CFAP299

protein-coding

cilia and flagella associated protein 299, the group of Cilia and flagella associated

Gene summary

Predicted to be located in cytoplasm. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

C4orf22

MANE transcript

NM_152770.3

Inheritance

—

ClinVar variants

U:2B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.05

Max pathogenic AF

—

Genomic locus

chr4:80,335,730-80,963,750

External References & Databases

Ensembl (ENSG00000197826)

Transcript & Mutation Effects

hg38 • Region Span ~628.0 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 CFAP299 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 5

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_152770.3. 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
missense			2 clinvar	2 clinvar		4
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	2	3	0	5

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 12 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_152770.3	RefSeq	NP_689983.2	6	MANE Select
ENST00000358105.8	Ensembl	ENSP00000350818.3	6	MANE Select
NM_001206997.2	RefSeq	NP_001193926.1	7	Standard
ENST00000508675.1	Ensembl	ENSP00000425786.1	7	Standard

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000508675
Coding exons: 7
Length: 628037
Individuals with no LoFs: 125295
Homozygous LoFs: 2
Heterozygous LoFs: 451
Defined: 125748
p: 0.00180

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.571	148	130	1.14	0.00000644	1631
Missense (PolyPhen)		45	42.842	1.0504		543
Synonymous	0.239	46	48.1	0.956	0.00000246	466
Loss of Function	-0.158	13	12.4	1.05	5.24e-7	165

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00025	0.00025	rare
Latino/Admixed American	0.0011	0.0010	notable
Ashkenazi Jewish	0.0027	0.0024	notable
East Asian	0.015	0.015	notable
Finnish	0	0.0	absent
European (Non-Finnish)	0.00059	0.00057	rare
South Asian	0.0014	0.0013	notable
Other	0.0022	0.0021	notable

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

RVIS EVS: 0.53
RVIS percentile EVS: 80.73

Essentials

Essential (gene trap): N