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

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	51134
Gene name	Centrosomal protein 83
Gene symbol	CEP83
Synonyms (NCBI Gene)	CCDC41NPHP18NY-REN-58
Chromosome	12
Chromosome location	12q22
Summary	The protein encoded by this gene is a centriolar protein involved in primary cilium assembly. Defects in this gene have been associated with infantile nephronophthisis and intellectual disability. [provided by RefSeq, Oct 2016]

Show/Hide all (11)

SNP ID	Visualize variation	Clinical significance	Consequence
rs200971081	T>A	Likely-pathogenic	Genic downstream transcript variant, non coding transcript variant, coding sequence variant, intron variant, missense variant, downstream transcript variant
rs368619022	G>A,T	Pathogenic	Non coding transcript variant, genic upstream transcript variant, coding sequence variant, 5 prime UTR variant, missense variant, stop gained
rs369483167	G>A	Pathogenic	5 prime UTR variant, stop gained, non coding transcript variant, coding sequence variant
rs587777486	G>A	Pathogenic	5 prime UTR variant, coding sequence variant, genic upstream transcript variant, intron variant, non coding transcript variant, stop gained
rs587777487	C>G,T	Pathogenic	Coding sequence variant, missense variant, non coding transcript variant, genic downstream transcript variant
rs587777488	G>T	Pathogenic	Coding sequence variant, stop gained, non coding transcript variant, genic downstream transcript variant
rs757301110	G>A,T	Pathogenic	Synonymous variant, intron variant, stop gained, non coding transcript variant, coding sequence variant
rs879255575	CAATTCCAATTTTTGTGG>-	Pathogenic	5 prime UTR variant, non coding transcript variant, genic upstream transcript variant, inframe deletion, upstream transcript variant, coding sequence variant, intron variant
rs879255576	GTT>-	Pathogenic	Non coding transcript variant, coding sequence variant, genic downstream transcript variant, inframe deletion
rs1064794347	->AT	Pathogenic	Non coding transcript variant, coding sequence variant, intron variant, downstream transcript variant, frameshift variant, genic downstream transcript variant
rs1207804224	G>A	Pathogenic	Genic downstream transcript variant, non coding transcript variant, stop gained, coding sequence variant

Show/Hide all (14)

miRTarBase ID	miRNA	Experiments	Reference
MIRT742070	hsa-miR-1306-5p	HITS-CLIP	23824327
MIRT742071	hsa-miR-5702	HITS-CLIP	23824327
MIRT742072	hsa-miR-937-5p	HITS-CLIP	23824327
MIRT742073	hsa-miR-7641	HITS-CLIP	23824327
MIRT754755	hsa-miR-548c-3p	PAR-CLIP	22291592
MIRT754756	hsa-miR-548a-3p	PAR-CLIP	22291592
MIRT754757	hsa-miR-548ar-3p	PAR-CLIP	22291592
MIRT754758	hsa-miR-548az-3p	PAR-CLIP	22291592
MIRT754759	hsa-miR-548e-3p	PAR-CLIP	22291592
MIRT754760	hsa-miR-548f-3p	PAR-CLIP	22291592
MIRT754761	hsa-miR-5582-3p	PAR-CLIP	22291592
MIRT754762	hsa-miR-4282	PAR-CLIP	22291592
MIRT754763	hsa-miR-590-3p	PAR-CLIP	22291592
MIRT754764	hsa-miR-4522	PAR-CLIP	22291592

Show/Hide all (22)

GO ID	Ontology	Definition	Evidence	Reference
GO:0005515	Function	Protein binding	IPI	23530209, 32296183
GO:0005737	Component	Cytoplasm	IEA
GO:0005794	Component	Golgi apparatus	IBA
GO:0005794	Component	Golgi apparatus	IDA	23530209
GO:0005813	Component	Centrosome	IBA
GO:0005814	Component	Centriole	IBA
GO:0005814	Component	Centriole	IDA	23348840, 23530209
GO:0005814	Component	Centriole	IEA
GO:0005829	Component	Cytosol	TAS
GO:0005856	Component	Cytoskeleton	IEA
GO:0030030	Process	Cell projection organization	IEA
GO:0042802	Function	Identical protein binding	IPI	32296183
GO:0048278	Process	Vesicle docking	IMP	23530209
GO:0051660	Process	Establishment of centrosome localization	IBA
GO:0051660	Process	Establishment of centrosome localization	IEA
GO:0060271	Process	Cilium assembly	IBA
GO:0060271	Process	Cilium assembly	IEA
GO:0060271	Process	Cilium assembly	IMP	23348840, 23530209
GO:0060271	Process	Cilium assembly	IMP	23348840, 23530209
GO:0071539	Process	Protein localization to centrosome	IMP	23348840, 23530209
GO:0097539	Component	Ciliary transition fiber	IBA
GO:0097539	Component	Ciliary transition fiber	IDA	23348840

MIM	HGNC	e!Ensembl
615847	17966	ENSG00000173588

Q9Y592

Protein name

Centrosomal protein of 83 kDa (Cep83) (Coiled-coil domain-containing protein 41) (Renal carcinoma antigen NY-REN-58)

Protein function

Component of the distal appendage region of the centriole involved in the initiation of primary cilium assembly. May collaborate with IFT20 in the trafficking of ciliary membrane proteins from the Golgi complex to the cilium during the initiatio

Family and domains

Sequence

MVVSTFTDMDTFPNNFPPGGDSGLTGSQSEFQKMLIDERLRCEHHKANYQTLKAEHTRLQ
NEHVKLQNELKHLFNEKQTQQEKLQLLLEELRGELVEKTKDLEEMKLQILTPQKLELLRA
QIQQELETPMRERFRNLDEEVEKYRAVYNKLRYEHTFLKSEFEHQKEEYARILDEGKIKY
ESEIARLEEDKEELRNQLLNVDLTKDSKRVEQLAREKVYLCQKLKGLEAEVAELKAEKEN
SEAQVENAQRIQVRQLAEMQATVRSLEAEKQSANLRAERLEKELQSSSEQNTFLINKLHK
AEREINTLSSKVKELKHSNKLEITDIKLETARAKSELERERNKIQSELDGLQSDNEILKA
AVEHHKVLLVEKDRELIRKVQAAKEEGYQKLVVLQDEKLELENRLADLEKMKVEHDVWRQ
SEKDQYEEKLRASQMAEEITRKELQSVRLKLQQQIVTIENAEKEKNENSDLKQQISSLQI
QVTSLAQSENDLLNSNQMLKEMVERLKQECRNFRSQAEKAQLEAEKTLEEKQIQWLEEKH
KLHERITDREEKYNQAKEKLQRAAIAQKKRKSLHENKLKRLQEKVEVLEAKKEELETENQ
VLNRQNVPFEDYTRLQKRLKDIQRRHNEFRSLILVPNMPPTASINPVSFQSSAMVPSMEL
PFPPHMQEEQHQRELSLLRKRLEELETTQRKQLEELGSSGE

Sequence length

701

Interactions

View interactions

	Reactome
			Anchoring of the basal body to the plasma membrane

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 (3)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Ciliopathy	Likely pathogenic	rs2541287399	RCV003984302	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Nephronophthisis	Pathogenic	rs780500128	RCV003483757	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Nephronophthisis 18	Pathogenic; Likely pathogenic	rs922686745, rs1276979881, rs750092874, rs1162641847, rs1555237944, rs2137575733, rs587777486, rs879255575, rs368619022, rs879255576, rs587777487, rs369483167, rs587777488, rs777412559, rs2061111812 View all (17 more)	RCV001383008 RCV001384613 RCV001385312 RCV001866359 RCV001974117 View all (27 more)	★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)

Show/Hide Unknown Diseases (15)

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.
CEP83-related disorder	Likely benign; Uncertain significance; Conflicting classifications of pathogenicity	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CILIOPATHIES	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
COLOR VISION DISORDER	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DEFICIENCY ANEMIA	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Familial cancer of breast	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
HEART CONDUCTION DISEASE	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Hepatocellular carcinoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant lymphoma, large B-cell, diffuse	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NEPHRONOPHTHISIS 2	—	CTD, Disgenet CTD, Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Nonpapillary renal cell carcinoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Ovarian serous cystadenocarcinoma	Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Sarcoma	Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Thymoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine corpus endometrial carcinoma	Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uveal melanoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Show/Hide Text Mining Associations (22)

Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Associations from Text Mining Disease associations identified through text mining
Chronic kidney disease stage 5	Kidney Disease	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Ciliopathies	Ciliopathy	Pubtator	33938610	Associate	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Congenital neurologic anomalies	Drachtman Weinblatt Sitarz syndrome	BEFREE	24882706		★★★★★ ★☆☆☆☆ Found in Text Mining only
Hydrocephalus	Hydrocephalus	Pubtator	24882706	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Infantile nephronophthisis	Nephronophthisis	Orphanet			★★★★★ ★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Mental retardation	BEFREE	24882706		★★★★★ ★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Intellectual developmental disorder	Pubtator	24882706	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Kidney Diseases	Kidney disease	Pubtator	33938610, 36222666	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Learning Disabilities	Learning disorders	Pubtator	24882706	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Nephritis, Tubulointerstitial	Nephritis	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Nephronophthisis	Nephronophthisis	HPO_DG			★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
NEPHRONOPHTHISIS 18	Nephronophthisis	GENOMICS_ENGLAND_DG	24882706		★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
NEPHRONOPHTHISIS 18	Nephronophthisis	UNIPROT_DG	24882706		★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
NEPHRONOPHTHISIS 18	Nephronophthisis	CLINVAR_DG			★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
NEPHRONOPHTHISIS 18	Nephronophthisis	CTD_human_DG			★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
NEPHRONOPHTHISIS 2	Nephronophthisis	BEFREE	24882706		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NEPHRONOPHTHISIS 2	Nephronophthisis	ORPHANET_DG	24882706		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Nephronophthisis 2	Nephronophthisis	Pubtator	24882706	Associate	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Nephronophthisis familial juvenile	Nephronophthisis	Pubtator	24882706, 33938610	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Retinal Degeneration	Retinal degeneration	Pubtator	36672815	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Retinal Diseases	Retinal detachment	Pubtator	33938610	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Retinitis Pigmentosa	Retinitis pigmentosa	Pubtator	33938610	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only

CEP83 (centrosomal protein 83)