CEP83

centrosomal protein 83

Basic information

Region (hg38): 12:94306449-94459988

Previous symbols: [ "CCDC41" ]

Links

ENSG00000173588 ∙ NCBI:51134 ∙ OMIM:615847 ∙ HGNC:17966 ∙ Uniprot:Q9Y592 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• nephronophthisis 18 (Strong), mode of inheritance: AR
• nephronophthisis 2 (Supportive), mode of inheritance: AR
• nephronophthisis 18 (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Nephronophthisis 18	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Gastrointestinal; Neurologic; Ophthalmologic; Renal	24882706

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CEP83 gene.

• Nephronophthisis 18 (29 variants)
• not provided (4 variants)
• Nephronophthisis (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CEP83 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				106	4	110
missense	1	1	183	8	3	196
nonsense	18	1				19
start loss						0
frameshift	11		1			12
inframe indel			5			5
splice donor/acceptor (+/-2bp)		2				2
splice region			11	17	1	29
non coding			1	64	29	94
Total	30	4	190	178	36

Highest pathogenic variant AF is 0.0000789

Variants in CEP83

This is a list of pathogenic ClinVar variants found in the CEP83 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
12-94308506-CA-C			Benign (Sep 06, 2019)
12-94308613-A-G			Likely benign (May 16, 2021)
12-94308820-C-T		Nephronophthisis 18	Uncertain significance (Nov 22, 2022)
12-94308821-C-T		Nephronophthisis 18	Uncertain significance (Aug 10, 2023)
12-94308822-G-A		Nephronophthisis 18	Likely benign (Jan 02, 2024)
12-94308828-T-C			Likely benign (Mar 02, 2018)
12-94308841-AGTT-A		Nephronophthisis 18	Pathogenic (Jun 05, 2014)
12-94308843-T-C		Nephronophthisis 18	Likely benign (Jul 31, 2023)
12-94308843-TTGTTTTCTTTG-T		Nephronophthisis 18	Uncertain significance (Feb 26, 2020)
12-94308853-T-C		Nephronophthisis 18	Uncertain significance (Mar 20, 2022)
12-94308858-T-C		Nephronophthisis 18	Likely benign (Mar 23, 2023)
12-94308873-T-C		Nephronophthisis 18	Likely benign (Sep 10, 2022)
12-94308874-A-G		Nephronophthisis 18	Uncertain significance (Aug 16, 2021)
12-94308876-T-A		Nephronophthisis 18	Uncertain significance (Aug 31, 2022)
12-94308880-T-C		Nephronophthisis 18	Uncertain significance (Oct 13, 2022)
12-94308883-C-T		Nephronophthisis 18	Likely benign (Mar 11, 2022)
12-94308884-G-A		Nephronophthisis 18 • Inborn genetic diseases	Uncertain significance (Jul 26, 2022)
12-94308888-T-C		Nephronophthisis 18	Likely benign (Feb 02, 2023)
12-94308891-A-G		Nephronophthisis 18	Likely benign (Feb 11, 2023)
12-94308892-G-C		Nephronophthisis 18	Uncertain significance (Jul 19, 2022)
12-94308895-A-G		Nephronophthisis 18	Likely pathogenic (-)
12-94308899-C-T		Nephronophthisis 18	Uncertain significance (Mar 02, 2022)
12-94308903-T-C		Nephronophthisis 18	Likely benign (Mar 17, 2022)
12-94308904-T-A		Inborn genetic diseases	Uncertain significance (Dec 15, 2022)
12-94308911-GT-G		Nephronophthisis 18	Pathogenic (Sep 04, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CEP83	protein_coding	protein_coding	ENST00000397809	15	153540

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.29e-14	0.912	124706	0	86	124792	0.000345

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.406	316	337	0.938	0.0000171	4612
Missense in Polyphen		87	100.71	0.86386		1510
Synonymous	-0.950	130	117	1.11	0.00000555	1197
Loss of Function	2.12	28	43.0	0.652	0.00000232	556

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000437	0.000437
Ashkenazi Jewish	0.0000994	0.0000993
East Asian	0.000449	0.000445
Finnish	0.000140	0.000139
European (Non-Finnish)	0.000487	0.000486
Middle Eastern	0.000449	0.000445
South Asian	0.000200	0.000196
Other	0.000339	0.000330

dbNSFP

Source: dbNSFP

• Function: 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 initiation of primary cilium assembly. {ECO:0000269|PubMed:23348840, ECO:0000269|PubMed:23530209}.
• Disease: DISEASE: Nephronophthisis 18 (NPHP18) [MIM:615862]: An autosomal recessive disorder characterized by chronic tubulointerstitial nephritis resulting in end-stage renal disease in early childhood. Extrarenal manifestations, including intellectual disability or liver changes, may occur in some patients. {ECO:0000269|PubMed:24882706}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Anchoring of the basal body to the plasma membrane;Cilium Assembly;Organelle biogenesis and maintenance (Consensus)

Recessive Scores

• pRec: 0.105

Intolerance Scores

• rvis_EVS: -0.11
• rvis_percentile_EVS: 45.49

Haploinsufficiency Scores

• pHI: 0.158
• hipred: N
• hipred_score: 0.393
• ghis: 0.564

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Cep83

Zebrafish Information Network

• Gene name: cep83
• Affected structure: olfactory pit
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: vesicle docking;cilium assembly;protein localization to centrosome;ciliary basal body-plasma membrane docking
• Cellular component: Golgi apparatus;centriole;cytosol;ciliary transition fiber
• Molecular function: molecular_function;protein binding