CFAP47

gene
On this page

Also known as FLJ36601RP13-11B7.1MGC34831

Summary

CFAP47 (cilia and flagella associated protein 47, HGNC:26708) is a protein-coding gene on chromosome Xp21.1, encoding Cilia- and flagella-associated protein 47 (Q6ZTR5). Plays a role in flagellar formation and sperm motility.

While this gene is well-supported by transcript data, no functional information on its protein product is currently available.

Source: NCBI Gene 286464 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): spermatogenic failure, X-linked, 3 (Limited, ClinGen) — +1 more curated relationship
  • Clinical variants (ClinVar): 173 total — 6 pathogenic
  • Phenotypes (HPO): 8
  • MANE Select transcript: NM_001304548

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:26708
Approved symbolCFAP47
Namecilia and flagella associated protein 47
LocationXp21.1
Locus typegene with protein product
StatusApproved
AliasesFLJ36601, RP13-11B7.1, MGC34831
Ensembl geneENSG00000165164
Ensembl biotypeprotein_coding
OMIM301057
Entrez286464

Gene structure

Transcript identifiers

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

ENST00000297866, ENST00000313548, ENST00000378653, ENST00000378660, ENST00000446478, ENST00000493930, ENST00000630521

RefSeq mRNA: 2 — MANE Select: NM_001304548 NM_001304548, NM_152632

CCDS: CCDS14237, CCDS83464

Canonical transcript exons

ENST00000378653 — 64 exons

ExonStartEnd
ENSE000010908833594831435948452
ENSE000010908843591973435920048
ENSE000010908853592601735926168
ENSE000010908863594128335941398
ENSE000012158443597186935971965
ENSE000012162633596656535966754
ENSE000012162683597158635971772
ENSE000012162753597076835970923
ENSE000012162793596761935967832
ENSE000012162893595596135956196
ENSE000012162953595359235953719
ENSE000012163023595180335951963
ENSE000012163103595113135951359
ENSE000014244913597514735975363
ENSE000014782493638479736385317
ENSE000014782513637935036379518
ENSE000014782543636133036361501
ENSE000014782553635352936353681
ENSE000014782563635003836350132
ENSE000014782653622862836228824
ENSE000015956963613834836138464
ENSE000015987893609975136099879
ENSE000016132773631920936319307
ENSE000016158853610449936104691
ENSE000016339313630677236306876
ENSE000016443923634812936348288
ENSE000016516963613795836138055
ENSE000016596143609879336098874
ENSE000016933493607313936073364
ENSE000017237773607182536071971
ENSE000017273733629897736299152
ENSE000017371073630107236301179
ENSE000017413093631083336310989
ENSE000017609083630384936303960
ENSE000017654643608531436085538
ENSE000035229403628562936285726
ENSE000035329553597567235975913
ENSE000035364043623668636236859
ENSE000036535193623593436236077
ENSE000036719183628048736280630
ENSE000036725933625133336251444
ENSE000037055253636696636367127
ENSE000037606913618862036188690
ENSE000037610263614910836149223
ENSE000037610813620127436201500
ENSE000037615273614521936145353
ENSE000037626373599319035993321
ENSE000037632393601477436014912
ENSE000037635313620495736205110
ENSE000037645703615942636159576
ENSE000037645883598931935989449
ENSE000037656083620037936200493
ENSE000037690833600028336000427
ENSE000037697613617934536179422
ENSE000037705263600161336001707
ENSE000037710993606564336065743
ENSE000037724453603898436039179
ENSE000037732223599182135991943
ENSE000037739863619005136190196
ENSE000037743543604685436047063
ENSE000037744003599731235997389
ENSE000037745183616068136160769
ENSE000037786353603125336031347
ENSE000037799823603569536035854

Expression profiles

Bgee: expression breadth broad, 95 present calls, max score 92.44.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.6298 / max 67.7533, expressed in 178 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
1958860.4005138
1958850.2294106

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
bronchial epithelial cellCL:000232892.44gold quality
bronchusUBERON:000218590.56gold quality
oviduct epitheliumUBERON:000480489.60gold quality
right uterine tubeUBERON:000130288.57gold quality
buccal mucosa cellCL:000233687.57gold quality
mucosa of paranasal sinusUBERON:000503080.37silver quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047378.54gold quality
olfactory segment of nasal mucosaUBERON:000538678.37gold quality
fallopian tubeUBERON:000388974.18gold quality
epithelium of nasopharynxUBERON:000195173.33silver quality
nasopharynxUBERON:000172873.32silver quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099171.87gold quality
secondary oocyteCL:000065570.27gold quality
ventricular zoneUBERON:000305368.43gold quality
pituitary glandUBERON:000000766.97gold quality
adenohypophysisUBERON:000219666.94gold quality
nasal cavity mucosaUBERON:000182661.85gold quality
caput epididymisUBERON:000435859.91gold quality
oocyteCL:000002358.56silver quality
nasal cavity epitheliumUBERON:000538458.17gold quality
corpus callosumUBERON:000233657.44gold quality
nucleus accumbensUBERON:000188256.29gold quality
vena cavaUBERON:000408755.62gold quality
skin of hipUBERON:000155455.49silver quality
right lungUBERON:000216755.21gold quality
hypothalamusUBERON:000189855.07gold quality
ganglionic eminenceUBERON:000402354.94gold quality
lower lobe of lungUBERON:000894954.92silver quality
spermCL:000001954.45gold quality
caudate nucleusUBERON:000187354.40gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes9.50

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

19 targeting CFAP47, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-1277-5P100.0073.955056
HSA-MIR-5692B100.0071.322622
HSA-MIR-5692C100.0071.322622
HSA-MIR-449399.9066.48977
HSA-MIR-391999.8769.452489
HSA-MIR-471999.7372.103329
HSA-MIR-1212499.6869.172700
HSA-MIR-54399.5269.032595
HSA-MIR-432599.4972.201342
HSA-MIR-892C-5P99.1670.562116
HSA-MIR-316899.0867.751384
HSA-MIR-6830-5P99.0168.731884
HSA-MIR-607498.8969.642187
HSA-MIR-6755-3P98.6166.90834
HSA-MIR-477398.3567.301710
HSA-MIR-4786-5P97.4567.89924
HSA-MIR-6750-3P96.7967.50740
HSA-MIR-4793-3P94.8765.85896
HSA-MIR-769-5P94.4564.56603

Literature-anchored findings (GeneRIF, showing 4)

  • Deleterious variants in X-linked CFAP47 induce asthenoteratozoospermia and primary male infertility. (PMID:33472045)
  • WDR87 interacts with CFAP47 protein in the middle piece of spermatozoa flagella to participate in sperm tail assembly. (PMID:36571501)
  • A novel mutation in CFAP47 causes male infertility due to multiple morphological abnormalities of the sperm flagella. (PMID:37424856)
  • Mutations in CFAP47, a previously reported MMAF causative gene, also contribute to the respiratory defects in patients with PCD. (PMID:37723893)

Cross-species orthologs

0 orthologs

Paralogs (2): DLEC1 (ENSG00000008226), HYDIN (ENSG00000157423)

Protein

Protein identifiers

Cilia- and flagella-associated protein 47Q6ZTR5 (reviewed: Q6ZTR5)

All UniProt accessions (3): A0A0D9SEI5, A0A182DWE8, Q6ZTR5

UniProt curated annotations — full annotation on UniProt →

Function. Plays a role in flagellar formation and sperm motility.

Subunit / interactions. Interacts with CFAP65.

Subcellular location. Cytoplasm. Cytoskeleton. Flagellum basal body.

Tissue specificity. Highly expressed in spermatzoa (at protein level).

Disease relevance. Spermatogenic failure, X-linked, 3 (SPGFX3) [MIM:301059] An infertility disorder characterized by asthenoteratozoospermia. Spermatozoa exhibit multiple morphologic abnormalities, including absent, short, coiled, and irregular-caliber flagella. The disease is caused by variants affecting the gene represented in this entry.

Isoforms (4)

UniProt IDNamesCanonical?
Q6ZTR5-55yes
Q6ZTR5-11
Q6ZTR5-22
Q6ZTR5-66

RefSeq proteins (2): NP_001291477, NP_689845 (=MANE)

Domains & families (InterPro)

IDNameType
IPR001715CH_domDomain
IPR013783Ig-like_foldHomologous_superfamily
IPR036872CH_dom_sfHomologous_superfamily
IPR056343CFAP47_domDomain
IPR058952Ig_CFAP47Domain

Pfam: PF24529, PF26579

UniProt features (20 total): sequence variant 8, splice variant 6, sequence conflict 2, chain 1, domain 1, region of interest 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

No AlphaFold model available for Q6ZTR5 — AlphaFold DB does not currently provide models for proteins above ~3000 aa.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 0 (showing top):

GO Biological Process (2): sperm axoneme assembly (GO:0007288), cilium assembly (GO:0060271)

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

GO Cellular Component (7): cilium (GO:0005929), sperm head-tail coupling apparatus (GO:0120212), cytoplasm (GO:0005737), cytoskeleton (GO:0005856), membrane (GO:0016020), motile cilium (GO:0031514), cell projection (GO:0042995)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure4
axoneme assembly2
developmental process involved in reproduction1
sperm flagellum assembly1
intraciliary transport involved in cilium assembly1
cilium organization1
protein localization to cilium1
organelle assembly1
trans-Golgi to periciliary membrane compartment transport1
plasma membrane bounded cell projection assembly1
ciliary transition zone assembly1
binding1
intraciliary transport particle1
membrane-bounded organelle1
plasma membrane bounded cell projection1
intracellular anatomical structure1
intracellular membraneless organelle1
cilium1

Protein interactions and networks

STRING

1242 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
CFAP47CFAP43Q8NDM7612
CFAP47TTC29Q8NA56612
CFAP47CFAP70Q5T0N1573
CFAP47CFAP65Q6ZU64570
CFAP47LRRC43Q8N309566
CFAP47CFAP44Q96MT7545
CFAP47FAM47BQ8NA70524
CFAP47DNAH1Q9P2D7524
CFAP47CFAP99D6REC4520
CFAP47CFAP251Q8TBY9519
CFAP47CFAP141Q5VU69506
CFAP47CFAP69A5D8W1505
CFAP47TTC21AQ8NDW8499
CFAP47FAM181AQ8N9Y4485
CFAP47CFAP91Q7Z4T9485

IntAct

7 interactions, top by confidence:

ABTypeScore
CFAP47UBBpsi-mi:“MI:0914”(association)0.560
CFAP47UBBpsi-mi:“MI:0915”(physical association)0.560
CFAP47RPL35psi-mi:“MI:0915”(physical association)0.400
CFAP47CFTRpsi-mi:“MI:0915”(physical association)0.370
ESR1TUBAL3psi-mi:“MI:0914”(association)0.350
ESR2PSMD11psi-mi:“MI:0914”(association)0.350

BioGRID (7): CXorf22 (Affinity Capture-MS), CXorf22 (Proximity Label-MS), CXorf22 (Affinity Capture-MS), CXorf22 (PCA), CXorf22 (Cross-Linking-MS (XL-MS)), CXorf22 (Cross-Linking-MS (XL-MS)), RPL35 (Cross-Linking-MS (XL-MS))

ESM2 similar proteins: A0A0G2JEB6, A0JM56, B0DOB4, B0FXQ5, B1ANS9, B4F7L9, B4GQJ7, B5DHW4, B7FF06, B7FF07, B7FF08, B7FF09, B7FF12, C5IAW9, F1LW30, F1P4W9, O08747, O95185, P0DM40, Q008S8, Q18264, Q32NR9, Q3V0B4, Q402B2, Q4G0P3, Q5R4M2, Q5T0N1, Q5XI14, Q6AXU1, Q6DCF6, Q6NRS1, Q6P2C0, Q6P5D8, Q6UXZ4, Q6ZTR5, Q6ZU64, Q761X5, Q7T2Z5, Q80W93, Q86YR7

Diamond homologs: A0A0G2JEB6, Q6ZTR5

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic6
Likely pathogenic0
Uncertain significance29
Likely benign29
Benign0

Top pathogenic / likely-pathogenic (6)

Variant IDHGVSClassification
1808493GRCh37/hg19 Xp21.1(chrX:32419533-37487291)x1Pathogenic
3062483GRCh37/hg19 Xp21.1-11.4(chrX:33027159-39840641)Pathogenic
3235121Single allelePathogenic
59258GRCh38/hg38 Xp21.1-11.4(chrX:31665506-37921988)x0Pathogenic
975141Single allelePathogenic
996916NM_001304548.2(CFAP47):c.7154T>A (p.Ile2385Asn)Pathogenic

SpliceAI

2748 predictions. Top by Δscore:

VariantEffectΔscore
X:35920044:CACAG:Cdonor_loss1.0000
X:35920045:ACAG:Adonor_loss1.0000
X:35920046:CAG:Cdonor_loss1.0000
X:35920047:AGGT:Adonor_loss1.0000
X:35920048:GGT:Gdonor_loss1.0000
X:35920049:G:Adonor_loss1.0000
X:35926010:A:AGacceptor_gain1.0000
X:35926012:T:Aacceptor_gain1.0000
X:35926015:A:AGacceptor_gain1.0000
X:35926016:G:GGacceptor_gain1.0000
X:35951934:GACT:Gdonor_gain1.0000
X:35951964:G:GGdonor_gain1.0000
X:35953586:TTACA:Tacceptor_loss1.0000
X:35953587:TACA:Tacceptor_loss1.0000
X:35953588:A:AGacceptor_gain1.0000
X:35953588:ACAG:Aacceptor_gain1.0000
X:35953589:C:Gacceptor_gain1.0000
X:35953589:CAGGC:Cacceptor_loss1.0000
X:35953590:A:AGacceptor_gain1.0000
X:35953590:AG:Aacceptor_gain1.0000
X:35953591:G:GCacceptor_gain1.0000
X:35953591:GG:Gacceptor_gain1.0000
X:35953591:GGC:Gacceptor_gain1.0000
X:35953591:GGCT:Gacceptor_gain1.0000
X:35953591:GGCTA:Gacceptor_gain1.0000
X:35953672:G:GTdonor_gain1.0000
X:35953715:CAAAA:Cdonor_gain1.0000
X:35953716:AAAA:Adonor_gain1.0000
X:35953716:AAAAG:Adonor_loss1.0000
X:35953717:AAA:Adonor_gain1.0000

AlphaMissense

21156 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
X:35951318:T:AW282R0.995
X:35951318:T:CW282R0.995
X:36228661:T:CF2284S0.994
X:36099850:T:AW1700R0.993
X:36099850:T:CW1700R0.993
X:35926017:T:CF84L0.992
X:35926019:C:AF84L0.992
X:35926019:C:GF84L0.992
X:35975859:T:AW887R0.992
X:35975859:T:CW887R0.992
X:36149180:T:CF1915L0.992
X:36149182:C:AF1915L0.992
X:36149182:C:GF1915L0.992
X:36201424:G:CR2196P0.992
X:35919944:T:CF49L0.991
X:35919945:T:CF49S0.991
X:35919946:C:AF49L0.991
X:35919946:C:GF49L0.991
X:35926018:T:CF84S0.991
X:35926086:T:GY107D0.991
X:36228724:G:CR2305P0.991
X:36301080:T:CF2624S0.991
X:35951296:T:AN274K0.990
X:35951296:T:GN274K0.990
X:36201428:G:CR2197S0.990
X:36201428:G:TR2197S0.990
X:36379400:T:CF3079S0.990
X:36159481:G:CA1948P0.989
X:36190077:T:CF2068L0.989
X:36190079:C:AF2068L0.989

dbSNP variants (sampled 300 via entrez): RS1000002870 (X:36222471 A>C), RS1000008288 (X:36169456 A>G), RS1000009577 (X:35973703 A>C,G), RS1000030327 (X:35940221 A>G), RS1000043210 (X:35986687 A>C,G), RS1000060710 (X:35926775 A>G), RS1000067172 (X:35923550 A>G), RS1000078553 (X:36006588 T>C,G), RS1000079907 (X:35956261 C>A,T), RS1000094150 (X:36297644 T>C), RS1000121806 (X:36110164 G>A), RS1000131156 (X:36050338 G>A), RS1000141245 (X:36361124 A>G), RS1000165795 (X:36361974 G>A), RS1000178193 (X:36275473 T>A)

Disease associations

OMIM: gene MIM:301057 | disease phenotypes: MIM:301059, MIM:300842, MIM:300029

GenCC curated gene-disease

DiseaseClassificationInheritance
spermatogenic failure, X-linked, 3LimitedX-linked
polycystic kidney diseaseLimitedX-linked

ClinGen Gene-Disease Validity (2)

Expert-panel classifications — Definitive > Strong > Moderate > Limited > Disputed > Refuted.

DiseaseClassificationInheritance
spermatogenic failure, X-linked, 3LimitedXL
polycystic kidney diseaseDisputedXL

Mondo (4): spermatogenic failure, X-linked, 3 (MONDO:0025354), XK-related neurodegenerative disease (MONDO:0018945), retinitis pigmentosa 3 (MONDO:0010227), polycystic kidney disease (MONDO:0020642)

Orphanet (2): McLeod neuroacanthocytosis syndrome (Orphanet:59306), Retinitis pigmentosa (Orphanet:791)

HPO phenotypes

8 total (8 of 8 shown, HPO-id order):

HPOTerm
HP:0000798Oligozoospermia
HP:0001419X-linked recessive inheritance
HP:0003251Male infertility
HP:0012207Reduced sperm motility
HP:0032558Absent sperm flagella
HP:0032559Short sperm flagella
HP:0032560Coiled sperm flagella
HP:0033393Irregularly shaped sperm tail

GWAS associations

0 associations (top):

MeSH disease descriptors (3)

DescriptorNameTree numbers
D007690Polycystic Kidney DiseasesC12.050.351.968.419.403.875; C12.200.777.419.403.875; C12.950.419.403.875; C16.131.077.717; C16.320.184.625
C564038Neuroacanthocytosis, Mcleod Type (supp.)
C564520Retinitis Pigmentosa 3 (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

16 total (human), top 16 by PubMed support.

ChemicalActions (top 5)PubMed papers
S-(1,2-dichlorovinyl)cysteineaffects cotreatment, increases expression1
Grape Seed Proanthocyanidinsaffects cotreatment, decreases expression1
Acetaminophendecreases expression1
Air Pollutantsincreases abundance, increases expression1
Benzo(a)pyreneaffects methylation, decreases methylation1
Catechindecreases expression, affects cotreatment1
Leaddecreases expression1
Lipopolysaccharidesaffects cotreatment, increases expression1
Silicon Dioxidedecreases expression1
Smokeincreases abundance, increases expression1
Tobacco Smoke Pollutiondecreases expression1
Triclosanincreases expression1
Valproic Aciddecreases methylation1
Aflatoxin B1decreases methylation1
Okadaic Aciddecreases expression1
Copper Sulfatedecreases expression1

Clinical trials (associated diseases)

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

TrialPhaseStatusTitle
NCT02140814PHASE2COMPLETEDUncontrolled, Open Label, Pilot and Feasibility Study of Niacinamide in Polycystic Kidney Disease
NCT02558595PHASE2COMPLETEDPilot Study of Niacinamide in Polycystic Kidney Disease (NIAC-PKD2)
NCT02697617PHASE2COMPLETEDUse of Low Dose Pioglitazone to Treat Autosomal Dominant Polycystic Kidney Disease
NCT02166489PHASE1COMPLETEDMesenchymal Stem Cells Transplantation in Patients With Chronic Renal Failure Due to Polycystic Kidney Disease
NCT01009957PHASE2/PHASE3TERMINATEDEverolimus on CKD Progression in ADPKD Patients
NCT01680250PHASE2/PHASE3UNKNOWNSirolimus for Massive Polycystic Liver
NCT00286156PHASE1/PHASE2COMPLETEDPilot Study of Rapamycin as Treatment for Autosomal Dominant Polycystic Kidney Disease (ADPKD)
NCT03423810EARLY_PHASE1COMPLETEDAssessing a Dose-Response Relationship of Hydralazine and Its Effects on DNA Methyltransferase 1 in Polycystic Kidney Disease Patients
NCT00792155Not specifiedRECRUITINGPolycystic Kidney Disease Data Repository
NCT01873235Not specifiedRECRUITINGPKD Clinical and Translational Core Study
NCT01931644Not specifiedCOMPLETEDAt-Home Research Study for Patients With Autoimmune, Inflammatory, Genetic, Hematological, Infectious, Neurological, CNS, Oncological, Respiratory, Metabolic Conditions
NCT02142101Not specifiedCOMPLETEDEvaluation of Gut Bacteria in Patients With Polycystic Kidney Disease
NCT02739750Not specifiedCOMPLETEDPioglitazone and Lumbar Bone Marrow Fat in Chronic Kidney Disease
NCT02936791Not specifiedRECRUITINGEarly PKD Observational Cohort Study
NCT03726463Not specifiedUNKNOWNEvaluation of Iliac and Renal Artery for Mechanism of Intracranial Aneurysm in ADPKD
NCT03889392Not specifiedCOMPLETEDEvaluation of Nephrectomy Specimen for Intracranial Aneurysm Development in ADPKD
NCT03948113Not specifiedCOMPLETEDOutcome of Autosomal Dominant Polycystic Kidney Disease Patients on Peritoneal Dialysis: a National Retrospective Study Based on Two French Registries (the French Language Peritoneal Dialysis Registry and the French Renal Epidemiology and Information Network).
NCT04039061Not specifiedRECRUITINGADPKD Patient Registry
NCT05215964Not specifiedUNKNOWNThe Association Between Skeletal Muscle Mass and Severity of Polycystic Liver Disease and Polycystic Kidney Disease
NCT06036992Not specifiedACTIVE_NOT_RECRUITINGStudy and Management of Cystic Complications in Autosomal Dominant Polycystic Kidney Disease
NCT06325644Not specifiedRECRUITINGWell-Formulated Ketogenic Diet Polycystic Kidney Disease
NCT06728228Not specifiedRECRUITINGAmnioinfusion for Fetal Renal Failure
NCT06841224Not specifiedENROLLING_BY_INVITATIONThe Factors Affecting IPP in Peritoneal Dialysis Patients with Polycystic Kidney Disease
NCT06867471Not specifiedRECRUITINGEffects of Exogenous Ketosis on Proteinuria and Renal Function
NCT07310641Not specifiedCOMPLETEDDescriptive Analysis of Preimplantation Genetic Test (PGT)in Couples With Polycystic Kidney Disease (PKD). In the ADPKD Subgroup Evaluation of Outcomes and Complications Comparing Couples in Which the Father is Affected With Couples in Which the Mother is Affected