CFAP119

protein-coding

cilia and flagella associated protein 119

Gene summary

Predicted to act upstream of or within gene expression; single fertilization; and sperm flagellum assembly. Predicted to be located in acrosomal vesicle and sperm principal piece. Predicted to be part of radial spoke. Predicted to be active in axoneme. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

C16orf93
CCDC189

MANE transcript

NM_001014979.3

Inheritance

—

ClinVar variants

U:62B:15

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.75

Max pathogenic AF

—

Genomic locus

chr16:30,757,423-30,762,221

External References & Databases

Ensembl (ENSG00000196118)

Transcript & Mutation Effects

hg38 • Region Span ~4.8 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CFAP119 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 65

not providedTotal: 4

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001014979.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	1 clinvar	1 clinvar	3
missense			57 clinvar	12 clinvar	1 clinvar	70
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	0	62	13	2	77

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 28 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001014979.3	RefSeq	NP_001014979.2	9	MANE Select
ENST00000543610.6	Ensembl	ENSP00000437532.1	9	MANE Select
NM_001195620.2	RefSeq	NP_001182549.1	4	Standard
ENST00000535476.6	Ensembl	ENSP00000442644.2	4	Standard

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000543610
Coding exons: 9
Length: 5288
Individuals with no LoFs: 125216
Homozygous LoFs: 6
Heterozygous LoFs: 526
Defined: 125748
p: 0.00212

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.00419	197	197	0.999	0.0000110	2135
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00068	0.00068	rare
Latino/Admixed American	0.00043	0.00043	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.022	0.022	notable
Finnish	0.00014	0.00014	rare
European (Non-Finnish)	0.00059	0.00059	rare
South Asian	0.00069	0.00069	rare
Other	0.0011	0.0011	notable

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

RVIS EVS: -0.12
RVIS percentile EVS: 45.13

Essentials

Essential (gene trap): N