CEP83 (centrosomal protein 83)

Gene

• Entrez ID: 51134
• Gene name: Centrosomal protein 83
• Gene symbol: CEP83
• Synonyms (NCBI Gene): CCDC41, NPHP18, NY-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]

SNPs

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

miRNA

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

Gene ontology (GO)

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

Other IDs

• MIM: 615847
• HGNC: 17966
• e!Ensembl: ENSG00000173588

Protein

• UniProt ID: 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
• Sequence:

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

• Sequence length: 701

Pathways

Reactome:

Anchoring of the basal body to the plasma membrane

Associated diseases

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Ciliopathy	Likely pathogenic	rs2541287399	RCV003984302
Nephronophthisis	Pathogenic	rs780500128	RCV003483757
Nephronophthisis 18	Pathogenic; Likely pathogenic	rs922686745, rs1276979881, rs750092874, rs1162641847, rs1555237944, rs2137575733, rs587777486, rs879255575, rs368619022, rs879255576, rs587777487, rs369483167, rs587777488, rs777412559, rs2061111812, rs2136515432, rs1187876547, rs1198459012, rs2137174483, rs2136488957, rs2136514301, rs2541064312, rs1216945458, rs1437433749, rs2541678147, rs763560797, rs2541287551, rs2541088599, rs1064794347, rs1207804224, rs780500128, rs2061113374	RCV001383008 RCV001384613 RCV001385312 RCV001866359 RCV001974117 RCV002002375 RCV000128439 RCV000128440 RCV000128441 RCV000128442 RCV000128443 RCV000128444 RCV000128445 RCV001925052 RCV001933612 RCV001941874 RCV001949012 RCV001932813 RCV001949388 RCV001979772 RCV001934053 RCV003112252 RCV002636025 RCV002881285 RCV003585524 RCV003585613 RCV003584078 RCV003584282 RCV001851184 RCV000701469 RCV001037716 RCV001060137

Unknown
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
CEP83-related disorder	Likely benign; Uncertain significance; Conflicting classifications of pathogenicity	rs199828197, rs550020211, rs371676456, rs1164166356, rs1383807925, rs2541673011, rs780167307, rs150415429, rs199617764, rs187309637, rs185058802	RCV003938726 RCV004757491 RCV003968820 RCV003896868 RCV003904549 RCV003902117 RCV003935528 RCV003937980 RCV003925866 RCV003936222 RCV003906156
Familial cancer of breast	Benign	rs12426243	RCV005913009
Hepatocellular carcinoma	Benign	rs12426243	RCV005913010
Malignant lymphoma, large B-cell, diffuse	Benign	rs12426243	RCV005913012
Nonpapillary renal cell carcinoma	Benign	rs200666634	RCV005909721
Ovarian serous cystadenocarcinoma	Likely benign	rs568769580, rs145510261	RCV005912778 RCV005917521
Sarcoma	Likely benign	rs145510261	RCV005917520
Thymoma	Benign	rs12426243	RCV005913013
Uterine corpus endometrial carcinoma	Likely benign	rs145510261	RCV005917522
Uveal melanoma	Benign	rs12426243	RCV005913011

Associations from Text Mining
Disease Name	Relationship Type	References
Ciliopathies	Associate	33938610
Fetal Alcohol Spectrum Disorders	Associate	24882706
Hydrocephalus	Associate	24882706
Immunologic Deficiency Syndromes	Inhibit	33938610
Intellectual Disability	Associate	24882706
Kidney Diseases	Associate	33938610, 36222666
Learning Disabilities	Associate	24882706
Nephronophthisis 2	Associate	24882706
Nephronophthisis familial juvenile	Associate	24882706, 33938610
Retinal Degeneration	Associate	36672815
Retinal Diseases	Associate	33938610
Retinitis Pigmentosa	Associate	33938610