CEP70

centrosomal protein 70

Basic information

Region (hg38): 3:138494344-138594538

Links

ENSG00000114107 ∙ NCBI:80321 ∙ OMIM:614310 ∙ HGNC:29972 ∙ Uniprot:Q8NHQ1 ∙ 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 CEP70 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CEP70 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				1		1
missense			28	4		32
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			2			2
Total	0	0	30	5	0

Variants in CEP70

This is a list of pathogenic ClinVar variants found in the CEP70 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-138495047-C-A		not specified	Uncertain significance (Nov 13, 2024)
3-138497922-TTCCAA-T		Median cleft lip and palate	Uncertain significance (Oct 16, 2019)
3-138497928-C-G		Median cleft lip and palate	Uncertain significance (Oct 16, 2019)
3-138498063-T-C		not specified	Uncertain significance (Jul 09, 2021)
3-138498109-T-C		not specified	Uncertain significance (Apr 20, 2024)
3-138500198-C-T		not specified	Uncertain significance (Oct 29, 2021)
3-138500224-T-C		not specified	Uncertain significance (Jul 06, 2021)
3-138500403-T-A		not specified	Uncertain significance (Feb 03, 2022)
3-138500408-A-T		not specified	Uncertain significance (Nov 09, 2024)
3-138500410-A-T			Likely benign (Jul 01, 2022)
3-138500425-C-T		not specified	Uncertain significance (Jul 25, 2023)
3-138500447-C-T		not specified	Uncertain significance (Apr 25, 2022)
3-138500467-T-C		not specified	Uncertain significance (Jun 12, 2023)
3-138500473-C-T		not specified	Uncertain significance (Jul 19, 2022)
3-138500501-C-T		not specified	Uncertain significance (May 14, 2024)
3-138500504-C-G		not specified	Uncertain significance (Jun 29, 2022)
3-138500511-C-T			Likely benign (Jul 01, 2022)
3-138500549-A-G		not specified	Uncertain significance (Aug 10, 2021)
3-138500551-T-C		not specified	Uncertain significance (Dec 12, 2023)
3-138500745-T-C		not specified	Uncertain significance (Jan 29, 2024)
3-138500766-G-C		not specified	Uncertain significance (Jun 17, 2024)
3-138500775-A-C		not specified	Uncertain significance (Sep 08, 2024)
3-138500859-G-A		not specified	Likely benign (Feb 28, 2024)
3-138505329-A-G		not specified	Uncertain significance (Nov 08, 2024)
3-138505374-T-G		not specified	Uncertain significance (Nov 26, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CEP70	protein_coding	protein_coding	ENST00000264982	16	100195

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.56e-15	0.496	125605	0	141	125746	0.000561

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0397	281	279	1.01	0.0000128	3946
Missense in Polyphen		81	83.413	0.97107		1245
Synonymous	-0.0928	100	98.8	1.01	0.00000473	990
Loss of Function	1.58	28	38.6	0.726	0.00000199	490

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00137	0.00136
Ashkenazi Jewish	0.00	0.00
East Asian	0.000223	0.000217
Finnish	0.00125	0.00125
European (Non-Finnish)	0.000491	0.000475
Middle Eastern	0.000223	0.000217
South Asian	0.000542	0.000523
Other	0.000517	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in the organization of both preexisting and nascent microtubules in interphase cells. During mitosis, required for the organization and orientation of the mitotic spindle.
• 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: 0.107

Intolerance Scores

• loftool: 0.973
• rvis_EVS: 0.11
• rvis_percentile_EVS: 62.1

Haploinsufficiency Scores

• pHI: 0.312
• hipred: N
• hipred_score: 0.144
• ghis: 0.478

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0303

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cep70

Zebrafish Information Network

• Gene name: cep70
• Affected structure: otolith
• Phenotype tag: abnormal
• Phenotype quality: mislocalised

Gene ontology

• Biological process: G2/M transition of mitotic cell cycle;regulation of G2/M transition of mitotic cell cycle;regulation of microtubule cytoskeleton organization;ciliary basal body-plasma membrane docking
• Cellular component: nucleoplasm;centrosome;cytosol;nuclear membrane
• Molecular function: protein binding;identical protein binding;gamma-tubulin binding