CFAP54

gene
On this page

Also known as FLJ31514FLJ44112

Summary

CFAP54 (cilia and flagella associated protein 54, HGNC:26456) is a protein-coding gene on chromosome 12q23.1, encoding Cilia- and flagella-associated protein 54 (Q96N23). Required for assembly and function of cilia and flagella. It is a selective cancer dependency (DepMap: 17.8% of cell lines).

Predicted to be involved in cilium assembly; cilium movement involved in cell motility; and spermatogenesis. Predicted to act upstream of or within epithelial cilium movement involved in extracellular fluid movement; establishment of localization in cell; and sperm flagellum assembly. Predicted to be located in axoneme.

Source: NCBI Gene 144535 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): ciliary dyskinesia, primary, 54 (Strong, ClinGen)
  • GWAS associations: 6
  • Clinical variants (ClinVar): 20 total — 9 pathogenic, 2 likely-pathogenic
  • Phenotypes (HPO): 21
  • Cancer dependency (DepMap): dependent in 17.8% of screened cell lines
  • MANE Select transcript: NM_001306084

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:26456
Approved symbolCFAP54
Namecilia and flagella associated protein 54
Location12q23.1
Locus typegene with protein product
StatusApproved
AliasesFLJ31514, FLJ44112
Ensembl geneENSG00000188596
Ensembl biotypeprotein_coding
OMIM621121
Entrez144535

Gene structure

Transcript identifiers

Ensembl transcripts: 9 — 3 retained_intron, 3 protein_coding, 2 protein_coding_CDS_not_defined, 1 non_stop_decay

ENST00000342887, ENST00000524981, ENST00000550977, ENST00000553778, ENST00000554108, ENST00000554621, ENST00000554821, ENST00000556591, ENST00000637336

RefSeq mRNA: 2 — MANE Select: NM_001306084 NM_001306084, NM_001367885

CCDS: CCDS76588

Canonical transcript exons

ENST00000524981 — 68 exons

ExonStartEnd
ENSE000010987189653838496538518
ENSE000010987209650692896507099
ENSE000010987229653406296534227
ENSE000010987239650083496500939
ENSE000010987259651298696513044
ENSE000010987279653379296533973
ENSE000010987289652208896522189
ENSE000010987299650388696504029
ENSE000010987309653551596535600
ENSE000010987329652185796521970
ENSE000010987349652724696527444
ENSE000010987359651892896519071
ENSE000021402999664417896644408
ENSE000021429689676507796765218
ENSE000021469469648957796489926
ENSE000021514849663055196630651
ENSE000021555859681173696811842
ENSE000021605909678667596786898
ENSE000021886279681777596817913
ENSE000021948629682901496829088
ENSE000021962479687511896875555
ENSE000022004979678471796784890
ENSE000022008379679232996792499
ENSE000022015489686081996860952
ENSE000034604749662571896625807
ENSE000034612969669372296693808
ENSE000034631999664787596648017
ENSE000034641739676415196764249
ENSE000034711969668464896684735
ENSE000034725589667960096679752
ENSE000034789539673995696740061
ENSE000034834089665821196658346
ENSE000034846339654083796540987
ENSE000034856079666383096663932
ENSE000035127819662376796623881
ENSE000035229319670474396704796
ENSE000035381969655418296554310
ENSE000035419319674402096744146
ENSE000035615559663009396630204
ENSE000035691149672040596720565
ENSE000035791209654790296547978
ENSE000035811359669997196700093
ENSE000035933949668502996685238
ENSE000035995299674340296743559
ENSE000036007319675645896756563
ENSE000036011589668891696688982
ENSE000036017919674373196743910
ENSE000036052679675374396753898
ENSE000036142689670860896708803
ENSE000036146889675749596757588
ENSE000036238039671844396718522
ENSE000036263709665158896651815
ENSE000036387709662681396626939
ENSE000036500219665788296658105
ENSE000036659919674243996742586
ENSE000036747859664989196650072
ENSE000036892029669112896691310
ENSE000037028559662159096621721
ENSE000037029799659429196594446
ENSE000037038179657658596576761
ENSE000037047699658092096581105
ENSE000037060919658942796589563
ENSE000037066299658059796580689
ENSE000037066789659864596598767
ENSE000037079369655467696554802
ENSE000037098639656464496564765
ENSE000037100129659249096592637
ENSE000037107769656446896564554

Expression profiles

Bgee: expression breadth ubiquitous, 166 present calls, max score 89.66.

FANTOM5 (CAGE): breadth broad, TPM avg 1.4739 / max 66.3116, expressed in 620 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
1274851.4739620

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047389.66gold quality
right uterine tubeUBERON:000130287.39gold quality
colonic epitheliumUBERON:000039780.55gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099180.10gold quality
olfactory segment of nasal mucosaUBERON:000538678.20gold quality
bone marrow cellCL:000209276.28gold quality
ventricular zoneUBERON:000305375.65gold quality
bronchial epithelial cellCL:000232874.50gold quality
bronchusUBERON:000218572.97gold quality
oviduct epitheliumUBERON:000480472.05gold quality
fallopian tubeUBERON:000388969.65gold quality
adenohypophysisUBERON:000219667.77gold quality
buccal mucosa cellCL:000233667.54silver quality
pituitary glandUBERON:000000766.00gold quality
testisUBERON:000047365.85gold quality
ganglionic eminenceUBERON:000402365.20gold quality
right testisUBERON:000453464.30gold quality
left testisUBERON:000453364.25gold quality
tonsilUBERON:000237263.98gold quality
left uterine tubeUBERON:000130363.89gold quality
calcaneal tendonUBERON:000370162.92gold quality
corpus callosumUBERON:000233662.91gold quality
stromal cell of endometriumCL:000225562.86gold quality
body of uterusUBERON:000985362.79gold quality
thyroid glandUBERON:000204662.40gold quality
lower esophagus muscularis layerUBERON:003583362.39gold quality
lower esophagusUBERON:001347362.34gold quality
left lobe of thyroid glandUBERON:000112061.74gold quality
right lungUBERON:000216761.71gold quality
right lobe of thyroid glandUBERON:000111960.85gold quality

Single-cell (SCXA)

Detected in 8 experiment(s), a significant marker in 5.

ExperimentMarker?Max mean expression
E-GEOD-180759yes3295.68
E-GEOD-81547yes131.46
E-MTAB-5061yes13.91
E-ANND-3yes11.11
E-HCAD-35yes7.09
E-ENAD-20no105.77
E-MTAB-9067no3.63
E-GEOD-137537no3.38

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

31 targeting CFAP54, 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-518D-5P100.0067.51979
HSA-MIR-518E-5P100.0067.66954
HSA-MIR-518F-5P100.0067.51979
HSA-MIR-519A-5P100.0067.66954
HSA-MIR-519B-5P100.0067.66954
HSA-MIR-519C-5P100.0067.66954
HSA-MIR-520C-5P100.0067.51979
HSA-MIR-522-5P100.0067.66954
HSA-MIR-523-5P100.0067.66954
HSA-MIR-526A-5P100.0067.51979
HSA-MIR-520G-5P99.9966.76658
HSA-MIR-1229-3P99.9766.49906
HSA-MIR-627-3P99.9071.423316
HSA-MIR-2681-5P99.7567.641655
HSA-MIR-580-3P99.6769.231841
HSA-MIR-432899.5771.064094
HSA-MIR-18A-3P99.5665.681092
HSA-MIR-469699.4867.481040
HSA-MIR-330-3P99.4169.952521
HSA-MIR-478499.1567.411733
HSA-MIR-7160-5P99.1167.172207
HSA-MIR-62298.9966.481050
HSA-MIR-3150B-3P98.8167.211728
HSA-MIR-6755-3P98.6166.90834
HSA-MIR-7158-3P98.4666.45728
HSA-MIR-138-1-3P98.2567.89867
HSA-MIR-4638-3P97.9065.75905
HSA-MIR-6511A-3P97.6066.61713
HSA-MIR-6511B-3P97.6066.61713
HSA-MIR-320E97.4965.96865

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 17.8% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 2)

  • Biallelic mutations in CFAP54 cause male infertility with severe MMAF and NOA. (PMID:36593121)
  • Lack of CFAP54 causes primary ciliary dyskinesia in a mouse model and human patients. (PMID:37725231)

Cross-species orthologs

2 orthologs

OrganismSymbolGene ID
mus_musculusCfap54ENSMUSG00000020014
rattus_norvegicusCfap54ENSRNOG00000024494

Protein

Protein identifiers

Cilia- and flagella-associated protein 54Q96N23 (reviewed: Q96N23)

All UniProt accessions (4): A0A0A0MTQ3, A0A1B0GU80, Q96N23, H0YIB5

UniProt curated annotations — full annotation on UniProt →

Function. Required for assembly and function of cilia and flagella.

Subcellular location. Cytoplasm. Cytoskeleton. Cilium axoneme.

Disease relevance. Spermatogenic failure 98 (SPGF98) [MIM:621124] An autosomal recessive, male infertility disorder characterized by abnormal sperm morphology, and reduced sperm concentration and motility. The disease may be caused by variants affecting the gene represented in this entry. Ciliary dyskinesia, primary, 54 (CILD54) [MIM:621125] An autosomal recessive form of primary ciliary dyskinesia, a disorder characterized by abnormalities of motile cilia. Respiratory infections leading to chronic inflammation and bronchiectasis are recurrent, due to defects in the respiratory cilia. CILD54 affected individuals suffer from rhinitis, sinusitis, asthma, in addition to bronchiectasis. The disease may be caused by variants affecting distinct genetic loci, including the gene represented in this entry.

Miscellaneous. Gene prediction based on partial mRNA data. Incomplete sequence.

Similarity. Belongs to the CFAP54 family.

Isoforms (2)

UniProt IDNamesCanonical?
Q96N23-11yes
Q96N23-22

RefSeq proteins (2): NP_001293013, NP_001354814 (=MANE)

Domains & families (InterPro)

IDNameType
IPR027912CFAP54Family

Pfam: PF14858

UniProt features (20 total): sequence variant 9, sequence conflict 5, region of interest 2, splice variant 2, chain 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

No AlphaFold model available for Q96N23 — AlphaFold DB does not currently provide models for proteins above ~3000 aa.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 116 (showing top): GOBP_RESPIRATORY_GASEOUS_EXCHANGE_BY_RESPIRATORY_SYSTEM, GOBP_RESPIRATORY_SYSTEM_PROCESS, GOBP_MALE_GAMETE_GENERATION, GOBP_CILIUM_ORGANIZATION, GOBP_CILIUM_MOVEMENT, GOBP_CILIUM_OR_FLAGELLUM_DEPENDENT_CELL_MOTILITY, GOBP_ORGANELLE_ASSEMBLY, GOBP_CELLULAR_PROCESS_INVOLVED_IN_REPRODUCTION_IN_MULTICELLULAR_ORGANISM, GOBP_DEVELOPMENTAL_PROCESS_INVOLVED_IN_REPRODUCTION, GOBP_MOTILE_CILIUM_ASSEMBLY, GOBP_CELL_PROJECTION_ORGANIZATION, GOCC_CYTOPLASMIC_REGION, GOCC_CILIUM, chr12q23, TCANNTGAY_SREBP1_01

GO Biological Process (9): spermatogenesis (GO:0007283), establishment of localization in cell (GO:0051649), cilium assembly (GO:0060271), cilium movement involved in cell motility (GO:0060294), cerebrospinal fluid circulation (GO:0090660), mucociliary clearance (GO:0120197), sperm flagellum assembly (GO:0120316), cell projection organization (GO:0030030), cell differentiation (GO:0030154)

GO Molecular Function (0):

GO Cellular Component (7): extracellular region (GO:0005576), axoneme (GO:0005930), cytoplasm (GO:0005737), cytoskeleton (GO:0005856), cilium (GO:0005929), membrane (GO:0016020), cell projection (GO:0042995)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure5
developmental process involved in reproduction2
epithelial cilium movement involved in extracellular fluid movement2
male gamete generation1
establishment of localization1
cellular localization1
axoneme 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
cilium movement1
cell motility1
cilium-dependent cell motility1
nervous system process1
respiratory system process1
spermatid development1
flagellated sperm motility1
motile cilium assembly1
cellular component organization1
cellular developmental process1
cytoskeleton1
microtubule1
ciliary plasm1
intracellular anatomical structure1
intracellular membraneless organelle1
intraciliary transport particle1
membrane-bounded organelle1
plasma membrane bounded cell projection1

Protein interactions and networks

STRING

1023 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
CFAP54SPEF2Q9C093707
CFAP54C1DQ13901587
CFAP54CFAP221Q4G0U5571
CFAP54CALML6Q8TD86484
CFAP54CALML3P27482484
CFAP54CALML5Q9NZT1484
CFAP54CALML4Q96GE6484
CFAP54CALM1P02593482
CFAP54SPAG6O75602479
CFAP54HYDINQ4G0P3479
CFAP54GALNT18Q6P9A2439
CFAP54RCL1Q9Y2P8438
CFAP54PMIS2A0A1W2PS18434
CFAP54CFAP52Q8N1V2421
CFAP54R3HDM2Q9Y2K5413

IntAct

4 interactions, top by confidence:

ABTypeScore
CFAP54NPM1psi-mi:“MI:0915”(physical association)0.400
CFAP54AP2B1psi-mi:“MI:0915”(physical association)0.400
CFAP54TSPY2psi-mi:“MI:0914”(association)0.350

ESM2 similar proteins: A0A571BF63, A1L0Z4, A1ZAG4, A4IF93, A4QP31, A5HEI1, D3IUT5, F4JS25, F4KCC2, F6S215, O00443, O65418, Q08AV6, Q0JF48, Q4R6I5, Q5FVR8, Q5Q0E6, Q5RAY1, Q5RD58, Q5TEA3, Q5ZKT1, Q61194, Q61QK6, Q640P7, Q69KN0, Q6DRD4, Q7TT23, Q7XZU2, Q8BMQ2, Q8C6S9, Q8GYU3, Q8H1U4, Q8L6Y4, Q8LLD0, Q8N957, Q8NB91, Q8NHS4, Q8RWM3, Q96N23, Q9FFF9

Diamond homologs: Q8C6S9, Q96N23

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic9
Likely pathogenic2
Uncertain significance2
Likely benign6
Benign0

Top pathogenic / likely-pathogenic (11)

Variant IDHGVSClassification
3767880NM_001306084.2(CFAP54):c.3317del (p.Phe1106fs)Pathogenic
3767881NM_001306084.2(CFAP54):c.878G>A (p.Arg293His)Pathogenic
3767882NM_001306084.2(CFAP54):c.955C>T (p.Arg319Cys)Pathogenic
3767883NM_001306084.2(CFAP54):c.937G>A (p.Gly313Arg)Pathogenic
3767884NM_001306084.2(CFAP54):c.4885C>T (p.Arg1629Cys)Pathogenic
3768007CFAP54, DEL/INS NT2649Pathogenic
3768008CFAP54, 18-BP INS, NT7312Pathogenic
3768009CFAP54, GLU1371ALAPathogenic
3768010CFAP54, PRO2187SERPathogenic
3778415NM_001306084.2(CFAP54):c.4713_4716del (p.Phe1571fs)Likely pathogenic
4526608NM_001306084.2(CFAP54):c.8644_8645del (p.Leu2882fs)Likely pathogenic

SpliceAI

11568 predictions. Top by Δscore:

VariantEffectΔscore
12:96489923:GTTG:Gdonor_gain1.0000
12:96489926:GGTA:Gdonor_loss1.0000
12:96489927:G:GGdonor_gain1.0000
12:96489928:T:Adonor_loss1.0000
12:96500936:GAAA:Gdonor_gain1.0000
12:96500937:AAAGT:Adonor_loss1.0000
12:96500938:AAGTA:Adonor_loss1.0000
12:96500939:AGT:Adonor_loss1.0000
12:96500940:G:Cdonor_loss1.0000
12:96500940:G:GGdonor_gain1.0000
12:96500941:T:Gdonor_loss1.0000
12:96503879:GTTTC:Gacceptor_loss1.0000
12:96503880:TTTCA:Tacceptor_loss1.0000
12:96503881:TTCA:Tacceptor_loss1.0000
12:96503882:TCA:Tacceptor_loss1.0000
12:96503883:CAGG:Cacceptor_loss1.0000
12:96503884:A:Cacceptor_loss1.0000
12:96503964:G:GTdonor_gain1.0000
12:96504001:GCTT:Gdonor_gain1.0000
12:96504030:G:GGdonor_gain1.0000
12:96506926:A:AGacceptor_gain1.0000
12:96506927:G:GGacceptor_gain1.0000
12:96527384:G:GTdonor_gain1.0000
12:96527428:A:Tdonor_gain1.0000
12:96527440:GA:Gdonor_gain1.0000
12:96527441:A:AGdonor_gain1.0000
12:96527441:A:Gdonor_gain1.0000
12:96527445:G:GGdonor_gain1.0000
12:96533790:A:AGacceptor_gain1.0000
12:96533791:G:GGacceptor_gain1.0000

AlphaMissense

20344 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
12:96626839:T:CF1335L0.997
12:96626841:T:AF1335L0.997
12:96626841:T:GF1335L0.997
12:96792452:T:AW2935R0.997
12:96792452:T:CW2935R0.997
12:96651612:T:AW1633R0.996
12:96651612:T:CW1633R0.996
12:96685045:T:AW1941R0.996
12:96685045:T:CW1941R0.996
12:96625772:T:AV1314D0.995
12:96658059:T:AW1760R0.995
12:96658059:T:CW1760R0.995
12:96757515:T:CL2656P0.995
12:96784827:T:AW2798R0.995
12:96784827:T:CW2798R0.995
12:96580986:G:CA986P0.994
12:96626840:T:CF1335S0.994
12:96644299:T:AW1480R0.994
12:96644299:T:CW1480R0.994
12:96651601:G:CR1629P0.994
12:96594339:A:CS1137R0.993
12:96594341:C:AS1137R0.993
12:96594341:C:GS1137R0.993
12:96658264:T:CL1793P0.993
12:96651595:C:AA1627D0.992
12:96651622:T:CL1636P0.992
12:96756538:A:CS2641R0.992
12:96756540:C:AS2641R0.992
12:96756540:C:GS2641R0.992
12:96786780:T:CL2854P0.992

dbSNP variants (sampled 300 via entrez): RS1000014607 (12:96570139 C>T), RS1000017026 (12:96705048 A>T), RS1000019277 (12:96544067 CCTAAAT>C), RS1000029484 (12:96534503 A>T), RS1000041661 (12:96841623 A>G), RS1000044297 (12:96574069 C>A,T), RS1000044617 (12:96759132 A>G), RS1000056564 (12:96617249 A>G), RS1000067706 (12:96703840 G>A), RS1000068183 (12:96794935 G>A,T), RS1000097066 (12:96622123 G>A), RS1000098343 (12:96704164 A>C), RS1000106746 (12:96616987 G>A), RS1000126338 (12:96845392 A>T), RS1000134255 (12:96604466 T>C)

Disease associations

OMIM: gene MIM:621121 | disease phenotypes: MIM:621124, MIM:621125

GenCC curated gene-disease

ClinGen Gene-Disease Validity (1)

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

DiseaseClassificationInheritance
ciliary dyskinesia, primary, 54StrongAR

Mondo (2): spermatogenic failure 98 (MONDO:0700290), ciliary dyskinesia, primary, 54 (MONDO:0100607)

Orphanet (0):

HPO phenotypes

21 total (21 of 21 shown, HPO-id order):

HPOTerm
HP:0000007Autosomal recessive inheritance
HP:0000798Oligozoospermia
HP:0002090Pneumonia
HP:0002099Asthma
HP:0002110Bronchiectasis
HP:0002837Recurrent bronchitis
HP:0003251Male infertility
HP:0011462Young adult onset
HP:0011463Childhood onset
HP:0012207Reduced sperm motility
HP:0025708Early young adult onset
HP:0031245Productive cough
HP:0032558Absent sperm flagella
HP:0032559Short sperm flagella
HP:0032560Coiled sperm flagella
HP:0033393Irregularly shaped sperm tail
HP:0033524Abnormal sperm axoneme morphology
HP:0034011Reduced progressive sperm motility
HP:0034811Bent sperm flagella
HP:0100750Atelectasis
HP:6000135Low semen volume

GWAS associations

6 associations (top):

StudyTraitp-value
GCST000837_3Weight4.000000e-06
GCST005050_6Obstructive sleep apnea during REM sleep (apnea hypopnea index)6.000000e-07
GCST007231_5Tuberculosis3.000000e-06
GCST007637_21Diffusing capacity of carbon monoxide2.000000e-06
GCST009222_4Corpus callosum posterior volume7.000000e-06
GCST009391_187Metabolite levels2.000000e-06

EFO canonical traits (4, from GWAS)

EFO IDTrait name
EFO:0004338body weight
EFO:0008455sleep apnea measurement during REM sleep
EFO:0009369diffusing capacity of the lung for carbon monoxide
EFO:0010482gamma-aminoisobutyric acid measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

9 total (human), top 9 by PubMed support.

ChemicalActions (top 5)PubMed papers
Smokedecreases expression, increases abundance, increases expression2
FR900359increases phosphorylation1
sodium arsenitedecreases expression1
2-palmitoylglycerolincreases expression1
Air Pollutantsincreases expression, increases abundance1
Arsenicaffects methylation1
Caffeineincreases phosphorylation1
Tobacco Smoke Pollutionaffects expression1
Aflatoxin B1decreases methylation1

Clinical trials (associated diseases)

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