CEP76

centrosomal protein 76

Basic information

Region (hg38): 18:12661833-12702777

Previous symbols: [ "C18orf9" ]

Links

ENSG00000101624 ∙ NCBI:79959 ∙ ∙ HGNC:25727 ∙ Uniprot:Q8TAP6 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CEP76 gene.

• not_specified (63 variants)
• CEP76-related_disorder (5 variants)
• Joubert_syndrome_1 (5 variants)
• Short_stature (3 variants)
• See_cases (3 variants)
• Retinitis_pigmentosa (3 variants)
• not_provided (2 variants)
• Bardet-Biedl_syndrome_1 (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CEP76 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000024899.4. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous	1			2	1	4
missense	1	8	63	2	2	76
nonsense						0
start loss						0
frameshift		3				3
splice donor/acceptor (+/-2bp)						0
Total	2	11	63	4	3

Highest pathogenic variant AF is 0.00005204274

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CEP76	protein_coding	protein_coding	ENST00000262127	12	40945

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.51e-9	0.998	125677	0	71	125748	0.000282

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.75	265	358	0.740	0.0000191	4246
Missense in Polyphen		54	104.45	0.51699		1223
Synonymous	1.31	104	122	0.850	0.00000621	1308
Loss of Function	2.75	20	38.4	0.521	0.00000246	419

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000892	0.000861
Ashkenazi Jewish	0.000200	0.000198
East Asian	0.000218	0.000217
Finnish	0.000140	0.000139
European (Non-Finnish)	0.000294	0.000290
Middle Eastern	0.000218	0.000217
South Asian	0.000341	0.000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Centrosomal protein involved in regulation of centriole duplication. Required to limit centriole duplication to once per cell cycle by preventing centriole reduplication. {ECO:0000269|PubMed:19460342}.
• Pathway: Regulation of PLK1 Activity at G2/M Transition;Recruitment of mitotic centrosome proteins and complexes;Loss of Nlp from mitotic centrosomes;Loss of proteins required for interphase microtubule organization from the centrosome;Centrosome maturation;AURKA Activation by TPX2;G2/M Transition;Mitotic G2-G2/M phases;Recruitment of NuMA to mitotic centrosomes;Mitotic Prometaphase;M Phase;Cell Cycle;Cell Cycle, Mitotic;Anchoring of the basal body to the plasma membrane;Cilium Assembly;Organelle biogenesis and maintenance (Consensus)

Recessive Scores

• pRec: 0.145

Intolerance Scores

• loftool: 0.625
• rvis_EVS: 0.26
• rvis_percentile_EVS: 70.44

Haploinsufficiency Scores

• pHI: 0.138
• hipred: Y
• hipred_score: 0.639
• ghis: 0.603

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.599

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Cep76
• Phenotype: immune system phenotype; hematopoietic system phenotype

Gene ontology

• Biological process: G2/M transition of mitotic cell cycle;regulation of G2/M transition of mitotic cell cycle;regulation of centriole replication;ciliary basal body-plasma membrane docking
• Cellular component: centrosome;centriole;cytosol;protein-containing complex
• Molecular function: protein binding