CEP20

centrosomal protein 20

Basic information

Region (hg38): 16:15865719-15888625

Previous symbols: [ "C16orf63", "FOPNL" ]

Links

ENSG00000133393 ∙ NCBI:123811 ∙ OMIM:617149 ∙ HGNC:26435 ∙ Uniprot:Q96NB1 ∙ 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 CEP20 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CEP20 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			19	1		20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	2	0

Variants in CEP20

This is a list of pathogenic ClinVar variants found in the CEP20 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-15867447-T-C		not specified	Uncertain significance (Mar 23, 2022)
16-15867465-T-C		not specified	Uncertain significance (Oct 16, 2023)
16-15867486-C-T		not specified	Uncertain significance (Mar 06, 2025)
16-15867510-T-C		not specified	Uncertain significance (Nov 08, 2022)
16-15873516-T-A		not specified	Uncertain significance (Aug 14, 2024)
16-15873538-G-A		not specified	Uncertain significance (Mar 29, 2023)
16-15873541-T-C		not specified	Uncertain significance (Dec 06, 2021)
16-15873574-A-G		not specified	Uncertain significance (Nov 07, 2022)
16-15873612-C-T			Likely benign (Oct 01, 2024)
16-15879855-T-C		not specified	Uncertain significance (Jul 25, 2023)
16-15879861-T-C		not specified	Uncertain significance (Sep 17, 2021)
16-15879868-G-A		not specified	Uncertain significance (Nov 30, 2022)
16-15884026-C-T		not specified	Uncertain significance (Aug 10, 2021)
16-15884106-C-G		not specified	Uncertain significance (Apr 29, 2022)
16-15884116-G-A		not specified	Uncertain significance (Jan 04, 2024)
16-15884131-C-T		not specified	Uncertain significance (Jan 23, 2024)
16-15884133-T-C		not specified	Likely benign (Jul 06, 2022)
16-15888565-C-A		not specified	Uncertain significance (Jan 31, 2024)
16-15888569-T-C		not specified	Uncertain significance (Feb 07, 2023)
16-15888570-C-G		not specified	Uncertain significance (Jan 08, 2024)
16-15888581-G-A		not specified	Uncertain significance (Aug 02, 2022)
16-15888581-G-C		not specified	Uncertain significance (Jun 20, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CEP20	protein_coding	protein_coding	ENST00000255759	5	22906

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000183	0.264	125699	0	48	125747	0.000191

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.589	103	87.5	1.18	0.00000425	1118
Missense in Polyphen		20	25.757	0.77648		329
Synonymous	0.352	30	32.6	0.922	0.00000149	326
Loss of Function	0.140	9	9.46	0.951	6.34e-7	110

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000216	0.000198
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.00	0.00
Finnish	0.00134	0.00134
European (Non-Finnish)	0.0000806	0.0000791
Middle Eastern	0.00	0.00
South Asian	0.000131	0.000131
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in the biogenesis of cilia (PubMed:20551181). Required for the recruitement of PLK1 to centrosomes and S phase progression (PubMed:24018379). {ECO:0000269|PubMed:20551181, ECO:0000269|PubMed:24018379}.

Intolerance Scores

• rvis_EVS: -0.07
• rvis_percentile_EVS: 48.12

Haploinsufficiency Scores

• pHI: 0.188
• hipred: N
• hipred_score: 0.174
• ghis: 0.650

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fopnl

Gene ontology

• Biological process: microtubule anchoring;cilium assembly
• Cellular component: nucleus;centrosome;centriole;motile cilium;centriolar satellite;ciliary basal body