PIBF1 (progesterone immunomodulatory binding factor 1)

Gene

• Entrez ID: 10464
• Gene name: Progesterone immunomodulatory binding factor 1
• Gene symbol: PIBF1
• Synonyms (NCBI Gene): C13orf24, CEP90, JBTS33, PIBF
• Chromosome: 13
• Chromosome location: 13q21.33-q22.1
• Summary: This gene encodes a protein that is induced by the steroid hormone progesterone and plays a role in the maintenance of pregnancy. The encoded protein regulates multiple facets of the immune system to promote normal pregnancy including cytokine synthesis,

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs17089782	G>A	Pathogenic, likely-pathogenic	Missense variant, coding sequence variant, non coding transcript variant
rs144610914	A>G	Pathogenic	3 prime UTR variant, missense variant, non coding transcript variant, coding sequence variant
rs147863910	A>C,T	Likely-pathogenic	5 prime UTR variant, missense variant, non coding transcript variant, coding sequence variant
rs539010725	C>A,G,T	Pathogenic	Non coding transcript variant, intron variant, stop gained, missense variant, coding sequence variant
rs863225214	C>-	Likely-pathogenic	Frameshift variant, coding sequence variant, genic downstream transcript variant, non coding transcript variant
rs911707459	A>T	Pathogenic	Missense variant, coding sequence variant, genic downstream transcript variant, intron variant, non coding transcript variant
rs987735817	A>C	Pathogenic	Non coding transcript variant, genic downstream transcript variant, intron variant, coding sequence variant, missense variant
rs1594219498	C>T	Pathogenic	Stop gained, genic downstream transcript variant, coding sequence variant, non coding transcript variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT2295686	hsa-miR-320e	CLIP-seq
MIRT2295687	hsa-miR-4680-3p	CLIP-seq
MIRT2295688	hsa-miR-587	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0002376	Process	Immune system process	IEA
GO:0005136	Function	Interleukin-4 receptor binding	IDA	16393965
GO:0005515	Function	Protein binding	IPI	17500595, 26297806, 26638075, 35709258
GO:0005576	Component	Extracellular region	IEA
GO:0005615	Component	Extracellular space	IDA	14634107
GO:0005634	Component	Nucleus	IDA	14634107
GO:0005634	Component	Nucleus	IEA
GO:0005737	Component	Cytoplasm	IEA
GO:0005813	Component	Centrosome	IDA	21399614
GO:0005813	Component	Centrosome	IEA
GO:0005815	Component	Microtubule organizing center	IBA
GO:0005856	Component	Cytoskeleton	IEA
GO:0007080	Process	Mitotic metaphase chromosome alignment	IMP	21224392
GO:0031393	Process	Negative regulation of prostaglandin biosynthetic process	IDA	3863495
GO:0032695	Process	Negative regulation of interleukin-12 production	IDA	14634107
GO:0032733	Process	Positive regulation of interleukin-10 production	IDA	14634107
GO:0032815	Process	Negative regulation of natural killer cell activation	IDA	12516630
GO:0034451	Component	Centriolar satellite	IDA	21224392
GO:0034451	Component	Centriolar satellite	IEA
GO:0036064	Component	Ciliary basal body	IDA
GO:0042531	Process	Positive regulation of tyrosine phosphorylation of STAT protein	IDA	16393965
GO:0042532	Process	Negative regulation of tyrosine phosphorylation of STAT protein	IDA	16393965
GO:0042976	Process	Activation of Janus kinase activity	IDA	16393965
GO:0060271	Process	Cilium assembly	IBA
GO:0060271	Process	Cilium assembly	IMP	26167768
GO:0071539	Process	Protein localization to centrosome	IMP	23110211
GO:0090307	Process	Mitotic spindle assembly	IMP	21224392
GO:1905515	Process	Non-motile cilium assembly	IMP	23110211

Other IDs

• MIM: 607532
• HGNC: 23352
• e!Ensembl: ENSG00000083535

Protein

• UniProt ID: Q8WXW3
• Protein name: Progesterone-induced-blocking factor 1 (PIBF) (Centrosomal protein of 90 kDa) (CEP90)
• Protein function: Plays a role in ciliogenesis. ; [Isoform 1]: Pericentriolar protein required to maintain mitotic spindle pole integrity (PubMed:21224392). Required for the centrosomal accumulation of PCM1 and the recruitm
• Tissue specificity: TISSUE SPECIFICITY: Expressed at highest levels in testis. Moderate expression is detected in spleen, thymus, prostate, ovary, small intestine, and colon (PubMed:11935316). Expressed in the first trimester pregnancy decidua (PubMed:12516630). Localized to
• Sequence:

  MSRKISKESKKVNISSSLESEDISLETTVPTDDISSSEEREGKVRITRQLIERKELLHNI
  QLLKIELSQKTMMIDNLKVDYLTKIEELEEKLNDALHQKQLLTLRLDNQLAFQQKDASKY
  QELMKQEMETILLRQKQLEETNLQLREKAGDVRRNLRDFELTEEQYIKLKAFPEDQLSIP
  EYVSVRFYELVNPLRKEICELQVKKNILAEELSTNKNQLKQLTETYEEDRKNYSEVQIRC
  QRLALELADTKQLIQQGDYRQENYDKVKSERDALEQEVIELRRKHEILEASHMIQTKERS
  ELSKEVVTLEQTVTLLQKDKEYLNRQNMELSVRCAHEEDRLERLQAQLEESKKAREEMYE
  KYVASRDHYKTEYENKLHDELEQIRLKTNQEIDQLRNASREMYERENRNLREARDNAVAE
  KERAVMAEKDALEKHDQLLDRYRELQLSTESKVTEFLHQSKLKSFESERVQLLQEETARN
  LTQCQLECEKYQKKLEVLTKEFYSLQASSEKRITELQAQNSEHQARLDIYEKLEKELDEI
  IMQTAEIENEDEAERVLFSYGYGANVPTTAKRRLKQSVHLARRVLQLEKQNSLILKDLEH
  RKDQVTQLSQELDRANSLLNQTQQPYRYLIESVRQRDSKIDSLTESIAQLEKDVSNLNKE
  KSALLQTKNQMALDLEQLLNHREELAAMKQILVKMHSKHSENSLLLTKTEPKHVTENQKS
  KTLNVPKEHEDNIFTPKPTLFTKKEAPEWSKKQKMKT

• Sequence length: 757

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
Cephalocele	Likely pathogenic; Pathogenic	rs144610914, rs911707459	RCV000779664 RCV000779665	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Dandy-Walker syndrome	Likely pathogenic; Pathogenic	rs144610914, rs911707459	RCV001257995 RCV001257996	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Joubert syndrome	Likely pathogenic	rs863225214	RCV000201708	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Joubert syndrome 33	Likely pathogenic; Pathogenic	rs2138204996, rs2137980593, rs2501854454, rs2041684401, rs987735817, rs144610914, rs539010725, rs911707459, rs1594219498, rs2037306370, rs751280996	RCV001806372 RCV002250906 RCV002810038 RCV003493336 RCV000515457 RCV000779664 RCV000735820 RCV000779665 RCV000995835 RCV001261421 RCV001782615	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
PIBF1-related disorder	Likely pathogenic; Pathogenic	rs2501854454, rs2501798819, rs987735817	RCV004754960 RCV003901636 RCV004754456	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
CILIOPATHIES	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CILIOPATHY	—	ClinGen, GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CONGENITAL CEREBRAL HERNIA	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
EMPHYSEMA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
FAMILIAL APLASIA OF THE VERMIS	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GOUT	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ISOLATED JOUBERT SYNDROME	—	Orphanet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant tumor of esophagus	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Astrocytoma	Astrocytoma	Pubtator	28168193	Associate	★☆☆☆☆ Found in Text Mining only
Blepharoptosis	Ptosis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Breast Carcinoma	Breast Carcinoma	BEFREE	15305375, 29107859		★☆☆☆☆ Found in Text Mining only
Congenital cerebral hernia	Congenital Cerebral Hernia	CLINVAR_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Congenital cerebral hernia	Congenital Cerebral Hernia	HPO_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Congenital coloboma of iris	Congenital Coloboma Of Iris	HPO_DG			★☆☆☆☆ Found in Text Mining only
Emphysema	Emphysema	Pubtator	34404834	Associate	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Familial aplasia of the vermis	Cerebellar vermis agenesis	ORPHANET_DG	26167768		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Familial aplasia of the vermis	Cerebellar vermis agenesis	GENOMICS_ENGLAND_DG	26167768		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Familial aplasia of the vermis	Cerebellar vermis agenesis	CLINVAR_DG	26167768		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Familial aplasia of the vermis	Cerebellar vermis agenesis	BEFREE	29695797, 30520571		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Glioblastoma	Glioblastoma	Pubtator	24474429, 28168193	Associate	★☆☆☆☆ Found in Text Mining only
Global developmental delay	Developmental Delay	GENOMICS_ENGLAND_DG	26167768		★☆☆☆☆ Found in Text Mining only
Global developmental delay	Developmental Delay	HPO_DG			★☆☆☆☆ Found in Text Mining only
Hirschsprung Disease	Hirschsprung Disease	HPO_DG			★☆☆☆☆ Found in Text Mining only
Hydrocephalus	Hydrocephalus	HPO_DG			★☆☆☆☆ Found in Text Mining only
Hypertension	Hypertension	Pubtator	24165912	Associate	★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Mental retardation	HPO_DG			★☆☆☆☆ Found in Text Mining only
Joubert syndrome	Joubert syndrome	Orphanet			★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Joubert syndrome 1	Joubert Syndrome	ORPHANET_DG	26167768		★☆☆☆☆ Found in Text Mining only
JOUBERT SYNDROME 33	Joubert syndrome	UNIPROT_DG	26167768		★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
JOUBERT SYNDROME 33	Joubert syndrome	GENOMICS_ENGLAND_DG	29695797		★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
JOUBERT SYNDROME 33	Joubert syndrome	CLINVAR_DG			★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Lung Neoplasms	Lung neoplasms	Pubtator	37478265	Associate	★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of breast	Breast Cancer	BEFREE	15305375, 29107859		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of stomach	Stomach Neoplasms	BEFREE	26980572		★☆☆☆☆ Found in Text Mining only
Mammary Neoplasms	Mammary Neoplasms	BEFREE	15305375		★☆☆☆☆ Found in Text Mining only
Mammary Neoplasms	Mammary Neoplasms	LHGDN	15305375		★☆☆☆☆ Found in Text Mining only
Microcephaly	Microcephaly	Pubtator	26297806	Associate	★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	15305375		★☆☆☆☆ Found in Text Mining only
Nystagmus	Nystagmus	HPO_DG			★☆☆☆☆ Found in Text Mining only
Oculomotor apraxia	Oculomotor apraxia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Oculovestibuloauditory syndrome	Oculovestibuloauditory Syndrome	HPO_DG			★☆☆☆☆ Found in Text Mining only
Oral cleft	Oral cleft	HPO_DG			★☆☆☆☆ Found in Text Mining only
Polydactyly of toes	Polydactyly Of Toes	HPO_DG			★☆☆☆☆ Found in Text Mining only
Polymicrogyria	Polymicrogyria	HPO_DG			★☆☆☆☆ Found in Text Mining only
Ptosis	Ptosis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Pulmonary Disease Chronic Obstructive	Chronic obstructive pulmonary disease	Pubtator	34404834	Associate	★☆☆☆☆ Found in Text Mining only
Scoliosis, unspecified	Scoliosis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Situs inversus totalis	Situs Inversus	HPO_DG			★☆☆☆☆ Found in Text Mining only
Stomach Carcinoma	Stomach Carcinoma	BEFREE	26980572		★☆☆☆☆ Found in Text Mining only
Stomach Neoplasms	Stomach neoplasms	Pubtator	26980572	Associate	★☆☆☆☆ Found in Text Mining only
Strabismus	Strabismus	HPO_DG			★☆☆☆☆ Found in Text Mining only