CFAP263

Summary

CFAP263 (cilia and flagella associated protein 263, HGNC:25002) is a protein-coding gene on chromosome 16q21, encoding Cilia- and flagella-associated protein 263 (Q9H0I3). Component of centriolar satellites contributing to primary cilium formation.

Involved in cilium assembly. Located in centriolar satellite and ciliary basal body. Part of protein-containing complex.

Source: NCBI Gene 29070 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 129 total
• MANE Select transcript: NM_014157

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:25002
Approved symbol	CFAP263
Name	cilia and flagella associated protein 263
Location	16q21
Locus type	gene with protein product
Status	Approved
Aliases	HSPC065, DKFZp434N1418
Ensembl gene	ENSG00000103021
Ensembl biotype	protein_coding
OMIM	616070
Entrez	29070

Gene structure

Transcript identifiers

Ensembl transcripts: 7 — 5 protein_coding, 1 nonsense_mediated_decay, 1 protein_coding_CDS_not_defined

ENST00000219299, ENST00000443128, ENST00000561517, ENST00000566498, ENST00000569374, ENST00000877446, ENST00000954260

RefSeq mRNA: 2 — MANE Select: NM_014157 NM_001142302, NM_014157

CCDS: CCDS10795, CCDS45497

Canonical transcript exons

ENST00000219299 — 9 exons

Exon	Start	End
ENSE00000686675	58253998	58254159
ENSE00000853017	58249936	58250115
ENSE00000921089	58278482	58278637
ENSE00001047062	58267479	58267586
ENSE00001860360	58279691	58283836
ENSE00003565088	58262385	58262540
ENSE00003575648	58258368	58258523
ENSE00003591159	58259854	58259934
ENSE00003675995	58252727	58252853

Expression profiles

Bgee: expression breadth ubiquitous, 229 present calls, max score 99.31.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 6.4349 / max 315.7795, expressed in 1472 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
154438	6.3513	1469
154439	0.0509	19
154441	0.0327	12

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
bronchial epithelial cell	CL:0002328	99.31	gold quality
bronchus	UBERON:0002185	98.97	gold quality
oviduct epithelium	UBERON:0004804	96.94	gold quality
mucosa of paranasal sinus	UBERON:0005030	95.21	gold quality
right uterine tube	UBERON:0001302	91.13	gold quality
endothelial cell	CL:0000115	89.87	gold quality
epithelium of nasopharynx	UBERON:0001951	89.82	gold quality
trachea	UBERON:0003126	89.51	gold quality
middle temporal gyrus	UBERON:0002771	89.17	gold quality
Brodmann (1909) area 23	UBERON:0013554	88.09	gold quality
caput epididymis	UBERON:0004358	86.94	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	86.30	gold quality
nasal cavity epithelium	UBERON:0005384	86.06	gold quality
fallopian tube	UBERON:0003889	85.39	gold quality
medial globus pallidus	UBERON:0002477	84.00	gold quality
nasal cavity mucosa	UBERON:0001826	83.08	gold quality
primary visual cortex	UBERON:0002436	82.88	gold quality
left testis	UBERON:0004533	82.70	gold quality
right testis	UBERON:0004534	82.31	gold quality
testis	UBERON:0000473	82.17	gold quality
occipital lobe	UBERON:0002021	81.82	gold quality
tibia	UBERON:0000979	81.71	gold quality
globus pallidus	UBERON:0001875	81.67	gold quality
superior frontal gyrus	UBERON:0002661	81.44	gold quality
superior vestibular nucleus	UBERON:0007227	81.38	gold quality
Brodmann (1909) area 46	UBERON:0006483	81.37	gold quality
postcentral gyrus	UBERON:0002581	80.92	gold quality
entorhinal cortex	UBERON:0002728	80.80	gold quality
parietal lobe	UBERON:0001872	80.64	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	79.77	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-CURD-114	yes	11.04
E-ANND-3	yes	8.42

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

106 targeting CFAP263, 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-4692	100.00	67.32	2066
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-4747-5P	100.00	67.90	2681
HSA-MIR-5196-5P	100.00	67.98	2761
HSA-MIR-4673	100.00	66.64	1490
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-4514	99.99	67.10	1870
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-548AW	99.99	72.57	3559
HSA-MIR-4500	99.99	72.72	2367
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-32-5P	99.98	75.21	1964
HSA-MIR-92A-3P	99.98	75.21	1960
HSA-MIR-92B-3P	99.98	75.25	1955
HSA-MIR-25-3P	99.98	74.60	1817
HSA-MIR-363-3P	99.98	74.72	1821
HSA-MIR-367-3P	99.98	74.83	1819
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-4645-5P	99.98	65.81	1284
HSA-MIR-4725-3P	99.96	69.53	2520
HSA-MIR-6780B-5P	99.96	69.60	2562
HSA-MIR-3658	99.96	73.87	4379
HSA-MIR-6825-5P	99.96	69.81	3431
HSA-MIR-767-5P	99.95	70.85	993
HSA-MIR-5010-5P	99.94	64.11	705
HSA-MIR-4525	99.94	64.38	675
HSA-MIR-6721-5P	99.93	68.92	2981
HSA-MIR-6753-3P	99.93	66.57	637
HSA-MIR-7107-3P	99.93	66.73	627

Literature-anchored findings (GeneRIF, showing 1)

• CCDC113 promotes colorectal cancer tumorigenesis and metastasis via TGF-beta signaling pathway. (PMID:39261464)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	cfap263	ENSDARG00000006981
mus_musculus	Ccdc113	ENSMUSG00000036598
rattus_norvegicus	Ccdc113	ENSRNOG00000051510

Protein

Protein identifiers

Cilia- and flagella-associated protein 263 — Q9H0I3 (reviewed: Q9H0I3)

All UniProt accessions (3): Q9H0I3, H3BMZ8, H3BQS9

UniProt curated annotations — full annotation on UniProt →

Function. Component of centriolar satellites contributing to primary cilium formation. In complex with CFAP263, acts as a regulator of ciliary beating that connects radial spoke 3 (RS3) to the inner dynein arm (IDA) and the nexin-dynein regulatory complex (N-DRC). The complex is positioned parallel to N-DRC and forms a connection between the arch at the base of RS3, the IDA tail and N-DRC.

Subunit / interactions. Forms a complex with CFAP184; the interaction is required for functional activity in cilia. Interacts with HAP1 and PCM1.

Subcellular location. Cytoplasm. Cytoskeleton. Microtubule organizing center. Centrosome. Centriolar satellite. Cell projection. Cilium.

Similarity. Belongs to the CFAP263 family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q9H0I3-1	1	yes
Q9H0I3-2	2

RefSeq proteins (2): NP_001135774, NP_054876* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR025254	CCDC113/CCDC96_CC	Domain
IPR051885	CC_CF	Family

Pfam: PF13870

UniProt features (7 total): coiled-coil region 2, sequence variant 2, chain 1, splice variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

1 structures.

PDB	Method	Resolution (Å)
8J07	ELECTRON MICROSCOPY	4.1

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9H0I3-F1	83.57	0.54

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 59 (showing top): GOCC_MICROTUBULE_ORGANIZING_CENTER, SENGUPTA_NASOPHARYNGEAL_CARCINOMA_DN, GOBP_CILIUM_ORGANIZATION, GOCC_CENTROSOME, TCCCCAC_MIR491, GOBP_ORGANELLE_ASSEMBLY, chr16q21, GOBP_CELL_PROJECTION_ORGANIZATION, GOCC_CYTOPLASMIC_REGION, GOCC_CILIUM, GOCC_CILIARY_BASAL_BODY, GOCC_CENTRIOLAR_SATELLITE, ROYLANCE_BREAST_CANCER_16Q_COPY_NUMBER_UP, DODD_NASOPHARYNGEAL_CARCINOMA_DN, KRIGE_RESPONSE_TO_TOSEDOSTAT_6HR_DN

GO Biological Process (2): cilium assembly (GO:0060271), cell projection organization (GO:0030030)

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

GO Cellular Component (8): axoneme (GO:0005930), protein-containing complex (GO:0032991), centriolar satellite (GO:0034451), ciliary basal body (GO:0036064), cytoplasm (GO:0005737), cytoskeleton (GO:0005856), cilium (GO:0005929), cell projection (GO:0042995)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	4
axoneme assembly	1
intraciliary transport involved in cilium assembly	1
cilium organization	1
protein localization to cilium	1
organelle assembly	1
trans-Golgi to periciliary membrane compartment transport	1
plasma membrane bounded cell projection assembly	1
ciliary transition zone assembly	1
cellular component organization	1
binding	1
cytoskeleton	1
microtubule	1
ciliary plasm	1
cellular_component	1
centrosome	1
microtubule organizing center	1
cilium	1
intracellular anatomical structure	1
intracellular membraneless organelle	1
intraciliary transport particle	1
membrane-bounded organelle	1
plasma membrane bounded cell projection	1

Protein interactions and networks

STRING

704 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CFAP263	DRC7	Q8IY82	644
CFAP263	DRC12	Q494R4	626
CFAP263	LRRC23	Q53EV4	607
CFAP263	SPMIP4	Q8N865	570
CFAP263	CCDC146	Q8IYE0	544
CFAP263	CCDC125	Q86Z20	540
CFAP263	SPAG17	Q6Q759	535
CFAP263	LYPD2	Q6UXB3	531
CFAP263	CFAP96	A7E2U8	527
CFAP263	CCDC81	Q6ZN84	513
CFAP263	CFAP184	Q2M329	504
CFAP263	CFAP70	Q5T0N1	494
CFAP263	LRRIQ1	Q96JM4	491
CFAP263	CCDC92	Q53HC0	488
CFAP263	LZTFL1	Q9NQ48	488

IntAct

19 interactions, top by confidence:

A	B	Type	Score
HSF2BP	CFAP263	psi-mi:“MI:0915”(physical association)	0.560
LTBR	ZNF724	psi-mi:“MI:0914”(association)	0.530
AIFM1	SEC16A	psi-mi:“MI:2364”(proximity)	0.420
CFAP263	H2BC21	psi-mi:“MI:0915”(physical association)	0.400
CFAP263	H1-0	psi-mi:“MI:0915”(physical association)	0.400
CFAP263	PPFIA3	psi-mi:“MI:0915”(physical association)	0.400
SMYD1	CFAP263	psi-mi:“MI:0915”(physical association)	0.370
LMTK2	HAL	psi-mi:“MI:0914”(association)	0.350
CFAP184	TARS3	psi-mi:“MI:0914”(association)	0.350
CFAP263	SPTBN2	psi-mi:“MI:0914”(association)	0.350
CANX	NACA	psi-mi:“MI:2364”(proximity)	0.270
CFAP263	HSF2BP	psi-mi:“MI:0915”(physical association)	0.000
CFAP263	GIT1	psi-mi:“MI:0915”(physical association)	0.000
CFAP263	HAP1	psi-mi:“MI:0915”(physical association)	0.000
CFAP263	IMMT	psi-mi:“MI:0915”(physical association)	0.000
CFAP263	PFN2	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (24): CCDC113 (Affinity Capture-MS), CCDC113 (Affinity Capture-MS), CCDC113 (Proximity Label-MS), CCDC113 (Proximity Label-MS), GIT1 (Two-hybrid), HAP1 (Two-hybrid), IMMT (Two-hybrid), PFN2 (Two-hybrid), HSF2BP (Two-hybrid), CCDC113 (Proximity Label-MS), CCDC113 (Proximity Label-MS), CCDC113 (Proximity Label-MS), CCDC113 (Affinity Capture-RNA), CCDC113 (Affinity Capture-MS), PPFIA3 (Affinity Capture-MS)

ESM2 similar proteins: A0JMY4, A2AJB1, A3KQH2, A7RNG8, B1H228, E9Q9F7, F1N2N9, F1RKB1, M1V4Y8, Q0VFX2, Q16VW9, Q17QH9, Q28G12, Q2TA00, Q2TAA8, Q3KPZ2, Q3SZX9, Q3T0L1, Q3USS3, Q3UX62, Q3UZ57, Q4R6I5, Q4R8Y5, Q4V7B0, Q502W7, Q5T1B0, Q5T5S1, Q5XIR6, Q5XIR8, Q66H60, Q68CZ6, Q6DCY9, Q6DHI2, Q6PA15, Q8BSN3, Q8C5T8, Q8CDN8, Q8CDV6, Q8IWF9, Q8NA47

Diamond homologs: I7M6D6, Q2M329, Q3SZX9, Q8C5T8, Q95LS7, Q9CR92, Q9H0I3, Q5XJN6

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	97
Likely benign	6
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1418 predictions. Top by Δscore:

Variant	Effect	Δscore
16:58250111:CTCAG:C	donor_loss	1.0000
16:58250112:TCAG:T	donor_loss	1.0000
16:58250113:CAG:C	donor_loss	1.0000
16:58250114:AG:A	donor_loss	1.0000
16:58250115:GGTAC:G	donor_loss	1.0000
16:58250117:T:A	donor_loss	1.0000
16:58252725:A:AG	acceptor_gain	1.0000
16:58252726:G:GG	acceptor_gain	1.0000
16:58252726:GCT:G	acceptor_gain	1.0000
16:58252726:GCTAT:G	acceptor_gain	1.0000
16:58252849:CACAG:C	donor_loss	1.0000
16:58252850:ACAG:A	donor_loss	1.0000
16:58252851:CAGG:C	donor_loss	1.0000
16:58252852:AGGTA:A	donor_loss	1.0000
16:58252853:GGT:G	donor_loss	1.0000
16:58252854:G:GC	donor_loss	1.0000
16:58252855:T:A	donor_loss	1.0000
16:58253988:T:TA	acceptor_gain	1.0000
16:58253989:G:A	acceptor_gain	1.0000
16:58258356:T:A	acceptor_gain	1.0000
16:58258465:G:GT	donor_gain	1.0000
16:58278607:G:GT	donor_gain	1.0000
16:58278620:A:T	donor_gain	1.0000
16:58278633:CAGAG:C	donor_loss	1.0000
16:58278634:AGAGG:A	donor_loss	1.0000
16:58278635:GAG:G	donor_gain	1.0000
16:58278635:GAGG:G	donor_loss	1.0000
16:58278636:AGGTG:A	donor_loss	1.0000
16:58278637:GGTGA:G	donor_loss	1.0000
16:58278639:T:A	donor_loss	1.0000

AlphaMissense

2493 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
16:58258368:G:C	A131P	0.996
16:58258383:G:C	A136P	0.996
16:58278632:G:C	A348P	0.990
16:58254133:G:C	A122P	0.987
16:58259894:T:C	L196P	0.986
16:58262485:T:C	L243P	0.983
16:58262494:T:C	L246P	0.983
16:58258425:T:C	F150L	0.978
16:58258427:T:A	F150L	0.978
16:58258427:T:G	F150L	0.978
16:58262445:G:C	A230P	0.977
16:58262431:T:C	L225S	0.976
16:58262527:T:C	L257P	0.976
16:58267486:T:C	L264P	0.976
16:58258393:G:C	R139P	0.974
16:58262420:T:A	D221E	0.973
16:58262420:T:G	D221E	0.973
16:58278536:T:C	F316L	0.970
16:58278538:C:A	F316L	0.970
16:58278538:C:G	F316L	0.970
16:58254140:G:C	R124P	0.969
16:58250091:T:C	L26P	0.967
16:58254077:T:C	L103P	0.967
16:58254146:T:C	L126P	0.967
16:58278564:T:A	V325D	0.967
16:58278516:T:C	L309P	0.966
16:58262419:A:G	D221G	0.963
16:58258426:T:C	F150S	0.962
16:58262421:T:C	F222L	0.962
16:58262423:T:A	F222L	0.962

dbSNP variants (sampled 300 via entrez): RS1000003641 (16:58280355 G>A), RS1000022059 (16:58196472 A>G), RS1000057731 (16:58229251 A>C), RS1000075756 (16:58280128 G>A,T), RS1000108314 (16:58229570 G>A), RS1000136449 (16:58196667 G>A), RS1000138856 (16:58210706 A>C), RS1000173474 (16:58242066 T>G), RS1000185513 (16:58208072 G>A,T), RS1000243231 (16:58201995 T>A), RS1000283943 (16:58235147 C>G,T), RS1000288465 (16:58207571 C>G,T), RS1000312404 (16:58223717 G>A,T), RS1000354468 (16:58248746 T>G), RS1000402320 (16:58235309 A>C)

Disease associations

OMIM: gene MIM:616070 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

3 associations (top):

Study	Trait	p-value
GCST004302_22	Primary biliary cholangitis	2.000000e-08
GCST005752_147	Systemic lupus erythematosus	3.000000e-06
GCST005752_34	Systemic lupus erythematosus	1.000000e-07

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

31 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, decreases expression, increases expression	4
mercuric bromide	decreases expression, affects cotreatment	2
Air Pollutants	increases abundance, increases expression	2
Phenylmercuric Acetate	affects cotreatment, decreases expression	2
Tretinoin	decreases expression	2
aristolochic acid I	increases expression	1
TAK-243	increases sumoylation	1
methylmercuric chloride	decreases expression	1
propionaldehyde	increases expression	1
trichostatin A	decreases expression, increases expression	1
3,4-dichloroaniline	decreases expression	1
potassium chromate(VI)	increases expression	1
CGP 52608	affects binding, increases reaction	1
perfluoro-n-nonanoic acid	increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
Arsenic	affects methylation	1
Benzo(a)pyrene	increases methylation	1
Diuron	decreases expression	1
Folic Acid	decreases expression	1
Niclosamide	increases expression	1
Oxygen	decreases expression	1
Silicon Dioxide	increases expression	1
Smoke	increases abundance, increases expression	1
Thimerosal	decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
Tunicamycin	increases expression	1
Cyclosporine	increases expression	1
Lactic Acid	decreases expression	1
Acrylamide	decreases expression	1

Clinical trials (associated diseases)

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