CFAP20

Summary

CFAP20 (cilia and flagella associated protein 20, HGNC:29523) is a protein-coding gene on chromosome 16q21, encoding Cilia- and flagella-associated protein 20 (Q9Y6A4). Cilium- and flagellum-specific protein that plays a role in axonemal structure organization and motility. It is a selective cancer dependency (DepMap: 67.2% of cell lines).

Enables RNA binding activity. Involved in several processes, including positive regulation of feeding behavior; protein polyglutamylation; and regulation of cilium beat frequency involved in ciliary motility. Located in microtubule cytoskeleton and nucleoplasm.

Source: NCBI Gene 29105 — automated summary from GO annotations (Alliance of Genome Resources).

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 27 total — 1 pathogenic
• GTEx eGene: eQTL in 13 tissues, sQTL in 5 (q < 0.05)
• Phenotypes (HPO): 51
• ChEMBL bioactivity: 1 clinical-phase molecule tested; no curated mechanism-of-action drug
• Cancer dependency (DepMap): dependent in 67.2% of screened cell lines
• Constraint (gnomAD): pLI 0.07 (LoF-tolerant), LOEUF 0.78 (unconstrained)
• MANE Select transcript: NM_013242
• Interaction hub: 2,552 STRING partners (top 4% of genes corpus-wide)

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:29523
Approved symbol	CFAP20
Name	cilia and flagella associated protein 20
Location	16q21
Locus type	gene with protein product
Status	Approved
Aliases	GTL3, fSAP23
Ensembl gene	ENSG00000070761
Ensembl biotype	protein_coding
OMIM	617906
Entrez	29105

Gene structure

Transcript identifiers

Ensembl transcripts: 12 — 7 protein_coding, 4 retained_intron, 1 protein_coding_CDS_not_defined

MANE Select: ENST00000262498

Transcript support level (Ensembl TSL; 1 = fully mRNA-supported): TSL 1: 1, TSL 2: 3, TSL 3: 1, TSL 5: 2

ENST00000262498, ENST00000562443, ENST00000562622, ENST00000564150, ENST00000565880, ENST00000567092, ENST00000567660, ENST00000896541, ENST00000933126, ENST00000933128, ENST00001007771, ENST00001134459

RefSeq mRNA: 1 — MANE Select: NM_013242 NM_013242

CCDS: CCDS10793

Canonical transcript exons

ENST00000262498 — 6 exons

Exon	Start	End
ENSE00000686445	58115269	58115457
ENSE00000921088	58113592	58114030
ENSE00001100813	58129032	58129381
ENSE00003523794	58116041	58116152
ENSE00003616717	58114810	58114920
ENSE00003674010	58116872	58116951

Expression profiles

Bgee: expression breadth ubiquitous, 288 present calls, max score 98.09.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 32.9700 / max 200.2936, expressed in 1817 samples.

Highest expression (Bgee): bronchial epithelial cell, sperm, epithelium of bronchus, ventricular zone, adult organism.

Genetic regulation across tissues (GTEx eQTL / sQTL)

CFAP20 is an eGene in GTEx v10 — its expression is genetically regulated (eQTL) in 13 tissues and its splicing (sQTL) in 5 (q < 0.05). Strongest associations first; slope = normalized effect of the lead variant’s alternative allele.

18 significant tissue × QTL associations:

Tissue	QTL	q-value	Slope	Lead variant
Brain Spinal cord cervical c-1	eqtl	3.8e-10	-0.74	16:58113995:AG:A
Skin Sun Exposed Lower leg	eqtl	3.1e-05	-0.39	16:58177462:T:G
Stomach	eqtl	2.6e-04	+0.19	16:57613631:C:T
Heart Atrial Appendage	eqtl	4.0e-04	+0.28	16:58129575:A:G
Thyroid	sqtl	4.0e-03	-1.50	16:57887939:G:A
Cells EBV-transformed lymphocytes	eqtl	5.4e-03	+0.13	16:58234532:C:T
Brain Hippocampus	eqtl	5.8e-03	+0.34	16:59004747:T:A
Brain Frontal Cortex BA9	eqtl	1.2e-02	+1.28	16:58589003:C:T
Artery Tibial	eqtl	1.4e-02	-0.21	16:58141695:T:C
Testis	sqtl	2.1e-02	+0.24	16:58252023:C:CAT
Esophagus Muscularis	eqtl	2.8e-02	-0.26	16:58183880:C:T
Adipose Subcutaneous	eqtl	3.0e-02	+0.14	16:58223322:C:T
Colon Transverse	sqtl	3.4e-02	+0.37	16:57985080:T:G
Skin Not Sun Exposed Suprapubic	eqtl	3.6e-02	-0.27	16:58171436:C:T
Muscle Skeletal	sqtl	3.8e-02	-0.91	16:57494226:G:T
Whole Blood	eqtl	4.2e-02	-0.18	16:57697522:C:T
Heart Left Ventricle	sqtl	4.2e-02	-0.69	16:58471583:GAGCCAGGAA:G
Pituitary	eqtl	4.5e-02	-0.17	16:57292357:A:G

FANTOM5 promoters

6 alternative TSS:

Promoter ID	TPM avg	Samples expressed
157601	20.8007	1803
157602	10.3199	1779
157603	1.2948	883
157600	0.3090	121
157599	0.2109	76
157596	0.0346	6

Top tissues by expression

showing 100 of 293 tissues by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
bronchial epithelial cell	CL:0002328	98.09	gold quality
sperm	CL:0000019	97.15	gold quality
epithelium of bronchus	UBERON:0002031	96.98	gold quality
ventricular zone	UBERON:0003053	96.73	gold quality
adult organism	UBERON:0007023	96.64	gold quality
bronchus	UBERON:0002185	96.49	gold quality
endothelial cell	CL:0000115	96.03	gold quality
cortical plate	UBERON:0005343	95.92	gold quality
left testis	UBERON:0004533	95.87	gold quality
ganglionic eminence	UBERON:0004023	95.81	gold quality
middle temporal gyrus	UBERON:0002771	95.61	gold quality
right testis	UBERON:0004534	95.55	gold quality
embryo	UBERON:0000922	95.41	gold quality
male germ cell	CL:0000015	95.33	gold quality
calcaneal tendon	UBERON:0003701	95.29	gold quality
right uterine tube	UBERON:0001302	95.16	gold quality
upper leg skin	UBERON:0004262	95.11	gold quality
testis	UBERON:0000473	94.86	gold quality
prefrontal cortex	UBERON:0000451	94.76	gold quality
pigmented layer of retina	UBERON:0001782	94.59	gold quality
retina	UBERON:0000966	94.56	gold quality
Brodmann (1909) area 23	UBERON:0013554	94.19	gold quality
pituitary gland	UBERON:0000007	94.11	gold quality
adenohypophysis	UBERON:0002196	94.05	gold quality
caput epididymis	UBERON:0004358	94.04	gold quality
skin of hip	UBERON:0001554	93.89	gold quality
epithelium of nasopharynx	UBERON:0001951	93.89	gold quality
metanephric glomerulus	UBERON:0004736	93.74	gold quality
left ventricle myocardium	UBERON:0006566	93.50	gold quality
frontal cortex	UBERON:0001870	93.39	gold quality
frontal lobe	UBERON:0016525	93.39	gold quality
renal glomerulus	UBERON:0000074	93.36	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	93.30	gold quality
tibia	UBERON:0000979	93.28	gold quality
parietal pleura	UBERON:0002400	93.28	gold quality
neocortex	UBERON:0001950	93.23	gold quality
amniotic fluid	UBERON:0000173	93.19	gold quality
caudate nucleus	UBERON:0001873	93.19	gold quality
hair follicle	UBERON:0002073	93.08	gold quality
Brodmann (1909) area 9	UBERON:0013540	93.07	gold quality
nucleus accumbens	UBERON:0001882	93.06	gold quality
right frontal lobe	UBERON:0002810	92.88	gold quality
cerebral cortex	UBERON:0000956	92.72	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	92.71	gold quality
placenta	UBERON:0001987	92.65	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	92.63	gold quality
hypothalamus	UBERON:0001898	92.53	gold quality
forebrain	UBERON:0001890	92.43	gold quality
primary visual cortex	UBERON:0002436	92.43	gold quality
visceral pleura	UBERON:0002401	92.37	gold quality
telencephalon	UBERON:0001893	92.34	gold quality
anterior cingulate cortex	UBERON:0009835	92.30	gold quality
pleura	UBERON:0000977	92.29	gold quality
myocardium	UBERON:0002349	92.24	gold quality
cingulate cortex	UBERON:0003027	92.21	gold quality
right lobe of liver	UBERON:0001114	92.17	gold quality
right atrium auricular region	UBERON:0006631	92.10	gold quality
metanephros	UBERON:0000081	92.07	gold quality
cardiac atrium	UBERON:0002081	92.02	gold quality
cartilage tissue	UBERON:0002418	91.96	gold quality
spinal cord	UBERON:0002240	91.89	gold quality
skin of abdomen	UBERON:0001416	91.86	gold quality
islet of Langerhans	UBERON:0000006	91.84	gold quality
brain	UBERON:0000955	91.82	gold quality
left ovary	UBERON:0002119	91.80	gold quality
heart right ventricle	UBERON:0002080	91.73	gold quality
corpus callosum	UBERON:0002336	91.64	gold quality
putamen	UBERON:0001874	91.60	gold quality
Ammon’s horn	UBERON:0001954	91.57	gold quality
cardiac muscle of right atrium	UBERON:0003379	91.47	gold quality
heart left ventricle	UBERON:0002084	91.46	gold quality
endocervix	UBERON:0000458	91.44	gold quality
cardiac ventricle	UBERON:0002082	91.39	gold quality
right ovary	UBERON:0002118	91.39	gold quality
heart	UBERON:0000948	91.31	gold quality
tendon	UBERON:0000043	91.16	gold quality
superior frontal gyrus	UBERON:0002661	91.12	gold quality
skin of leg	UBERON:0001511	90.99	gold quality
zone of skin	UBERON:0000014	90.98	gold quality
ovary	UBERON:0000992	90.97	gold quality
mucosa of paranasal sinus	UBERON:0005030	90.97	gold quality
Brodmann (1909) area 46	UBERON:0006483	90.95	gold quality
ectocervix	UBERON:0012249	90.92	gold quality
omental fat pad	UBERON:0010414	90.88	gold quality
peritoneum	UBERON:0002358	90.87	gold quality
cervix squamous epithelium	UBERON:0006922	90.84	silver quality
adipose tissue of abdominal region	UBERON:0007808	90.84	gold quality
peripheral nervous system	UBERON:0000010	90.81	gold quality
tibial nerve	UBERON:0001323	90.81	gold quality
right hemisphere of cerebellum	UBERON:0014890	90.77	gold quality
cerebellar hemisphere	UBERON:0002245	90.72	gold quality
cerebellar cortex	UBERON:0002129	90.69	gold quality
left uterine tube	UBERON:0001303	90.66	gold quality
left lobe of thyroid gland	UBERON:0001120	90.51	gold quality
apex of heart	UBERON:0002098	90.51	gold quality
stromal cell of endometrium	CL:0002255	90.46	gold quality
cerebellum	UBERON:0002037	90.44	gold quality
thyroid gland	UBERON:0002046	90.29	gold quality
postcentral gyrus	UBERON:0002581	90.29	gold quality
mucosa of transverse colon	UBERON:0004991	90.24	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-GEOD-81547	yes	11.89
E-CURD-89	no	1104.20
E-ANND-3	no	0.00

HPA expression

RNA tissue specificity: Low tissue specificity

showing 60 of 79 HPA tissues / cells by nTPM:

Tissue / cell	Axis	nTPM	Protein (IHC)
Cerebral cortex	tissue	61.3	medium
Somatosensory cortex	tissue	61.3
Pons	tissue	59.6
Thalamus	tissue	58.6
Midbrain	tissue	58.5
Prefrontal cortex	tissue	57.8
Hippocampal formation	tissue	57.4
Putamen	tissue	54.9
Superior colliculi	tissue	54.5
Occipital cortex	tissue	54.0
Basal ganglia	tissue	53.2	medium
Motor cortex	tissue	51.8
Septum	tissue	51.5
Spinal cord	tissue	51.0
Substantia nigra	tissue	50.2
Entorhinal cortex	tissue	50.2
Temporal cortex	tissue	50.1
Retrosplenial and cingulate cortex	tissue	49.9
Ventral forebrain	tissue	48.0
Medulla oblongata	tissue	47.5
Hypothalamus	tissue	45.8
Periaqueductal gray	tissue	45.7
Retrosplenial cortex	tissue	44.4
Caudate putamen	tissue	42.0
Corpus callosum	tissue	41.4
Heart muscle	tissue	40.4	medium
Insular cortex	tissue	40.4
Frontal cortex	tissue	36.8
Thymus	tissue	36.6
Fallopian tube	tissue	34.1	medium
Amygdala	tissue	33.0
Parathyroid gland	tissue	32.6	low
Cerebellum	tissue	32.1	not detected
Olfactory bulb	tissue	31.9
Ovary	tissue	31.8	not detected
Nucleus accumbens	tissue	31.7
Liver	tissue	31.7	medium
Pituitary gland	tissue	31.4
Locus coeruleus	tissue	28.8
Testis	tissue	28.5	medium
Placenta	tissue	28.4	medium
Retina	tissue	26.4
Postcentral gyrus	tissue	26.1
Choroid plexus	tissue	25.7
Thyroid gland	tissue	24.9	low
Bone marrow	tissue	24.6	not detected
Lymph node	tissue	23.9	not detected
Hippocampus	tissue	23.8	medium
Adrenal gland	tissue	22.5	low
Epididymis	tissue	21.9	high
Tonsil	tissue	20.5	high
Breast	tissue	19.6	low
Cervix	tissue	19.5	high
Lung	tissue	19.3	low
Kidney	tissue	19.2	medium
Endometrium 1	tissue	18.9	low
Tongue	tissue	18.7
Vagina	tissue	18.2	medium
Adipose tissue	tissue	17.9	not detected
Esophagus	tissue	17.8	medium

Brain sub-regions (HPA Brain Atlas): detected in 191; highest nTPM — Dorsal hippocampus (57.4), Ventral spinal cord (51.0), Subiculum (47.5), Ventral hippocampus (46.7), Dorsal spinal cord (44.8).

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): E2F4, RELA, TADA2A, TBP

miRNA regulators (miRDB)

Targeting CFAP20 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific).

showing 30 of 39 miRNAs:

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-5692B	100.00	71.32	2622
HSA-MIR-5692C	100.00	71.32	2622
HSA-MIR-513A-5P	100.00	69.77	2465
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-9983-3P	99.94	71.48	3631
HSA-MIR-6753-3P	99.93	66.57	637
HSA-MIR-7107-3P	99.93	66.73	627
HSA-MIR-129-5P	99.88	70.26	3273
HSA-MIR-3180-5P	99.82	69.12	2422
HSA-MIR-4760-5P	99.80	69.88	1619
HSA-MIR-577	99.78	69.13	2479
HSA-MIR-3680-3P	99.75	72.51	3095
HSA-MIR-4527	99.66	67.43	714
HSA-MIR-6848-3P	99.64	66.49	885
HSA-MIR-6503-5P	99.62	66.96	597
HSA-MIR-425-5P	99.59	67.67	900
HSA-MIR-12123	99.52	71.79	2990
HSA-MIR-5571-5P	99.49	66.99	1764
HSA-MIR-1206	99.30	69.32	1016
HSA-MIR-488-5P	99.28	68.12	821
HSA-MIR-410-3P	99.27	69.98	2457
HSA-MIR-6843-3P	99.26	66.42	915
HSA-MIR-664A-3P	99.22	71.08	2696
HSA-MIR-122B-3P	99.21	68.90	1333
HSA-MIR-21-3P	99.21	68.95	1312
HSA-MIR-6792-3P	98.41	66.86	1359

Functional genomics

gnomAD constraint: pLI 0.0692, LOEUF 0.783, missense Z 1.78 — population loss-of-function intolerance (pLI ≥ 0.9 = LoF-intolerant; lower LOEUF = more constrained). gnomAD

Regional missense constraint (gnomAD RMC): no regional variation along ENST00000262498 — one region, missense o/e 0.73. DepMap (CRISPR cell-line fitness): dependent in 67.2% of screened cell lines.

Most-dependent cell lines (DepMap gene-effect, lower = stronger; ≤ −0.5 shown): B-CPAP (-1.427), HCC-827-GR5 (-1.337), LN-428 (-1.333), SU-DHL-4 (-1.33), TEN (-1.317), NCI-H82 (-1.293), HCC1143 (-1.29), SNU-1196 (-1.289), HSC-4 (-1.285), CL-11 (-1.283), COV362 (-1.274), TC-71 (-1.258), HUP-T3 (-1.25), RL (-1.244), Panc 03.27 (-1.226).

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	cfap20	ENSDARG00000100514
mus_musculus	Cfap20	ENSMUSG00000031796
rattus_norvegicus	Cfap20	ENSRNOG00000042179
drosophila_melanogaster	Bug22	FBGN0032248
caenorhabditis_elegans		WBGENE00008288

Paralogs (1): CFAP20DC (ENSG00000163689)

Additional cross-species homologs

Sequence homologs in species beyond Ensembl Compara’s model organisms, by Diamond local protein alignment (% sequence identity; best hit per species). Lower-identity rows are more distant homologs. The matched accessions’ gene symbols aren’t in biobtree yet, so each row shows the UniProt accession.

Organism	UniProt	Identity	Method
Bos taurus	Q6B857	100.0%	Diamond
Xenopus tropicalis	Q6GL74	100.0%	Diamond
Xenopus laevis	Q6GPY6	100.0%	Diamond
Gallus gallus	Q5ZHP3	99.5%	Diamond
Caenorhabditis briggsae	Q61JK7	99.5%	Diamond
Paramecium tetraurelia	A0CDD4	92.1%	Diamond
Chlamydomonas reinhardtii	A8IU92	90.5%	Diamond

Genomic neighbors (locus context)

Genes flanking this one on the chromosome (NCBI/Entrez gene neighborhood). Positional context only — some neighbors share regulatory elements (bidirectional promoters, antisense/overlapping transcripts), but chromosomal adjacency is not itself a functional relationship (see Interactions for that).

Symbol	Type	Entrez
CSNK2A2	protein-coding	1459
MMP15	protein-coding	4324
ZNF319	protein-coding	57567
USB1	protein-coding	79650
PRSS54	protein-coding	221191
CFAP263	protein-coding	29070
SPMIP8	protein-coding	374739

Protein

Protein identifiers

Cilia- and flagella-associated protein 20 — Q9Y6A4 (reviewed: Q9Y6A4)

Alternative names: Basal body up-regulated protein 22, Transcription factor IIB

All UniProt accessions (2): Q9Y6A4, H3BPA3

UniProt curated annotations — full annotation on UniProt →

Function. Cilium- and flagellum-specific protein that plays a role in axonemal structure organization and motility. Microtubule inner protein (MIP) part of the dynein-decorated doublet microtubules (DMTs) in cilia axoneme, which is required for motile cilia beating. Involved in the regulation of the size and morphology of cilia. Required for axonemal microtubules polyglutamylation.

Subunit / interactions. Microtubule inner protein component of sperm flagellar doublet microtubules. Interacts with CFAP65.

Subcellular location. Nucleus. Cytoplasm. Cytoskeleton. Microtubule organizing center. Centrosome. Centriole. Cilium basal body. Cilium axoneme. Flagellum axoneme.

Similarity. Belongs to the CFAP20 family.

RefSeq proteins (1): NP_037374* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR007714	CFA20_dom	Domain
IPR040441	CFA20/CFAP20DC	Family

Pfam: PF05018

UniProt features (1 total): chain 1

Structure

Experimental structures (PDB)

3 structures by resolution:

PDB	Title	Method	Resolution (Å)
7UNG	48-nm repeat of the human respiratory doublet microtubule	ELECTRON MICROSCOPY	3.6
8J07	96nm repeat of human respiratory doublet microtubule and associated axonemal complexes	ELECTRON MICROSCOPY	4.1
11YJ	In situ subtomogram average of the transition zone doublet microtubule in human airway …	ELECTRON MICROSCOPY	7.3

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9Y6A4-F1	91.81	0.83

Human Protein Atlas

Protein class: Predicted intracellular proteins, Essential proteins

Protein evidence: Evidence at protein level

Subcellular location (HPA, imaging): nucleoplasm; principal piece; equatorial segment

Antibody reliability (HPA): IH uncertain · IF supported

Function

Pathways and Gene Ontology

Reactome pathways

0 curated (TAS) of 0; 0 disease pathways. Curated-first; evidence = TAS (manually curated) vs IEA (electronic inference).

MSigDB gene sets: 188 (showing top): GOBP_BEHAVIOR, GOBP_REGULATION_OF_MICROTUBULE_BASED_PROCESS, CMYB_01, RACCACAR_AML_Q6, GOBP_POSITIVE_REGULATION_OF_BEHAVIOR, GOCC_MICROTUBULE_ORGANIZING_CENTER, WEI_MYCN_TARGETS_WITH_E_BOX, PAX8_B, GOBP_REGULATION_OF_BEHAVIOR, GOBP_REGULATION_OF_FEEDING_BEHAVIOR, AML_Q6, GOBP_CILIUM_ORGANIZATION, GOBP_CILIUM_MOVEMENT, GOBP_REGULATION_OF_MICROTUBULE_BASED_MOVEMENT, GOBP_CILIUM_OR_FLAGELLUM_DEPENDENT_CELL_MOTILITY

GO Biological Process (6): protein polyglutamylation (GO:0018095), flagellated sperm motility (GO:0030317), cilium assembly (GO:0060271), regulation of cilium beat frequency involved in ciliary motility (GO:0060296), positive regulation of cell motility (GO:2000147), positive regulation of feeding behavior (GO:2000253)

GO Molecular Function (2): RNA binding (GO:0003723), protein binding (GO:0005515)

GO Cellular Component (12): nucleoplasm (GO:0005654), centriole (GO:0005814), axonemal microtubule (GO:0005879), cilium (GO:0005929), motile cilium (GO:0031514), ciliary basal body (GO:0036064), sperm flagellum (GO:0036126), extracellular exosome (GO:0070062), axonemal B tubule inner sheath (GO:0160112), nucleus (GO:0005634), microtubule (GO:0005874), axoneme (GO:0005930)

GO top-level categories

44 GO namespaces:

Category	Terms
cellular anatomical structure	3
microtubule organizing center	2
cilium	2
peptidyl-glutamic acid modification	1
cilium-dependent cell motility	1
cilium movement involved in cell motility	1
sperm motility	1
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
regulation of cilium beat frequency	1
regulation of cilium movement involved in cell motility	1
regulation of biological quality	1
positive regulation of locomotion	1
positive regulation of cellular process	1
cell motility	1
regulation of cell motility	1
feeding behavior	1
positive regulation of behavior	1
regulation of feeding behavior	1
nucleic acid binding	1
binding	1
nuclear lumen	1
intracellular membraneless organelle	1
cytoplasmic microtubule	1
axoneme	1
intraciliary transport particle	1
membrane-bounded organelle	1
plasma membrane bounded cell projection	1
9+2 motile cilium	1
extracellular vesicle	1
A axonemal microtubule	1
axonemal microtubule doublet inner sheath	1
intracellular membrane-bounded organelle	1
microtubule cytoskeleton	1
polymeric cytoskeletal fiber	1
cytoskeleton	1
microtubule	1
ciliary plasm	1

Experimentally-supported GO annotations

GO terms backed by direct experimental evidence (ECO experimental codes) — 12 of 20 annotations. The rest are phylogenetic / computational / electronic (IEA).

12 experimentally-supported GO terms:

GO term	NS	Evidence
cilium assembly	BP	mutant phenotype
positive regulation of cell motility	BP	direct assay
positive regulation of feeding behavior	BP	direct assay
protein polyglutamylation	BP	mutant phenotype
regulation of cilium beat frequency involved in ciliary motility	BP	direct assay
axonemal microtubule	CC	direct assay
centriole	CC	direct assay
ciliary basal body	CC	direct assay
cilium	CC	direct assay
extracellular exosome	CC	high-throughput assay
nucleoplasm	CC	direct assay
RNA binding	MF	high-throughput assay

Protein interactions and networks

STRING

showing 15 of 2,552 interactions by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CFAP20	GTF2B	Q00403	864
CFAP20	DRAP1	Q14919	789
CFAP20	TBP	P20226	760
CFAP20	DR1	Q01658	713
CFAP20	CFAP52	Q8N1V2	571
CFAP20	CFAP161	Q6P656	545
CFAP20	TBC1D32	Q96NH3	528
CFAP20	PACRG	Q96M98	526
CFAP20	CFAP184	Q2M329	513
CFAP20	EFHC1	Q5JVL4	505
CFAP20	CFAP45	Q9UL16	503
CFAP20	CFAP263	Q9H0I3	489
CFAP20	CFAP53	Q96M91	476
CFAP20	CFAP57	Q96MR6	473
CFAP20	SPAG8	Q99932	472

IntAct

Human interaction partners of CFAP20 in IntAct, one row per partner (best MIscore; records = supporting IntAct interaction records).

28 partners by confidence:

Partner	Interaction type	MIscore	Records
ARL2BP	physical association	0.790	4
CLASRP	physical association	0.790	4
SFSWAP	association	0.620	2
YWHAG	physical association	0.590	2
LRRK2	direct interaction	0.590	1
KPNA4	association	0.510	2
SF3A2	physical association	0.400	1
TFCP2L1	physical association	0.370	1
PRPF40A	association	0.350	1
RABEPK	association	0.350	1
CDK20	physical association	0.000	1
DCAF1	physical association	0.000	1
DDA1	physical association	0.000	1
DICER1	physical association	0.000	1
FOXJ1	physical association	0.000	1
HNRNPUL1	physical association	0.000	1
HSF1	physical association	0.000	1
MRPS28	physical association	0.000	1
MRPS31	physical association	0.000	1
MRPS35	physical association	0.000	1
PDHB	physical association	0.000	1
PLK1	physical association	0.000	1
PRPF38A	physical association	0.000	1
RFX3	physical association	0.000	1
SART3	physical association	0.000	1
SNRPD3	physical association	0.000	1
TARBP2	physical association	0.000	1
TBC1D32	physical association	0.000	1

BioGRID (132 interactions; top human partners by supporting records): ARL2BP (Affinity Capture-MS; 5 records), CLASRP (Affinity Capture-MS; 5 records), SFSWAP (Affinity Capture-MS; 5 records), CDK20 (Affinity Capture-MS; 3 records), TBC1D32 (Affinity Capture-MS; 3 records), FAM149B1 (Affinity Capture-MS; 2 records), FOXJ1 (Affinity Capture-MS; 2 records), KRAS (Synthetic Lethality; 2 records), PNN (Affinity Capture-MS; 2 records), RABEPK (Affinity Capture-MS; 2 records), ACIN1 (Affinity Capture-MS), ADCK1 (Affinity Capture-MS), ARRDC3 (Affinity Capture-MS), ATG16L1 (Affinity Capture-MS), ATG5 (Proximity Label-MS)

Protein complexes (CORUM) (1)

Experimentally-characterized complexes this protein is a subunit of (★ = the complex contains a known drug target).

1 complexes by size:

Complex	Subunits	Members
Spliceosome, A complex	112	RBM39, SAP30BP, CDK11A, CHERP, HNRNPA1, HNRNPK, HNRNPR, HNRNPU, RBM25, SF3A1, DDX46, HNRNPA3, RNPS1, SART1, SF1, SF3A2, SF3B4, SNRPB, ACIN1, CCAR2, DHX9, ELAVL1, ILF2, SF3B3, SRSF5, HNRNPA2B1, CD2BP2, DDX5, PUF60, RBM17, SNRPA1, TCERG1, ZC3H18, SNRPD1, SRSF2, SYNCRIP, ZNF207, CTNNBL1, HSPA8, NCBP2, SF3B2, TRA2B, YBX1, RBM10, SF3A3, SRRM1, SRSF6, SRSF7, SUGP1, DDX42, DNAJC8, EFTUD2, PRCC, SF3B5, SMNDC1, SNRNP200, WBP11, CDC5L, PPP1R8, PRPF6, BCAS2, NCBP1, PRPF19, PRPF3, SNRPD3, SRSF4, U2AF2, HNRNPUL1, NRIP2, PHF5A, RBM5, RBMX, SNRPA, SRRM2, U2AF1, CCAR1, CFAP20, CIRBP, DDX23, SF3B1, SF3B6, SNRPB2, SNRPE, BUB3, DHX15, PCBP1, PPP1CA, PQBP1, SNRNP70, SRSF1, U2SURP, DDX17, SNRPC, SNRPD2, SNRPF, SNRPG, SRRT, SRSF3, SRSF9, AGGF1, FUS, HNRNPC, HTATSF1, ILF3, PLRG1, SEC31B, TRIR, CWC15, HNRNPAB, PNN, PRPF40A, PRPF8

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 28 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

GO biological processes:

GO term	Partners	Fold	FDR
mRNA splicing, via spliceosome	5	16.4×	2e-03

Disease & clinical

Genetic variants

Variant evidence for CFAP20: 27 ClinVar records (1 pathogenic / likely pathogenic); 1 GWAS association. Per-variant detail is on Sugi Variant.

ClinVar

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

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	18
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (1)

Showing all 1 pathogenic / likely-pathogenic ClinVar records, ranked by ClinVar review status (expert panel → multiple submitters → single submitter), then by number of submitting labs.

Variant ID	HGVS	Classification	Review	Submitters
4849896	CFAP20, ARG113TRP (767845554)	Pathogenic	no assertion criteria provided	1

Per-variant reference — Sugi Variant

Explore CFAP20’s pathogenic and likely-pathogenic variants individually — each with its ClinVar classification and conditions, applied ACMG criteria (ClinGen expert panel, where curated), the calibrated in-silico predictors (AlphaMissense, REVEL, SaProt, conservation), gnomAD frequency, and the predictor-disagreement QC signal — on Sugi Variant.

SpliceAI

Top 10 splice-impact sites by Δscore (adjacent positions with the same effect merged into one range; 33 predictions of 320):

Position(s)	Effect	Δscore	Sites
16:58115267–58115268	donor_loss	1.0000	4
16:58115271	donor_gain	1.0000
16:58115458–58115460	acceptor_gain	1.0000	2
16:58115458–58115459	acceptor_loss	1.0000	3
16:58115465	acceptor_gain	1.0000
16:58116153–58116154	acceptor_loss	1.0000	5
16:58116870–58116871	donor_loss	1.0000	3
16:58116952–58116953	acceptor_loss	1.0000	3
16:58114031–58114032	acceptor_loss	0.9900	6
16:58114808–58114809	donor_loss	0.9900	5

AlphaMissense

876 missense substitutions predicted likely pathogenic (of 1,276 scored), across 175 residues. Top 20 hotspot residues, ranked by the number of likely-pathogenic substitutions (of those reachable by a single-nucleotide change), then by mean score:

Residue	Likely-pathogenic substitutions	Mean am_pathogenicity	Max am_pathogenicity
M121	9	0.909	0.996
D95	8	0.992	0.997
D39	8	0.988	0.997
F103	8	0.972	1.000
F2	8	0.967	0.995
N130	8	0.966	0.998
F167	8	0.966	0.994
S106	8	0.965	0.999
F89	8	0.959	0.994
H157	8	0.952	0.995
F134	8	0.949	0.998
F139	8	0.931	0.991
F87	8	0.929	0.992
S16	8	0.918	0.999
D138	8	0.917	0.980
D126	8	0.861	0.969
D169	8	0.816	0.970
W129	7	0.999	1.000
W25	7	0.994	1.000
F181	7	0.988	0.995

HPA cancer prognostics

RNA cancer specificity: Low cancer specificity

Disease associations

OMIM: gene MIM:617906 | disease phenotypes:

Genomics England panels (PanelApp)

Clinical diagnostic gene panels including this gene (1 panels, 1 green/diagnostic-grade). Confidence: green = diagnostic, amber = moderate.

1 panels:

Panel	Rating
Retinal disorders	green

HPO phenotypes

51 phenotypes (HPO-id order):

HPO	Term
HP:0000007	Autosomal recessive inheritance
HP:0000405	Conductive hearing impairment
HP:0000407	Sensorineural hearing impairment
HP:0000501	Glaucoma
HP:0000505	Visual impairment
HP:0000512	Abnormal electroretinogram
HP:0000543	Optic disc pallor
HP:0000546	Retinal degeneration
HP:0000551	Color vision defect
HP:0000563	Keratoconus
HP:0000602	Ophthalmoplegia
HP:0000613	Photophobia
HP:0000618	Blindness
HP:0000639	Nystagmus
HP:0000646	Amblyopia
HP:0000648	Optic atrophy
HP:0000662	Nyctalopia
HP:0000798	Oligozoospermia
HP:0000842	Hyperinsulinemia
HP:0001105	Retinal atrophy
HP:0001133	Constriction of peripheral visual field
HP:0001264	Spastic diplegia
HP:0001270	Motor delay
HP:0001276	Hypertonia
HP:0002069	Bilateral tonic-clonic seizure
HP:0002194	Delayed gross motor development
HP:0007663	Reduced visual acuity
HP:0007675	Progressive night blindness
HP:0007703	Abnormal retinal pigmentation
HP:0007722	Retinal pigment epithelial atrophy
HP:0007737	Spicular pigmentation of the retina
HP:0007787	Posterior subcapsular cataract
HP:0007843	Attenuation of retinal blood vessels
HP:0007994	Peripheral visual field loss
HP:0008046	Abnormal retinal vascular morphology
HP:0008209	Premature ovarian insufficiency
HP:0011003	High myopia
HP:0011505	Cystoid macular edema
HP:0012426	Optic disc drusen
HP:0025573	Mild myopia
HP:0030465	Undetectable light-adapted electroretinogram
HP:0030466	Abnormal full-field electroretinogram
HP:0030474	Undetectable dark-adapted electroretinogram
HP:0030488	Abnormal central response of multifocal electroretinogram
HP:0030515	Moderately reduced visual acuity
HP:0030610	Photoreceptor outer segment loss on macular OCT
HP:0030786	Photopsia
HP:0032037	Mildly reduced visual acuity
HP:0032286	Ultra-low vision with retained light perception
HP:0033725	Thin corpus callosum
HP:5200044	Reduced attention regulation

GWAS associations

1 associations:

Study	Trait	p-value
GCST005790_13	Rosacea symptom severity	2e-6

EFO canonical traits (from GWAS)

1 canonical traits:

EFO ID	Trait name
EFO:0009180	rosacea severity measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL5724749 (SINGLE PROTEIN)

Molecules with ChEMBL bioactivity

Phase ≥1, by development phase (incl. off-target/promiscuous compounds). Patent mentions across the top 20 by phase: 1,601 (via chembl_molecule»patent_compound — counts attach to the compound, not the gene–compound relationship, so off-target/promiscuous molecules can dominate).

1 molecules by phase:

Molecule	Name	Phase	Patents
CHEMBL1232461	MOLIBRESIB	2	1,601

PharmGKB: 1 entry (CPIC guideline: no)

ChEMBL bioactivities

2 potent at pChembl≥5 of 2 total, top 2 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChembl	Type	Value	Unit	Molecule
7.38	Kd	42	nM	MOLIBRESIB
7.10	IC50	80	nM	MOLIBRESIB

PubChem BioAssay actives

2 with measured affinity, of 7 total; 1 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

Compound	Assay	Type	Value	Unit
2-[(4S)-6-(4-chlorophenyl)-8-methoxy-1-methyl-4H-[1,2,4]triazolo[4,3-a][1,4]benzodiazepin-4-yl]-N-ethylacetamide	2179219: Binding affinity against C16ORF80 (unknown origin) assessed as apparent dissociation constant incubated for 1 hr by colloidal coomassie staining based LC-MS/MS analysis	kd	0.0420	uM

CTD chemical–gene interactions

28 total (human), top 28 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Acetaminophen	increases expression, affects response to substance	3
Smoke	increases abundance, increases expression, decreases expression	3
sodium arsenite	affects expression, increases expression	2
Air Pollutants	decreases expression, increases abundance, increases expression	2
bisphenol A	affects cotreatment, increases methylation	1
2-methyl-4-isothiazolin-3-one	increases expression	1
arsenite	increases reaction, affects binding	1
butyraldehyde	increases expression	1
di-n-butylphosphoric acid	affects expression	1
abrine	increases expression	1
licochalcone B	increases expression	1
Fulvestrant	affects cotreatment, increases methylation	1
Air Pollutants, Occupational	increases expression	1
Cisplatin	increases expression	1
Coumestrol	increases expression	1
Dimethyl Sulfoxide	increases expression	1
Doxorubicin	increases expression	1
Methyl Methanesulfonate	increases expression	1
Nickel	increases expression	1
Thiram	increases expression	1
Tobacco Smoke Pollution	decreases expression	1
Tretinoin	decreases expression	1
Urethane	increases expression	1
Valproic Acid	increases expression	1
Cyclosporine	decreases expression	1
Copper Sulfate	decreases expression	1
Vitamin K 3	affects expression	1
Particulate Matter	decreases expression, increases abundance	1

ChEMBL screening assays

7 unique, capped per target: 7 binding

Representative assays (with source publication via chembl_document):

Assay ID	Type	Description	Source paper
CHEMBL5697589	Binding	Inhibition of C16ORF80 (unknown origin) assessed as fold change at 10 uM incubated for 1 hr by colloidal coomassie staining based LC-MS/MS analysis	Inhibition of BET recruitment to chromatin as an effective treatment for MLL-fusion leukaemia. — *Nature*

Clinical trials (associated diseases)

Via MONDO — disease-level, not drug-specific.

Predicted chemistry — Sugi Predict

The predicted patent-compound landscape for CFAP20 across ~30M SureChEMBL compounds — explore on Sugi Predict.