CFAP119

cilia and flagella associated protein 119

Basic information

Region (hg38): 16:30757423-30762221

Previous symbols: [ "C16orf93", "CCDC189" ]

Links

ENSG00000196118 ∙ NCBI:90835 ∙ OMIM:618318 ∙ HGNC:28078 ∙ Uniprot:A1A4V9 ∙ 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 CFAP119 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CFAP119 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			32	6	1	39
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1			1
non coding			4	2		6
Total	0	0	36	8	2

Variants in CFAP119

This is a list of pathogenic ClinVar variants found in the CFAP119 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-30757522-C-T		not specified	Likely benign (Oct 22, 2021)
16-30757573-C-T		not specified	Likely benign (Oct 09, 2024)
16-30757591-T-C		not specified	Uncertain significance (Dec 28, 2023)
16-30757615-A-G		not specified	Uncertain significance (Aug 21, 2024)
16-30757621-G-A		not specified	Uncertain significance (Dec 03, 2021)
16-30757636-C-T			Benign (Jul 01, 2023)
16-30757643-C-T		Glycogen phosphorylase kinase deficiency	Uncertain significance (Jun 14, 2016)
16-30757687-G-A		Glycogen phosphorylase kinase deficiency	Likely benign (Jun 14, 2016)
16-30757943-A-G		Glycogen phosphorylase kinase deficiency	Uncertain significance (Jun 14, 2016)
16-30758232-C-T		Glycogen phosphorylase kinase deficiency	Uncertain significance (Jun 14, 2016)
16-30759017-T-C		not specified	Uncertain significance (Jan 22, 2025)
16-30759040-C-G		not specified	Uncertain significance (Oct 22, 2024)
16-30759042-C-G		not specified	Uncertain significance (Jun 22, 2024)
16-30759051-C-G			Likely benign (Jul 01, 2022)
16-30759080-A-G		not specified	Uncertain significance (Aug 12, 2024)
16-30759081-T-A		not specified	Uncertain significance (Aug 28, 2024)
16-30759086-T-G		not specified	Uncertain significance (Sep 18, 2024)
16-30759180-G-A		not specified	Likely benign (Sep 06, 2022)
16-30759195-C-A		not specified	Uncertain significance (Mar 01, 2023)
16-30759220-T-C		not specified	Uncertain significance (Jun 07, 2024)
16-30759247-C-G		not specified	Uncertain significance (Dec 03, 2021)
16-30759251-G-A		Glycogen phosphorylase kinase deficiency	Uncertain significance (Jun 14, 2016)
16-30759356-C-T		not specified	Uncertain significance (Jul 12, 2022)
16-30759379-C-T		not specified	Uncertain significance (Mar 05, 2025)
16-30759398-C-T		not specified	Uncertain significance (Jan 18, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CFAP119	protein_coding	protein_coding	ENST00000543610	9	5288

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.76e-8	0.504	125216	6	526	125748	0.00212

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.00419	197	197	0.999	0.0000110	2135
Missense in Polyphen		53	61.175	0.86636		740
Synonymous	0.582	78	84.8	0.920	0.00000499	653
Loss of Function	0.983	14	18.6	0.754	8.83e-7	210

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00111	0.00111
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.0225	0.0224
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000592	0.000589
Middle Eastern	0.0225	0.0224
South Asian	0.000687	0.000686
Other	0.00114	0.00114

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: -0.12
• rvis_percentile_EVS: 45.13

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.123
• ghis: 0.509

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Ccdc189