CFAP20

cilia and flagella associated protein 20, the group of Cilia and flagella associated

Basic information

Region (hg38): 16:58113592-58129381

Previous symbols: [ "C16orf80" ]

Links

ENSG00000070761 ∙ NCBI:29105 ∙ OMIM:617906 ∙ HGNC:29523 ∙ Uniprot:Q9Y6A4 ∙ 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 CFAP20 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CFAP20 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			8			8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	8	0	0

Variants in CFAP20

This is a list of pathogenic ClinVar variants found in the CFAP20 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-58114905-G-T		not specified	Uncertain significance (May 27, 2022)
16-58115277-T-C		Rod-cone dystrophy	Likely pathogenic (Jul 28, 2022)
16-58115336-TG-T		Rod-cone dystrophy	Likely pathogenic (Jul 28, 2022)
16-58115371-C-T		not specified	Uncertain significance (Apr 23, 2024)
16-58115372-A-G		not specified	Uncertain significance (Feb 20, 2025)
16-58115397-G-A		Rod-cone dystrophy	Uncertain significance (Sep 29, 2021)
16-58115429-C-T		Rod-cone dystrophy	Likely pathogenic (Jul 28, 2022)
16-58115433-G-A		not specified	Uncertain significance (Aug 16, 2021)
16-58116060-T-C		Rod-cone dystrophy	Likely pathogenic (Jul 28, 2022)
16-58116070-G-C		not specified	Uncertain significance (May 03, 2023)
16-58116871-C-T		Rod-cone dystrophy	Likely pathogenic (Jul 28, 2022)
16-58116876-C-T		not specified	Uncertain significance (Aug 19, 2024)
16-58116921-C-T		not specified	Uncertain significance (Nov 13, 2023)
16-58129054-G-C		not specified	Uncertain significance (Oct 27, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CFAP20	protein_coding	protein_coding	ENST00000262498	6	15859

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00211	0.923	125717	0	30	125747	0.000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.07	56	120	0.467	0.00000749	1274
Missense in Polyphen		17	38.942	0.43654		361
Synonymous	0.547	39	43.6	0.895	0.00000242	364
Loss of Function	1.55	6	11.7	0.511	6.70e-7	122

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.000323	0.000323
European (Non-Finnish)	0.0000792	0.0000791
Middle Eastern	0.0000544	0.0000544
South Asian	0.000359	0.000359
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Cilium- and flagellum-specific protein that plays a role in axonemal structure organization and motility. Involved in the regulation of the size and morphology of cilia (PubMed:24414207). Required for axonemal microtubules polyglutamylation (PubMed:24414207). {ECO:0000269|PubMed:24414207}.

Recessive Scores

• pRec: 0.136

Intolerance Scores

• rvis_EVS: 0.01
• rvis_percentile_EVS: 54.63

Haploinsufficiency Scores

• pHI: 0.283
• hipred: Y
• hipred_score: 0.754
• ghis: 0.663

Essentials

• essential_gene_gene_trap: E

Mouse Genome Informatics

• Gene name: Cfap20

Gene ontology

• Biological process: multicellular organism development;protein polyglutamylation;cilium assembly;regulation of cilium beat frequency involved in ciliary motility;positive regulation of cell motility;positive regulation of feeding behavior
• Cellular component: nucleus;centriole;microtubule;cilium;motile cilium;ciliary basal body;extracellular exosome
• Molecular function: RNA binding;protein binding