CFAP299

Summary

CFAP299 (cilia and flagella associated protein 299, HGNC:28554) is a protein-coding gene on chromosome 4q21.21, encoding Cilia- and flagella-associated protein 299 (Q6V702). May be involved in spermatogenesis.

Predicted to be located in cytoplasm.

Source: NCBI Gene 255119 — RefSeq curated summary.

At a glance

• GWAS associations: 15
• Clinical variants (ClinVar): 15 total
• MANE Select transcript: NM_152770

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28554
Approved symbol	CFAP299
Name	cilia and flagella associated protein 299
Location	4q21.21
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000197826
Ensembl biotype	protein_coding
Entrez	255119

Gene structure

Transcript identifiers

Ensembl transcripts: 8 — 4 protein_coding_CDS_not_defined, 2 protein_coding, 2 nonsense_mediated_decay

ENST00000358105, ENST00000502497, ENST00000503883, ENST00000508314, ENST00000508675, ENST00000512931, ENST00000513920, ENST00000514249

RefSeq mRNA: 2 — MANE Select: NM_152770 NM_001206997, NM_152770

CCDS: CCDS3587, CCDS56336

Canonical transcript exons

ENST00000358105 — 6 exons

Exon	Start	End
ENSE00001410586	80944810	80944939
ENSE00001415278	80963517	80963750
ENSE00001685943	80335730	80335879
ENSE00003513146	80583093	80583183
ENSE00003585984	80869993	80870135
ENSE00003672667	80362754	80362884

Expression profiles

Bgee: expression breadth ubiquitous, 157 present calls, max score 96.86.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.6459 / max 104.7445, expressed in 158 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
48535	0.6459	158

Top tissues by expression

254 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
bronchial epithelial cell	CL:0002328	96.86	gold quality
bronchus	UBERON:0002185	94.36	gold quality
sperm	CL:0000019	93.31	gold quality
buccal mucosa cell	CL:0002336	91.30	silver quality
left testis	UBERON:0004533	88.82	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	88.60	gold quality
right uterine tube	UBERON:0001302	88.58	gold quality
right testis	UBERON:0004534	87.98	gold quality
testis	UBERON:0000473	86.26	gold quality
mucosa of paranasal sinus	UBERON:0005030	82.65	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	82.43	gold quality
oviduct epithelium	UBERON:0004804	79.57	gold quality
fallopian tube	UBERON:0003889	75.71	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	75.24	gold quality
epithelium of nasopharynx	UBERON:0001951	73.66	gold quality
adult organism	UBERON:0007023	73.52	gold quality
stromal cell of endometrium	CL:0002255	68.11	gold quality
nasal cavity mucosa	UBERON:0001826	67.88	gold quality
corpus callosum	UBERON:0002336	65.53	gold quality
right lung	UBERON:0002167	64.75	gold quality
sural nerve	UBERON:0015488	64.42	gold quality
nasal cavity epithelium	UBERON:0005384	64.11	silver quality
cerebellar cortex	UBERON:0002129	63.58	gold quality
cerebellar hemisphere	UBERON:0002245	63.43	gold quality
ventricular zone	UBERON:0003053	62.29	gold quality
cerebellum	UBERON:0002037	61.87	gold quality
right hemisphere of cerebellum	UBERON:0014890	61.71	gold quality
caput epididymis	UBERON:0004358	61.50	gold quality
left uterine tube	UBERON:0001303	59.78	gold quality
hypothalamus	UBERON:0001898	57.14	gold quality

Single-cell (SCXA)

Detected in 4 experiment(s), a significant marker in 3.

Experiment	Marker?	Max mean expression
E-GEOD-180759	yes	5299.01
E-ANND-2	yes	3752.20
E-ANND-3	yes	10.21
E-MTAB-7381	no	67.62

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

11 targeting CFAP299, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-4795-3P	100.00	74.62	4024
HSA-MIR-126-5P	100.00	72.71	3180
HSA-MIR-576-5P	99.84	70.46	2582
HSA-MIR-4729	99.69	72.18	4233
HSA-MIR-12124	99.68	69.17	2700
HSA-MIR-4437	99.52	65.29	1266
HSA-MIR-4297	98.77	66.95	2013
HSA-MIR-374B-3P	98.63	68.24	1360
HSA-MIR-5691	98.23	67.02	1335
HSA-MIR-6805-3P	98.23	67.02	1334
HSA-MIR-5088-5P	97.97	64.28	487

Cross-species orthologs

7 orthologs

Organism	Symbol	Gene ID
danio_rerio	cfap299	ENSDARG00000088753
mus_musculus	Cfap299	ENSMUSG00000057816
rattus_norvegicus	Cfap299	ENSRNOG00000067409
drosophila_melanogaster	CG3528	FBGN0031430
drosophila_melanogaster	CG14013	FBGN0031720
drosophila_melanogaster	CG14017	FBGN0031721
drosophila_melanogaster	CG8138	FBGN0038122

Protein

Protein identifiers

Cilia- and flagella-associated protein 299 — Q6V702 (reviewed: Q6V702)

All UniProt accessions (3): E7EPK2, G5E9Y8, Q6V702

UniProt curated annotations — full annotation on UniProt →

Function. May be involved in spermatogenesis.

Subcellular location. Cytoplasm. Nucleus.

Miscellaneous. May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay.

Isoforms (3)

UniProt ID	Names	Canonical?
Q6V702-2	2	yes
Q6V702-1	1
Q6V702-3	3

RefSeq proteins (2): NP_001193926, NP_689983* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR027887	DUF4464	Family

Pfam: PF14713

UniProt features (9 total): splice variant 3, sequence conflict 3, sequence variant 2, chain 1

Structure

Experimental structures (PDB)

2 structures.

PDB	Method	Resolution (Å)
9FGP	X-RAY DIFFRACTION	1.49
8J07	ELECTRON MICROSCOPY	4.1

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6V702-F1	87.40	0.53

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 50 (showing top): SENGUPTA_NASOPHARYNGEAL_CARCINOMA_DN, WHN_B, chr4q21, DODD_NASOPHARYNGEAL_CARCINOMA_DN, MEISSNER_BRAIN_HCP_WITH_H3K4ME3_AND_H3K27ME3, HOXB4_TARGET_GENES, MAFG_TARGET_GENES, PAX3_TARGET_GENES, PAX7_TARGET_GENES, PRDM12_TARGET_GENES, ZNF22_TARGET_GENES, ZNF577_TARGET_GENES, ZNF781_TARGET_GENES, MIR4795_3P, CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_2

GO Biological Process (0):

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (2): nucleus (GO:0005634), cytoplasm (GO:0005737)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1
intracellular membrane-bounded organelle	1
intracellular anatomical structure	1
cellular anatomical structure	1

Protein interactions and networks

STRING

610 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CFAP299	CFAP90	A4QMS7	625
CFAP299	CFAP96	A7E2U8	618
CFAP299	C4orf36	Q96KX1	611
CFAP299	CFAP184	Q2M329	601
CFAP299	C10orf120	Q5SQS8	507
CFAP299	TMEM33	P57088	504
CFAP299	SHISA3	A0PJX4	483
CFAP299	C5orf47	Q569G3	477
CFAP299	SLC30A9	Q6PML9	472
CFAP299	ACOXL	Q9NUZ1	464
CFAP299	PRR27	Q6MZM9	462
CFAP299	CFAP263	Q9H0I3	443
CFAP299	CCDC27	Q2M243	418
CFAP299	ANTXR2	P58335	418
CFAP299	CLXN	Q9HAE3	413
CFAP299	RTP5	Q14D33	413

IntAct

5 interactions, top by confidence:

A	B	Type	Score
NFE2L2	CFAP299	psi-mi:“MI:0915”(physical association)	0.510
CFAP299	UBB	psi-mi:“MI:0914”(association)	0.350

BioGRID (9): C4orf22 (Affinity Capture-MS), C4orf22 (Two-hybrid), C4orf22 (Affinity Capture-Western), ACAD11 (Affinity Capture-MS), UBB (Affinity Capture-MS), ANKRD30B (Affinity Capture-MS), C4orf22 (Affinity Capture-RNA), APP (Reconstituted Complex), C4orf22 (Affinity Capture-Luminescence)

ESM2 similar proteins: A0Q8H0, A2BUS3, A3M5C1, A4IVZ4, A7NEK8, A8AZ80, A9N8X1, B0JPD8, B0VDY4, B0VPM5, B1X4R3, B1XPU8, B2I0B1, B2SEV1, B7H3B2, B7I5W1, B8GZA6, B8ZUM0, O18559, O41647, O68557, P04030, P08523, P0C1A0, P13141, P22026, P26146, P31036, P32373, Q04262, Q0BK53, Q14K36, Q21YC5, Q2A1F2, Q2YA25, Q3MGF7, Q5NIN3, Q64288, Q6MEB9, Q6V702

Diamond homologs: A2AVJ0, Q2YDG2, Q5PQ44, Q6V702, Q810M1

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

15 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	8
Likely benign	4
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

4031 predictions. Top by Δscore:

Variant	Effect	Δscore
4:80362751:TAGG:T	acceptor_loss	1.0000
4:80362751:TAGGA:T	acceptor_gain	1.0000
4:80362752:A:AG	acceptor_gain	1.0000
4:80362752:A:T	acceptor_loss	1.0000
4:80362752:AG:A	acceptor_gain	1.0000
4:80362752:AGGAT:A	acceptor_gain	1.0000
4:80362753:G:GT	acceptor_gain	1.0000
4:80362753:GG:G	acceptor_gain	1.0000
4:80362753:GGA:G	acceptor_gain	1.0000
4:80362753:GGAT:G	acceptor_gain	1.0000
4:80362753:GGATG:G	acceptor_gain	1.0000
4:80362880:CAAAA:C	donor_gain	1.0000
4:80362881:AAAA:A	donor_gain	1.0000
4:80362881:AAAAG:A	donor_loss	1.0000
4:80362882:AAA:A	donor_gain	1.0000
4:80362883:AA:A	donor_gain	1.0000
4:80362883:AAGT:A	donor_loss	1.0000
4:80362884:AGTA:A	donor_loss	1.0000
4:80362885:G:GG	donor_gain	1.0000
4:80362885:GTAA:G	donor_loss	1.0000
4:80362886:T:A	donor_loss	1.0000
4:80378797:GAT:G	donor_gain	1.0000
4:80500311:A:T	donor_gain	1.0000
4:80583087:TTACA:T	acceptor_loss	1.0000
4:80583090:CA:C	acceptor_loss	1.0000
4:80583091:A:AG	acceptor_gain	1.0000
4:80583091:A:AT	acceptor_loss	1.0000
4:80583091:AG:A	acceptor_gain	1.0000
4:80583091:AGGAC:A	acceptor_gain	1.0000
4:80583092:G:GT	acceptor_gain	1.0000

AlphaMissense

1536 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
4:80870009:G:C	R117P	0.995
4:80870042:G:A	G128E	0.995
4:80870066:T:C	L136P	0.993
4:80870038:T:C	S127P	0.992
4:80362767:C:A	A42D	0.991
4:80583153:A:C	R101S	0.991
4:80583153:A:T	R101S	0.991
4:80583167:G:C	R106P	0.991
4:80335817:T:C	F17L	0.990
4:80335819:C:A	F17L	0.990
4:80335819:C:G	F17L	0.990
4:80362826:T:C	F62L	0.990
4:80362828:T:A	F62L	0.990
4:80362828:T:G	F62L	0.990
4:80362770:G:C	R43P	0.989
4:80870002:T:C	F115L	0.989
4:80870004:T:A	F115L	0.989
4:80870004:T:G	F115L	0.989
4:80870117:C:A	P153Q	0.989
4:80944896:T:C	F188S	0.989
4:80583145:G:C	A99P	0.988
4:80944850:A:C	S173R	0.988
4:80944852:T:A	S173R	0.988
4:80944852:T:G	S173R	0.988
4:80870000:T:A	I114N	0.987
4:80870048:T:A	I130N	0.987
4:80870006:T:A	I116N	0.986
4:80870129:A:T	D157V	0.985
4:80870041:G:A	G128R	0.984
4:80870041:G:C	G128R	0.984

dbSNP variants (sampled 300 via entrez): RS1000004217 (4:80381752 C>G), RS10000078 (4:80733827 A>G), RS1000012730 (4:80760740 C>T), RS1000017836 (4:80620711 C>T), RS1000024320 (4:80920016 A>C,G), RS1000036296 (4:80943130 G>A), RS1000036973 (4:80599360 T>A), RS1000045269 (4:80637473 A>G), RS1000046243 (4:80465337 G>T), RS1000049664 (4:80332744 G>T), RS1000056843 (4:80324849 G>T), RS1000062314 (4:80471909 C>G,T), RS1000062318 (4:80340127 T>C,G), RS1000062458 (4:80595413 T>A,C), RS1000068413 (4:80676462 T>C)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

15 associations (top):

Study	Trait	p-value
GCST000394_1	Diastolic blood pressure	1.000000e-21
GCST001762_696	Obesity-related traits	4.000000e-06
GCST003075_116	Cognitive decline rate in late mild cognitive impairment	5.000000e-07
GCST003075_4	Cognitive decline rate in late mild cognitive impairment	8.000000e-07
GCST006291_12	Spherical equivalent or myopia (age of diagnosis)	3.000000e-08
GCST006291_140	Spherical equivalent or myopia (age of diagnosis)	6.000000e-21
GCST006661_68	Male-pattern baldness	2.000000e-09
GCST006976_123	Macular thickness	9.000000e-11
GCST006988_133	Blond vs. brown/black hair color	4.000000e-14
GCST008361_8	Response to cognitive-behavioural therapy in major depressive disorder	5.000000e-06
GCST008596_2	Opioid overdose severity score	9.000000e-06
GCST008596_5	Opioid overdose severity score	1.000000e-06
GCST009959_6	Retinal detachment or retinal break	5.000000e-06
GCST90000025_269	Appendicular lean mass	1.000000e-22
GCST90014268_14	Cataracts	3.000000e-12

EFO canonical traits (9, from GWAS)

EFO ID	Trait name
EFO:0006336	diastolic blood pressure
EFO:0004620	vitamin B12 measurement
EFO:0007710	cognitive decline measurement
EFO:0004847	age at onset
EFO:0003924	hair color
EFO:0007820	cognitive behavioural therapy
EFO:0010140	opioid overdose severity measurement
EFO:0010698	retinal break
EFO:0004980	appendicular lean mass

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

15 total (human), top 15 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	affects methylation	2
Tobacco Smoke Pollution	decreases expression, decreases methylation	2
bisphenol A	affects cotreatment, decreases methylation, increases methylation	1
aflatoxin B2	increases methylation	1
MT19c compound	decreases expression	1
Sunitinib	decreases expression	1
Fulvestrant	affects cotreatment, decreases methylation	1
Air Pollutants	increases abundance, increases expression	1
Arsenic	affects methylation	1
Diethylhexyl Phthalate	decreases expression	1
Lead	affects methylation	1
Smoke	increases abundance, increases expression	1
Valproic Acid	increases expression	1
Aflatoxin B1	decreases methylation	1
Antirheumatic Agents	increases expression	1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.