CEP15

centrosomal protein 15

Basic information

Region (hg38): 3:62319015-62336213

Previous symbols: [ "C3orf14" ]

Links

ENSG00000114405 ∙ NCBI:57415 ∙ ∙ HGNC:25024 ∙ Uniprot:Q9HBI5 ∙ 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 CEP15 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CEP15 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			1			1
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	1	0	0

Variants in CEP15

This is a list of pathogenic ClinVar variants found in the CEP15 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-62333367-T-C		not specified	Uncertain significance (Jul 20, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CEP15	protein_coding	protein_coding	ENST00000494481	4	17241

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000160	0.257	125644	0	89	125733	0.000354

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.349	57	64.9	0.878	0.00000326	824
Missense in Polyphen		11	13.968	0.78749		197
Synonymous	0.397	18	20.3	0.888	8.67e-7	236
Loss of Function	-0.173	7	6.52	1.07	2.75e-7	84

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000158	0.000157
Ashkenazi Jewish	0.00	0.00
East Asian	0.00375	0.00376
Finnish	0.00	0.00
European (Non-Finnish)	0.0000887	0.0000879
Middle Eastern	0.00375	0.00376
South Asian	0.000131	0.000131
Other	0.000328	0.000326

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.598
• rvis_EVS: 0.68
• rvis_percentile_EVS: 84.81

Haploinsufficiency Scores

• pHI: 0.112
• hipred: N
• hipred_score: 0.215
• ghis: 0.416

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: 3830406C13Rik