 21667357, 22332926, 24968150, 25007323, 26634552, 28242392, 28696707		★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Osteogenesis Imperfecta	Osteogenesis imperfecta	Pubtator	19781681, 20089953, 20188343, 21282188, 21829228, 22718341, 26634552, 28802583, 30993352, 39245686	Associate	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Osteogenesis imperfecta type 2	Osteogenesis Imperfecta	Orphanet			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Osteogenesis imperfecta type 3	Osteogenesis Imperfecta	Orphanet			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Osteogenesis imperfecta type 4	Osteogenesis Imperfecta	Orphanet			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Osteogenesis imperfecta type III (disorder)	Osteogenesis Imperfecta	ORPHANET_DG	21438135		★☆☆☆☆ Found in Text Mining only
Osteogenesis imperfecta type IV (disorder)	Osteogenesis Imperfecta	ORPHANET_DG	21282188		★☆☆☆☆ Found in Text Mining only
Osteogenesis Imperfecta Type IX	Osteogenesis imperfecta	Pubtator	22718341, 28802583	Associate	★☆☆☆☆ Found in Text Mining only
Osteogenesis imperfecta, dominant perinatal lethal	Osteogenesis Imperfecta	ORPHANET_DG	21438135		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OSTEOGENESIS IMPERFECTA, TYPE IX (disorder)	Osteogenesis Imperfecta	UNIPROT_DG	19781681, 20089953		★☆☆☆☆ Found in Text Mining only
OSTEOGENESIS IMPERFECTA, TYPE IX (disorder)	Osteogenesis Imperfecta	BEFREE	22718341, 24968150, 28242392		★☆☆☆☆ Found in Text Mining only
OSTEOGENESIS IMPERFECTA, TYPE IX (disorder)	Osteogenesis Imperfecta	CTD_human_DG			★☆☆☆☆ Found in Text Mining only
OSTEOGENESIS IMPERFECTA, TYPE IX (disorder)	Osteogenesis Imperfecta	CLINVAR_DG			★☆☆☆☆ Found in Text Mining only
OSTEOGENESIS IMPERFECTA, TYPE IX (disorder)	Osteogenesis Imperfecta	GENOMICS_ENGLAND_DG			★☆☆☆☆ Found in Text Mining only
Osteogenesis imperfecta, type VIII	Osteogenesis Imperfecta	BEFREE	28802583		★☆☆☆☆ Found in Text Mining only
Pancreatic carcinoma	Pancreatic carcinoma	BEFREE	31043353		★☆☆☆☆ Found in Text Mining only
Periodontitis	Periodontitis	Pubtator	29116140	Associate	★☆☆☆☆ Found in Text Mining only
Scoliosis, unspecified	Scoliosis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Squamous Cell Carcinoma of Head and Neck	Squamous cell carcinoma	Pubtator	22241958	Associate	★☆☆☆☆ Found in Text Mining only
Stomach Carcinoma	Stomach Carcinoma	BEFREE	26125731		★☆☆☆☆ Found in Text Mining only