CEP72

centrosomal protein 72

Basic information

Region (hg38): 5:612340-667168

Links

ENSG00000112877 ∙ NCBI:55722 ∙ OMIM:616475 ∙ HGNC:25547 ∙ Uniprot:Q9P209 ∙ 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 CEP72 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CEP72 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						0
missense			51	3		54
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	51	3	0

Variants in CEP72

This is a list of pathogenic ClinVar variants found in the CEP72 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-612366-C-G		not specified	Uncertain significance (Nov 05, 2021)
5-612368-C-G		not specified	Uncertain significance (Dec 08, 2023)
5-612377-C-T		not specified	Uncertain significance (Jan 02, 2024)
5-612386-G-A		not specified	Uncertain significance (Apr 15, 2024)
5-612411-C-G		not specified	Uncertain significance (May 18, 2023)
5-612441-T-C		not specified	Uncertain significance (Feb 27, 2024)
5-618996-T-G		not specified	Uncertain significance (Oct 26, 2022)
5-619095-G-A		not specified	Uncertain significance (Jul 09, 2021)
5-620115-A-G		not specified	Uncertain significance (Mar 04, 2024)
5-620144-C-T		not specified	Uncertain significance (Jan 03, 2024)
5-620195-G-A		not specified	Uncertain significance (Apr 17, 2024)
5-620220-G-A		not specified	Uncertain significance (Apr 20, 2023)
5-624472-C-T			Benign (Jun 06, 2017)
5-624473-G-A		not specified	Uncertain significance (Mar 25, 2024)
5-624477-G-A		not specified	Uncertain significance (Sep 09, 2021)
5-624482-G-A		not specified	Uncertain significance (Mar 05, 2024)
5-624498-G-A		not specified	Uncertain significance (Apr 07, 2023)
5-624520-T-G		not specified	Uncertain significance (Jul 05, 2023)
5-624539-G-A		not specified	Uncertain significance (May 17, 2023)
5-633788-A-G		not specified	Uncertain significance (May 27, 2022)
5-633810-A-G		not specified	Uncertain significance (Feb 16, 2023)
5-633821-G-A		not specified	Uncertain significance (Sep 20, 2023)
5-633831-C-T		not specified	Uncertain significance (Apr 06, 2022)
5-633868-C-G		not specified	Uncertain significance (Sep 01, 2021)
5-633921-G-A		not specified	Uncertain significance (Oct 05, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CEP72	protein_coding	protein_coding	ENST00000264935	12	54897

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.58e-19	0.00297	125433	3	312	125748	0.00125

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.892	432	383	1.13	0.0000236	4204
Missense in Polyphen		115	96.84	1.1875		1187
Synonymous	-0.122	178	176	1.01	0.0000125	1279
Loss of Function	0.0379	29	29.2	0.992	0.00000141	357

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000387	0.000387
Ashkenazi Jewish	0.000399	0.000298
East Asian	0.000926	0.000925
Finnish	0.000236	0.000231
European (Non-Finnish)	0.000599	0.000598
Middle Eastern	0.000926	0.000925
South Asian	0.00701	0.00688
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in the recruitment of key centrosomal proteins to the centrosome. Provides centrosomal microtubule-nucleation activity on the gamma-tubulin ring complexes (gamma-TuRCs) and has critical roles in forming a focused bipolar spindle, which is needed for proper tension generation between sister chromatids. Required for localization of KIZ, AKAP9 and gamma-tubulin ring complexes (gamma-TuRCs) (PubMed:19536135). Involved in centriole duplication. Required for CDK5RAP22, CEP152, WDR62 and CEP63 centrosomal localization and promotes the centrosomal localization of CDK2 (PubMed:26297806). {ECO:0000269|PubMed:19536135, ECO:0000269|PubMed:26297806}.
• Pathway: miR-targeted genes in epithelium - TarBase;miR-targeted genes in lymphocytes - TarBase;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: 0.116

Intolerance Scores

• loftool: 0.854
• rvis_EVS: -0.17
• rvis_percentile_EVS: 40.68

Haploinsufficiency Scores

• pHI: 0.0811
• hipred: N
• hipred_score: 0.123
• ghis: 0.544

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.489

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cep72

Gene ontology

• Biological process: G2/M transition of mitotic cell cycle;spindle organization;centriole replication;regulation of G2/M transition of mitotic cell cycle;gamma-tubulin complex localization;ciliary basal body-plasma membrane docking;regulation of protein localization to centrosome
• Cellular component: centrosome;cytosol;centriolar satellite
• Molecular function: protein binding;identical protein binding