CFAP44

gene
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Also known as FLJ11142

Summary

CFAP44 (cilia and flagella associated protein 44, HGNC:25631) is a protein-coding gene on chromosome 3q13.2, encoding Cilia- and flagella-associated protein 44 (Q96MT7). Flagellar protein involved in sperm flagellum axoneme organization and function.

Enables peptidase activity. Involved in sperm axoneme assembly. Acts upstream of or within microtubule cytoskeleton organization. Predicted to be located in cytoplasm; cytoskeleton; and motile cilium. Implicated in spermatogenic failure 20.

Source: NCBI Gene 55779 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): spermatogenic failure 20 (Moderate, GenCC) — +1 more curated relationship
  • GWAS associations: 4
  • Clinical variants (ClinVar): 229 total — 9 pathogenic, 7 likely-pathogenic
  • Phenotypes (HPO): 6
  • MANE Select transcript: NM_001164496

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:25631
Approved symbolCFAP44
Namecilia and flagella associated protein 44
Location3q13.2
Locus typegene with protein product
StatusApproved
AliasesFLJ11142
Ensembl geneENSG00000206530
Ensembl biotypeprotein_coding
OMIM617559
Entrez55779

Gene structure

Transcript identifiers

Ensembl transcripts: 13 — 6 nonsense_mediated_decay, 3 protein_coding, 3 retained_intron, 1 protein_coding_CDS_not_defined

ENST00000295868, ENST00000393845, ENST00000461734, ENST00000465186, ENST00000465510, ENST00000473143, ENST00000475568, ENST00000479422, ENST00000484923, ENST00000488854, ENST00000489244, ENST00000489938, ENST00000490481

RefSeq mRNA: 2 — MANE Select: NM_001164496 NM_001164496, NM_018338

CCDS: CCDS2972, CCDS54624

Canonical transcript exons

ENST00000393845 — 35 exons

ExonStartEnd
ENSE00001912682113286930113291748
ENSE00003548737113433565113433669
ENSE00003793620113341744113341918
ENSE00003796467113330168113330668
ENSE00003797033113344516113344712
ENSE00003797687113363145113363307
ENSE00003798616113333406113333583
ENSE00003799968113327616113327819
ENSE00003801243113420017113420179
ENSE00003801935113306201113306331
ENSE00003802208113366039113366309
ENSE00003802209113400545113400644
ENSE00003802467113396518113396727
ENSE00003802727113303916113304117
ENSE00003802789113363477113363532
ENSE00003803501113380899113381060
ENSE00003803720113305036113305152
ENSE00003804338113416525113416627
ENSE00003805666113441453113441493
ENSE00003805792113427187113427339
ENSE00003806044113373411113373556
ENSE00003806219113308158113308268
ENSE00003807637113358745113358875
ENSE00003807905113426124113426277
ENSE00003807960113326445113326640
ENSE00003808478113294687113294821
ENSE00003809202113409106113409322
ENSE00003809589113403852113404016
ENSE00003809680113395750113395860
ENSE00003809947113401584113401739
ENSE00003810589113296725113296885
ENSE00003810745113401240113401287
ENSE00003811125113399906113400000
ENSE00003811219113379306113379551
ENSE00003811379113406927113407041

Expression profiles

Bgee: expression breadth ubiquitous, 208 present calls, max score 96.87.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.4455 / max 43.0965, expressed in 120 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter IDTPM avgSamples expressed
438440.359098
438420.063323
438430.023114

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
right uterine tubeUBERON:000130296.87gold quality
bronchial epithelial cellCL:000232892.67gold quality
olfactory segment of nasal mucosaUBERON:000538691.69gold quality
mucosa of paranasal sinusUBERON:000503088.63gold quality
epithelium of bronchusUBERON:000203188.32gold quality
spermCL:000001988.27gold quality
calcaneal tendonUBERON:000370188.24gold quality
sural nerveUBERON:001548887.95gold quality
bronchusUBERON:000218587.28gold quality
adenohypophysisUBERON:000219685.04gold quality
male germ cellCL:000001585.01gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047384.82gold quality
minor salivary glandUBERON:000183084.23gold quality
body of pancreasUBERON:000115084.22gold quality
pituitary glandUBERON:000000783.55gold quality
endocervixUBERON:000045882.39gold quality
right testisUBERON:000453482.38gold quality
left testisUBERON:000453382.34gold quality
rectumUBERON:000105282.24gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099182.20gold quality
body of stomachUBERON:000116181.79gold quality
saliva-secreting glandUBERON:000104481.35gold quality
transverse colonUBERON:000115781.30gold quality
testisUBERON:000047380.55gold quality
right lungUBERON:000216780.50gold quality
small intestine Peyer’s patchUBERON:000345480.47gold quality
left uterine tubeUBERON:000130380.41gold quality
tibial nerveUBERON:000132379.93gold quality
body of uterusUBERON:000985379.92gold quality
right lobe of thyroid glandUBERON:000111979.69gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes9.08
E-MTAB-9388yes6.39

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

16 targeting CFAP44, 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-4425100.0067.591049
HSA-MIR-450A-1-3P100.0069.331837
HSA-MIR-196A-1-3P99.9972.152772
HSA-MIR-3065-5P99.9771.563281
HSA-MIR-495-3P99.9672.814197
HSA-MIR-568899.9673.234504
HSA-MIR-990299.8969.152250
HSA-MIR-5010-3P99.8370.602357
HSA-MIR-4668-5P99.7970.583782
HSA-MIR-505-3P99.1969.71896
HSA-MIR-59998.3266.991037
HSA-MIR-1022698.2566.50811
HSA-MIR-138-1-3P98.2567.89867
HSA-MIR-6771-3P98.2066.53971
HSA-MIR-392097.7569.021168
HSA-MIR-59296.5967.59817

Literature-anchored findings (GeneRIF, showing 5)

  • Results show that the rs13064411 polymorphism in the WDR52 gene was associated with a modified effect of statin therapy on serum LDL and total cholesterol levels. (PMID:25602530)
  • biallelic mutations in either CFAP43 or CFAP44 can cause sperm flagellar abnormalities and impair sperm motility. (PMID:28552195)
  • Study demonstrated that biallelic mutations in CFAP44 and CFAP43 cause multiple morphological abnormalities of the sperm flagella (MMAF). These results provide researchers with a new insight to understand the genetic etiology of MMAF and to identify new loci for genetic counselling of MMAF. (PMID:29277146)
  • demonstrate that CFAP43 and CFAP44 have a similar structure with a unique axonemal localization and are necessary to produce functional flagella in species ranging from Trypanosoma to human (PMID:29449551)
  • important cause of multiple morphological abnormalities of the sperm flagellum in the Chinese population (PMID:30904354)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
mus_musculusCfap44ENSMUSG00000071550
rattus_norvegicusCfap44ENSRNOG00000028077
drosophila_melanogasterCG34124FBGN0083960

Paralogs (9): EML1 (ENSG00000066629), EML2 (ENSG00000125746), EML4 (ENSG00000143924), EML3 (ENSG00000149499), CFAP251 (ENSG00000158023), WDR90 (ENSG00000161996), EML5 (ENSG00000165521), CFAP52 (ENSG00000166596), EML6 (ENSG00000214595)

Protein

Protein identifiers

Cilia- and flagella-associated protein 44Q96MT7 (reviewed: Q96MT7)

Alternative names: WD repeat-containing protein 52

All UniProt accessions (8): Q96MT7, A0A1D5RMR1, C9K0A4, F8WEX0, H0Y883, H0Y896, H7C512, H7C591

UniProt curated annotations — full annotation on UniProt →

Function. Flagellar protein involved in sperm flagellum axoneme organization and function.

Subcellular location. Cell projection. Cilium. Flagellum. Cytoplasm. Cytoskeleton. Flagellum axoneme.

Tissue specificity. Testis-specific.

Disease relevance. Spermatogenic failure 20 (SPGF20) [MIM:617593] An infertility disorder caused by spermatogenesis defects and characterized by abnormally shaped spermatozoa in the semen of affected individuals. SPGF20 patients have spermatozoa with absent, short, coiled, bent, and/or irregular-caliber flagella, which impair sperm motility. The disease is caused by variants affecting the gene represented in this entry.

Similarity. Belongs to the CFAP44 family.

Isoforms (2)

UniProt IDNamesCanonical?
Q96MT7-22yes
Q96MT7-11

RefSeq proteins (2): NP_001157968, NP_060808 (=MANE)

Domains & families (InterPro)

IDNameType
IPR001680WD40_rptRepeat
IPR015943WD40/YVTN_repeat-like_dom_sfHomologous_superfamily
IPR019775WD40_repeat_CSConserved_site
IPR036322WD40_repeat_dom_sfHomologous_superfamily
IPR055439Beta-prop_EML_1stDomain

Pfam: PF00400, PF23409

UniProt features (30 total): repeat 9, compositionally biased region 7, region of interest 5, sequence variant 4, splice variant 2, chain 1, coiled-coil region 1, modified residue 1

Structure

Experimental structures (PDB)

1 structures.

PDBMethodResolution (Å)
8J07ELECTRON MICROSCOPY4.1

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q96MT7-F174.870.27

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (1): 1083

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 122 (showing top): GSE45365_HEALTHY_VS_MCMV_INFECTION_CD8_TCELL_IFNAR_KO_UP, MODULE_511, GOBP_MALE_GAMETE_GENERATION, GOBP_NUCLEUS_ORGANIZATION, 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_MICROTUBULE_BUNDLE_FORMATION, GOBP_DEVELOPMENTAL_PROCESS_INVOLVED_IN_REPRODUCTION, GOBP_MOTILE_CILIUM_ASSEMBLY, GOBP_CELL_PROJECTION_ORGANIZATION, GOBP_AXONEME_ASSEMBLY, GOCC_CYTOPLASMIC_REGION

GO Biological Process (7): microtubule cytoskeleton organization (GO:0000226), cell morphogenesis (GO:0000902), nucleus organization (GO:0006997), sperm axoneme assembly (GO:0007288), spermatogenesis (GO:0007283), flagellated sperm motility (GO:0030317), cilium organization (GO:0044782)

GO Molecular Function (2): peptidase activity (GO:0008233), protein binding (GO:0005515)

GO Cellular Component (5): motile cilium (GO:0031514), cytoplasm (GO:0005737), cytoskeleton (GO:0005856), cilium (GO:0005929), cell projection (GO:0042995)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
organelle organization2
developmental process involved in reproduction2
cellular anatomical structure2
cytoskeleton organization1
microtubule-based process1
anatomical structure morphogenesis1
axoneme assembly1
sperm flagellum assembly1
male gamete generation1
cilium-dependent cell motility1
cilium movement involved in cell motility1
sperm motility1
plasma membrane bounded cell projection organization1
hydrolase activity1
catalytic activity, acting on a protein1
binding1
cilium1
intracellular anatomical structure1
intracellular membraneless organelle1
intraciliary transport particle1
membrane-bounded organelle1
plasma membrane bounded cell projection1

Protein interactions and networks

STRING

1772 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
CFAP44QRICH2Q9H0J4795
CFAP44CFAP69A5D8W1786
CFAP44DNAH1Q9P2D7777
CFAP44TTC29Q8NA56661
CFAP44CFAP70Q5T0N1652
CFAP44TTC21AQ8NDW8649
CFAP44FSIP2Q5CZC0641
CFAP44ARMC2Q8NEN0633
CFAP44AKAP4Q5JQC9611
CFAP44CFAP43Q8NDM7608
CFAP44CFAP58Q5T655594
CFAP44SPEF2Q9C093588
CFAP44DNAH17Q9UFH2582
CFAP44CFAP91Q7Z4T9581
CFAP44CCDC39Q9UFE4568

IntAct

4 interactions, top by confidence:

ABTypeScore
GADD45GCFAP44psi-mi:“MI:0915”(physical association)0.560
CFAP44GADD45Gpsi-mi:“MI:0915”(physical association)0.560

BioGRID (18): CFAP44 (Affinity Capture-MS), CFAP44 (Affinity Capture-MS), CFAP44 (Affinity Capture-MS), CFAP44 (Affinity Capture-MS), CFAP44 (Two-hybrid), CFAP44 (Proximity Label-MS), CFAP44 (Proximity Label-MS), CFAP44 (Affinity Capture-MS), CFAP44 (Affinity Capture-MS), CFAP44 (Proximity Label-MS), CFAP44 (Cross-Linking-MS (XL-MS)), CFAP44 (Cross-Linking-MS (XL-MS)), CFAP44 (Cross-Linking-MS (XL-MS)), CFAP44 (Cross-Linking-MS (XL-MS)), FAM98A (Cross-Linking-MS (XL-MS))

ESM2 similar proteins: A2AC93, B2RY71, E7F6H7, E9PYY5, E9Q5M6, O14576, O43815, O55106, O88485, O88487, P27766, P36872, P70483, Q0III3, Q13409, Q13610, Q16959, Q16960, Q29RQ3, Q2HJ56, Q32KS2, Q32LP9, Q4QR00, Q4V8G4, Q5DQR4, Q5NVM2, Q5SQE2, Q5VTH9, Q5XIL8, Q5ZLK1, Q62871, Q63100, Q66HC9, Q6GPB9, Q8BPM2, Q8C0M8, Q8C0P5, Q8IVH8, Q8IWG1, Q92828

Diamond homologs: E9Q5M6, Q96MT7

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic9
Likely pathogenic7
Uncertain significance113
Likely benign43
Benign19

Top pathogenic / likely-pathogenic (16)

Variant IDHGVSClassification
1013486NM_001164496.2(CFAP44):c.1170+1G>APathogenic
2055515NM_001164496.2(CFAP44):c.535C>T (p.Arg179Ter)Pathogenic
2058075NM_001164496.2(CFAP44):c.259C>T (p.Gln87Ter)Pathogenic
430938NM_001164496.2(CFAP44):c.2005_2006del (p.Met669fs)Pathogenic
523150NC_000003.12:g.113358867_113358876delPathogenic
523151NM_001164496.2(CFAP44):c.1769T>A (p.Leu590Gln)Pathogenic
523152NM_001164496.2(CFAP44):c.1387G>T (p.Glu463Ter)Pathogenic
523153NM_001164496.2(CFAP44):c.3175C>T (p.Arg1059Ter)Pathogenic
523154NM_001164496.2(CFAP44):c.2818dup (p.Glu940fs)Pathogenic
1339091NM_001164496.2(CFAP44):c.670C>T (p.Arg224Ter)Likely pathogenic
2632408NM_001164496.2(CFAP44):c.2616del (p.Leu873fs)Likely pathogenic
3065141NM_001164496.2(CFAP44):c.1303G>T (p.Gly435Ter)Likely pathogenic
3352580NM_001164496.2(CFAP44):c.5540_5541dup (p.Glu1848fs)Likely pathogenic
3893052NM_001164496.2(CFAP44):c.408-2A>TLikely pathogenic
3893053NM_001164496.2(CFAP44):c.5078-2A>GLikely pathogenic
4845865NM_001164496.2(CFAP44):c.2813_2816del (p.Met938fs)Likely pathogenic

SpliceAI

3068 predictions. Top by Δscore:

VariantEffectΔscore
3:113363303:CGATA:Cacceptor_gain1.0000
3:113363306:TA:Tacceptor_gain1.0000
3:113363308:C:CCacceptor_gain1.0000
3:113363471:CCATA:Cdonor_loss1.0000
3:113363472:CATA:Cdonor_loss1.0000
3:113363473:ATAC:Adonor_loss1.0000
3:113363474:TA:Tdonor_loss1.0000
3:113363475:ACCTG:Adonor_loss1.0000
3:113363476:CCTGT:Cdonor_loss1.0000
3:113363528:CCAAA:Cacceptor_gain1.0000
3:113363529:CAAA:Cacceptor_gain1.0000
3:113363529:CAAAC:Cacceptor_gain1.0000
3:113363531:AA:Aacceptor_gain1.0000
3:113363533:C:CCacceptor_gain1.0000
3:113363535:A:Cacceptor_gain1.0000
3:113373409:A:ACdonor_gain1.0000
3:113373410:C:CCdonor_gain1.0000
3:113396516:ACC:Adonor_gain1.0000
3:113396517:CCC:Cdonor_gain1.0000
3:113399900:ACTT:Adonor_loss1.0000
3:113399901:CTTA:Cdonor_loss1.0000
3:113399903:TACC:Tdonor_loss1.0000
3:113399936:T:TAdonor_gain1.0000
3:113399996:AGAGC:Aacceptor_gain1.0000
3:113399997:GAGC:Gacceptor_gain1.0000
3:113399998:AGC:Aacceptor_gain1.0000
3:113399999:GC:Gacceptor_gain1.0000
3:113400000:CC:Cacceptor_gain1.0000
3:113400001:C:CCacceptor_gain1.0000
3:113400001:CT:Cacceptor_loss1.0000

AlphaMissense

12367 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
3:113401736:A:GW392R0.999
3:113401736:A:TW392R0.999
3:113403980:A:GW348R0.999
3:113403980:A:TW348R0.999
3:113341765:C:GR1139P0.998
3:113304017:A:GL1659P0.997
3:113304029:C:GR1655P0.997
3:113305130:A:GL1594P0.997
3:113327692:A:GL1415P0.997
3:113403978:C:AW348C0.997
3:113403978:C:GW348C0.997
3:113409221:A:GW259R0.997
3:113409221:A:TW259R0.997
3:113303954:A:GL1680P0.996
3:113303963:C:GR1677P0.996
3:113304038:A:GL1652P0.996
3:113327785:A:GL1384P0.996
3:113333490:C:AK1177N0.996
3:113333490:C:GK1177N0.996
3:113333522:C:GA1167P0.996
3:113396675:C:GR541P0.996
3:113403985:A:GL346P0.996
3:113407037:A:GW299R0.996
3:113407037:A:TW299R0.996
3:113409227:A:GW257R0.996
3:113409227:A:TW257R0.996
3:113305094:C:GR1606P0.995
3:113306292:C:GR1556P0.995
3:113366262:C:GR831P0.995
3:113401262:A:GL451P0.995

dbSNP variants (sampled 300 via entrez): RS1000057792 (3:113313708 A>C,T), RS1000108264 (3:113368406 A>G), RS1000124400 (3:113441864 C>T), RS1000128218 (3:113398899 G>C), RS1000149208 (3:113386556 G>A,T), RS1000161099 (3:113346207 C>T), RS1000161855 (3:113423843 G>A), RS1000173270 (3:113300567 G>T), RS1000179539 (3:113369994 T>C), RS1000184101 (3:113312763 G>A,C), RS1000191490 (3:113299854 C>T), RS1000271492 (3:113325428 A>C), RS1000276247 (3:113374661 G>A,T), RS1000278358 (3:113405726 C>T), RS1000299523 (3:113306231 G>A)

Disease associations

OMIM: gene MIM:617559 | disease phenotypes: MIM:617593

GenCC curated gene-disease

DiseaseClassificationInheritance
spermatogenic failure 20ModerateAutosomal recessive
non-syndromic male infertility due to sperm motility disorderSupportiveAutosomal recessive

Mondo (2): spermatogenic failure 20 (MONDO:0054724), (MONDO:0017173)

Orphanet (0):

HPO phenotypes

6 total (6 of 6 shown, HPO-id order):

HPOTerm
HP:0000007Autosomal recessive inheritance
HP:0003251Male infertility
HP:0011462Young adult onset
HP:0032558Absent sperm flagella
HP:0032559Short sperm flagella
HP:0032560Coiled sperm flagella

GWAS associations

4 associations (top):

StudyTraitp-value
GCST001942_7Prostate cancer4.000000e-13
GCST002642_1Response to simvastatin treatment (PCSK9 protein level change)8.000000e-08
GCST005149_18Colorectal cancer6.000000e-07
GCST012034_4Sleep (1/2-day periodicity)4.000000e-09

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0006899PCSK9 protein measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

PharmGKB clinical annotations

1 annotations.

VariantTypeLevelDrugsPhenotypes
rs13064411Efficacy3HMG-CoA reductase inhibitors

PharmGKB variants

1 variants.

VariantGenesLevelScore#Clin annotsDrugs
rs13064411CFAP4432.501HMG-CoA reductase inhibitors

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects cotreatment, increases expression, affects expression, increases methylation5
sodium arsenitedecreases expression2
perfluorooctane sulfonic aciddecreases expression, increases expression2
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamideincreases expression1
GSK-J4decreases expression1
triphenyl phosphateaffects expression1
trichostatin Aincreases expression1
tris(2-butoxyethyl) phosphateaffects expression1
beta-lapachonedecreases expression1
ferrous chloridedecreases expression1
nickel sulfatedecreases expression1
hydroquinonedecreases expression1
pentanaldecreases expression1
entinostatincreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideincreases expression, affects cotreatment1
abrinedecreases expression1
dorsomorphinaffects cotreatment, increases expression1
jinfukangaffects cotreatment, increases expression1
Resveratrolaffects cotreatment, increases expression1
Vorinostatincreases expression1
Benzo(a)pyreneincreases methylation1
Cisplatinaffects cotreatment, increases expression1
Diethylhexyl Phthalatedecreases expression1
Methotrexateincreases expression1
Plant Extractsaffects cotreatment, increases expression1
Thimerosalincreases expression1
Thiramdecreases expression1
Tobacco Smoke Pollutiondecreases expression1
Tretinoindecreases expression1
Triclosanincreases expression1

Clinical trials (associated diseases)

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