CFAP20DC

Summary

CFAP20DC (CFAP20 domain containing, HGNC:24763) is a protein-coding gene on chromosome 3p14.2, encoding Protein CFAP20DC (Q6ZVT6).

At a glance

• GWAS associations: 9
• Clinical variants (ClinVar): 26 total
• MANE Select transcript: NM_001394063

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:24763
Approved symbol	CFAP20DC
Name	CFAP20 domain containing
Location	3p14.2
Locus type	gene with protein product
Status	Approved
Aliases	FLJ42117, FLJ42930
Ensembl gene	ENSG00000163689
Ensembl biotype	protein_coding
Entrez	200844

Gene structure

Transcript identifiers

Ensembl transcripts: 14 — 7 protein_coding, 6 nonsense_mediated_decay, 1 protein_coding_CDS_not_defined

ENST00000295966, ENST00000460459, ENST00000468415, ENST00000470454, ENST00000472469, ENST00000478363, ENST00000479931, ENST00000482387, ENST00000484535, ENST00000486145, ENST00000491845, ENST00000495572, ENST00000938701, ENST00000938702

RefSeq mRNA: 7 — MANE Select: NM_001394063 NM_001351530, NM_001351531, NM_001351532, NM_001351533, NM_001351534, NM_001394063, NM_198463

CCDS: CCDS33776, CCDS93302

Canonical transcript exons

ENST00000482387 — 17 exons

Exon	Start	End
ENSE00001077358	58806395	58806456
ENSE00001077361	58753769	58753863
ENSE00001168509	58742008	58742572
ENSE00001658730	58870173	58870309
ENSE00001690840	58913708	58913864
ENSE00001809732	59049611	59050025
ENSE00003463398	58867817	58867936
ENSE00003510621	59039557	59039629
ENSE00003512470	59046229	59046322
ENSE00003515802	59047165	59047254
ENSE00003560646	58831686	58831889
ENSE00003565702	58884545	58884709
ENSE00003598481	58869328	58869490
ENSE00003602079	58863558	58863892
ENSE00003605325	58937648	58937762
ENSE00003614949	58849032	58849409
ENSE00003628981	58866566	58866688

Expression profiles

Bgee: expression breadth ubiquitous, 171 present calls, max score 89.85.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 1.7645 / max 45.1085, expressed in 946 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
42755	1.6818	923
42754	0.0826	34

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
lower esophagus mucosa	UBERON:0035834	89.85	gold quality
left testis	UBERON:0004533	89.71	gold quality
right testis	UBERON:0004534	89.67	gold quality
sperm	CL:0000019	89.62	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	89.16	gold quality
testis	UBERON:0000473	87.16	gold quality
esophagus mucosa	UBERON:0002469	81.00	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	80.59	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	79.15	gold quality
esophagus squamous epithelium	UBERON:0006920	74.45	gold quality
mucosa of paranasal sinus	UBERON:0005030	74.16	gold quality
adrenal tissue	UBERON:0018303	74.16	gold quality
islet of Langerhans	UBERON:0000006	73.54	gold quality
bronchial epithelial cell	CL:0002328	73.03	gold quality
bronchus	UBERON:0002185	71.57	gold quality
pancreatic ductal cell	CL:0002079	71.09	silver quality
ventricular zone	UBERON:0003053	69.71	gold quality
ganglionic eminence	UBERON:0004023	69.60	gold quality
stromal cell of endometrium	CL:0002255	67.52	gold quality
right adrenal gland	UBERON:0001233	67.02	gold quality
oviduct epithelium	UBERON:0004804	66.88	gold quality
right adrenal gland cortex	UBERON:0035827	66.76	gold quality
endothelial cell	CL:0000115	66.65	gold quality
cerebellar vermis	UBERON:0004720	66.47	silver quality
epithelium of nasopharynx	UBERON:0001951	65.99	silver quality
cortical plate	UBERON:0005343	65.87	gold quality
pituitary gland	UBERON:0000007	65.82	gold quality
esophagus	UBERON:0001043	65.76	gold quality
left adrenal gland	UBERON:0001234	65.65	gold quality
oral cavity	UBERON:0000167	65.14	silver quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	6.68
E-GEOD-111727	no	43.57

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

21 targeting CFAP20DC, 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-6833-3P	100.00	70.63	3197
HSA-MIR-4768-5P	100.00	69.49	2861
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-4789-3P	99.99	70.75	2484
HSA-MIR-548AW	99.99	72.57	3559
HSA-MIR-548P	99.98	72.25	3784
HSA-MIR-141-3P	99.94	72.79	2421
HSA-MIR-200A-3P	99.94	72.68	2420
HSA-MIR-8063	99.91	69.76	3146
HSA-MIR-10527-5P	99.91	72.28	3754
HSA-MIR-4503	99.85	71.45	1869
HSA-MIR-374C-5P	99.80	72.06	2910
HSA-MIR-655-3P	99.80	72.19	2909
HSA-MIR-4699-3P	99.71	70.15	3142
HSA-MIR-1283	99.69	72.42	3009
HSA-MIR-5590-5P	98.81	68.78	969
HSA-MIR-4742-3P	98.73	69.82	1803
HSA-MIR-1-5P	98.70	68.66	1017
HSA-MIR-3668	98.52	68.76	951
HSA-MIR-4678	97.59	68.31	902
HSA-MIR-1913	97.07	66.20	1417

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	cfap20dc	ENSDARG00000026086
mus_musculus	Cfap20dc	ENSMUSG00000021747
rattus_norvegicus	Cfap20dc	ENSRNOG00000007206

Paralogs (1): CFAP20 (ENSG00000070761)

Protein

Protein identifiers

Protein CFAP20DC — Q6ZVT6 (reviewed: Q6ZVT6)

Alternative names: Uncharacterized protein C3orf67

All UniProt accessions (11): A0A2U3TZK7, C9IYJ1, C9J3M8, Q6ZVT6, F5H9F7, F8WF72, H0Y8H3, H7C4Q4, H7C4R0, H7C586, H7C5H9

UniProt curated annotations — full annotation on UniProt →

Isoforms (2)

UniProt ID	Names	Canonical?
Q6ZVT6-1	1	yes
Q6ZVT6-2	2

RefSeq proteins (7): NP_001338459, NP_001338460, NP_001338461, NP_001338462, NP_001338463, NP_001380992, NP_940865 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR007714	CFA20_dom	Domain
IPR040441	CFA20/CFAP20DC	Family

Pfam: PF05018

UniProt features (14 total): compositionally biased region 5, sequence variant 4, region of interest 3, chain 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6ZVT6-F1	53.59	0.08

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 53 (showing top): GOZGIT_ESR1_TARGETS_DN, SCHAEFFER_PROSTATE_DEVELOPMENT_48HR_UP, RFX1_02, chr3p14, RFX1_01, CAGTGTT_MIR141_MIR200A, DODD_NASOPHARYNGEAL_CARCINOMA_DN, MEISSNER_NPC_HCP_WITH_H3K4ME2, DELACROIX_RAR_BOUND_ES, DURAND_STROMA_S_UP, FOXD2_TARGET_GENES, ZSCAN31_TARGET_GENES, MIR1283, MIR655_3P, MIR374C_5P

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

825 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CFAP20DC	DENND2C	Q68D51	543
CFAP20DC	CCDC70	Q6NSX1	537
CFAP20DC	PLEKHN1	Q494U1	512
CFAP20DC	ZNF396	Q96N95	506
CFAP20DC	PTPDC1	A2A3K4	474
CFAP20DC	SYT16	Q17RD7	469
CFAP20DC	AP2A1	O95782	454
CFAP20DC	TMEM212	A6NML5	447
CFAP20DC	C12orf60	Q5U649	447
CFAP20DC	CDH22	Q9UJ99	447
CFAP20DC	NAA11	Q9BSU3	444
CFAP20DC	DPH6	Q7L8W6	436
CFAP20DC	KCNT1	Q5JUK3	436
CFAP20DC	NPM3	O75607	422
CFAP20DC	SLC5A10	A0PJK1	406

IntAct

3 interactions, top by confidence:

A	B	Type	Score
CDK16	CFAP20DC	psi-mi:“MI:0915”(physical association)	0.370
VPS35	DDX3Y	psi-mi:“MI:0914”(association)	0.350

BioGRID (4): C3orf67 (Biochemical Activity), C3orf67 (Affinity Capture-RNA), C3orf67 (Affinity Capture-MS), C3orf67 (Affinity Capture-RNA)

ESM2 similar proteins: A0A0A6YY25, A0A5K7RLP0, A6NMK8, A8MVX0, B2RQL2, B2RXH4, C9JSJ3, D2J0Y4, O54824, P97303, Q01954, Q05AH6, Q0VET5, Q14005, Q1W617, Q2YDE2, Q3MHT3, Q3U0P1, Q3ULM6, Q3UXL4, Q4R7L6, Q5RC05, Q5T0L3, Q68CR7, Q6GQV1, Q6NS69, Q6NZK5, Q6P1D7, Q6PG16, Q6ZVT6, Q7Z4V0, Q80W88, Q80XI1, Q811R2, Q86T90, Q86YN6, Q8BHP2, Q8BLK9, Q8BP99, Q8BW86

Diamond homologs: Q4V7B1, Q6P2K3, Q6ZVT6, Q95JY0

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	13
Likely benign	2
Benign	2

Top pathogenic / likely-pathogenic (0)

SpliceAI

4528 predictions. Top by Δscore:

Variant	Effect	Δscore
3:58806389:TCTTA:T	donor_loss	1.0000
3:58806390:CTTAC:C	donor_loss	1.0000
3:58806391:TTACC:T	donor_loss	1.0000
3:58806392:TACCG:T	donor_loss	1.0000
3:58806393:A:AC	donor_gain	1.0000
3:58806393:A:C	donor_loss	1.0000
3:58806394:C:A	donor_loss	1.0000
3:58806394:C:CC	donor_gain	1.0000
3:58806453:CAGG:C	acceptor_gain	1.0000
3:58806455:GG:G	acceptor_gain	1.0000
3:58806457:C:CC	acceptor_gain	1.0000
3:58831684:A:AC	donor_gain	1.0000
3:58831685:C:CC	donor_gain	1.0000
3:58831895:C:CT	acceptor_gain	1.0000
3:58831896:A:T	acceptor_gain	1.0000
3:58884707:CAG:C	acceptor_gain	1.0000
3:58913706:ACCAT:A	donor_gain	1.0000
3:58913707:CCATC:C	donor_gain	1.0000
3:58913710:T:TA	donor_gain	1.0000
3:58913862:CCA:C	acceptor_gain	1.0000
3:58913863:CAC:C	acceptor_gain	1.0000
3:58913865:C:CC	acceptor_gain	1.0000
3:58937639:GATAC:G	donor_loss	1.0000
3:58937640:ATACT:A	donor_loss	1.0000
3:58937641:TACTT:T	donor_loss	1.0000
3:58937642:ACTTA:A	donor_loss	1.0000
3:58937643:CT:C	donor_loss	1.0000
3:58937644:TTA:T	donor_loss	1.0000
3:58937645:TACA:T	donor_loss	1.0000
3:58937646:A:AC	donor_gain	1.0000

AlphaMissense

5357 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000006411 (3:59023157 G>A,T), RS1000009518 (3:58949852 A>G), RS1000017724 (3:58988410 C>T), RS1000024802 (3:59045892 A>C,G), RS1000025604 (3:59004764 A>G), RS1000029977 (3:58761318 T>G), RS1000033020 (3:58847538 G>C), RS1000041920 (3:58970905 A>G), RS1000043831 (3:58937558 T>C,G), RS1000061707 (3:58802675 G>A), RS1000066850 (3:59000404 T>C), RS1000067282 (3:58774405 G>A), RS1000068218 (3:58729675 T>C), RS1000080722 (3:58824372 C>T), RS1000091409 (3:58960990 TTA>T)

Disease associations

OMIM: gene `` | disease phenotypes: MIM:613254, MIM:244400

GenCC curated gene-disease

Mondo (2): tuberous sclerosis 2 (MONDO:0013199), primary ciliary dyskinesia (MONDO:0016575)

Orphanet (2): Tuberous sclerosis complex (Orphanet:805), Primary ciliary dyskinesia (Orphanet:244)

HPO phenotypes

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

GWAS associations

9 associations (top):

Study	Trait	p-value
GCST002783_13	Body mass index	9.000000e-06
GCST003059_7	Parkinson’s disease	1.000000e-06
GCST003518_82	Daytime sleep phenotypes	8.000000e-06
GCST003542_43	Night sleep phenotypes	4.000000e-06
GCST005051_11	Obstructive sleep apnea trait (apnea hypopnea index)	8.000000e-07
GCST005051_12	Obstructive sleep apnea trait (apnea hypopnea index)	1.000000e-06
GCST005651_4	Urinary metabolite levels in chronic kidney disease	4.000000e-08
GCST007843_5	Rheumatoid arthritis	8.000000e-13
GCST010396_139	Gut microbiota (bacterial taxa, hurdle binary method)	2.000000e-06

EFO canonical traits (5, from GWAS)

EFO ID	Trait name
EFO:0004340	body mass index
EFO:0007828	daytime rest measurement
EFO:0007817	sleep apnea measurement
EFO:0005116	urinary metabolite measurement
EFO:0007874	gut microbiome measurement

MeSH disease descriptors (3)

Descriptor	Name	Tree numbers
D002925	Ciliary Motility Disorders	C08.200; C09.150; C16.131.077.245.500; C16.320.184.500
D007619	Kartagener Syndrome	C08.127.384.500; C08.200.531; C08.695.501; C09.150.531; C14.240.400.280.500; C14.280.400.280.500; C16.131.077.245.500.531; C16.131.240.400.280.500; C16.131.740.501; C16.131.810.250.500; C16.320.184.500.531; C16.320.480
C566021	Tuberous Sclerosis 2 (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

25 total (human), top 25 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, increases expression, affects expression	6
trichostatin A	increases expression	2
Vorinostat	affects cotreatment, increases expression	2
Smoke	decreases expression, increases abundance, increases expression	2
urushiol	increases expression	1
methylmercuric chloride	decreases expression	1
methyleugenol	decreases expression	1
bisphenol A	increases expression	1
3,4-dichloroaniline	increases expression	1
sodium arsenite	increases abundance, increases expression	1
butyraldehyde	decreases expression	1
aflatoxin B2	increases methylation	1
2-palmitoylglycerol	increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	increases expression, affects cotreatment, decreases expression	1
belinostat	increases expression	1
dorsomorphin	affects cotreatment, decreases expression, increases expression	1
Air Pollutants	increases abundance, increases expression	1
Arsenic	increases abundance, increases expression	1
Benzo(a)pyrene	decreases methylation, increases methylation	1
Diuron	increases expression	1
Estradiol	affects cotreatment, increases expression	1
N-Nitrosopyrrolidine	decreases expression	1
Phenylmercuric Acetate	decreases expression, affects cotreatment	1
Tobacco Smoke Pollution	affects expression	1
Vanadates	increases expression	1

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT02201212	PHASE2	COMPLETED	Everolimus for Cancer With TSC1 or TSC2 Mutation
NCT05103358	PHASE2	ACTIVE_NOT_RECRUITING	Phase 2 Basket Trial of Nab-sirolimus in Patients With Malignant Solid Tumors With Pathogenic Alterations in TSC1/TSC2 Genes (PRECISION 1)
NCT02871778	PHASE2	COMPLETED	Clearing Lungs With ENaC Inhibition in Primary Ciliary Dyskinesia
NCT07318974	PHASE2	ACTIVE_NOT_RECRUITING	Melatonin Therapy for Improving ICSI Outcomes in Women With Diminished Ovarian Reserve
NCT05737485	PHASE1	COMPLETED	Study Evaluating the Safety and Tolerability of RCT1100 in Healthy and PCD Subjects
NCT06600425	PHASE1	COMPLETED	A Study to Assess the Safety, Tolerability, Ciliary Rescue, and Pharmacodynamics of RCT1100 in Adults With PCD
NCT06633757	PHASE1	COMPLETED	Study of Inhaled RCT1100 in Adults With PCD Caused by Pathogenic Mutations in the DNAI1 Gene to Measure Mucociliary Clearance
NCT03655223	Not specified	ENROLLING_BY_INVITATION	Early Check: Expanded Screening in Newborns
NCT03817515	Not specified	APPROVED_FOR_MARKETING	Expanded Access for ABI-009 in Patients With Advanced PEComa and Patients With a Malignancy With Relevant Genetic Mutations or mTOR Pathway Activation
NCT04901715	EARLY_PHASE1	COMPLETED	Functional Studies of Novel Genes Mutated in Primary Ciliary Dyskinesia II: Genotype to Phenotype
NCT00005650	Not specified	COMPLETED	Genetic Study of Patients With Primary Ciliary Dyskinesia
NCT00323167	Not specified	COMPLETED	Rare Genetic Disorders of the Breathing Airways
NCT00368446	Not specified	COMPLETED	Genetic Disorders of Mucociliary Clearance in Nontuberculous Mycobacterial Lung Disease
NCT00450918	Not specified	COMPLETED	Evaluating Progression of and Diagnostic Tools for Primary Ciliary Dyskinesia in Children and Adolescents
NCT00608556	Not specified	COMPLETED	Dyskinesia, Heterotaxy and Congenital Heart Disease
NCT00686309	Not specified	UNKNOWN	Comparison of On-line and Off-line Measurements of Exhaled Nitric Oxide (NO)
NCT00722878	Not specified	COMPLETED	Long-term Lung Function and Disease Progression in Children With Early Onset Primary Ciliary Dyskinesia Lung Disease
NCT00739817	Not specified	UNKNOWN	Screening for Primary Ciliary Dyskinesia Using Nasal Nitric Oxide
NCT00783887	Not specified	COMPLETED	Diagnosis of Primary Ciliary Dyskinesia
NCT00807482	Not specified	RECRUITING	Pathogenesis of Primary Ciliary Dyskinesia (PCD) Lung Disease
NCT01070914	Not specified	UNKNOWN	Early Detection and Characterization of Primary Ciliary Dyskinesia
NCT01155115	Not specified	COMPLETED	Inflammatory and Microbiologic Markers in Sputum: Comparing Cystic Fibrosis With Primary Ciliary Dyskinesia
NCT01246258	Not specified	COMPLETED	Otolith Function in Patients With Primary Ciliary Dyskinesia
NCT01929356	Not specified	RECRUITING	Chest Physiotherapy and Lung Function in Primary Ciliary Dyskinesia
NCT02389049	Not specified	COMPLETED	Genetics of Primary Ciliary Dyskinesia
NCT02419365	Not specified	RECRUITING	International Primary Ciliary Dyskinesia (PCD) Registry
NCT02699177	Not specified	UNKNOWN	In Vivo Measurements of Nasal Ciliary Beat Frequency by Using Interferometry
NCT02704455	Not specified	NOT_YET_RECRUITING	Registry Study on Primary Ciliary Dyskinesia in Chinese Children
NCT03271840	Not specified	COMPLETED	Registry for Primary Ciliary Dyskinesia
NCT03279965	Not specified	UNKNOWN	MRI in Cystic Fibrosis and Primary Ciliary Dyskinesia
NCT03320382	Not specified	UNKNOWN	Multiple Breath Washout, a Clinimetric Dataset
NCT03370029	Not specified	COMPLETED	Respiratory Muscle Strength, Exercise Capacity and Physical Activity Levels in Children Primary Ciliary Dyskinesia
NCT03494894	Not specified	COMPLETED	Bacteriological Link Between Upper and Lower Airways in Cystic Fibrosis and Primary Ciliary Dyskinesia
NCT03517865	Not specified	ACTIVE_NOT_RECRUITING	International Primary Ciliary Dyskinesia Cohort
NCT03606200	Not specified	RECRUITING	Swiss Primary Ciliary Dyskinesia Registry
NCT03704207	Not specified	RECRUITING	Utility of PCD Diagnostics to Improve Clinical Care
NCT03704896	Not specified	UNKNOWN	PRospective Observational Multicentre Study on VAriability of Lung Function in Stable PCD Patients
NCT03801395	Not specified	COMPLETED	PCD New Gene Discovery
NCT03809091	Not specified	UNKNOWN	WGS of Korean Idiopathic Bronchiectasis
NCT03832491	Not specified	COMPLETED	Effect of Game Based Approach on Oxygenation, Functional Capacity and Quality of Life in Primary Ciliary Dyskinesia