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.

• not_specified (57 variants)
• Glycogen_phosphorylase_kinase_deficiency (9 variants)
• not_provided (3 variants)

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. These statistics are base on transcript: NM_001014979.3. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					1	1
missense			50	9	1	60
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	50	9	2

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