CFAP54
geneOn 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
| Field | Value |
|---|---|
| HGNC ID | HGNC:26456 |
| Approved symbol | CFAP54 |
| Name | cilia and flagella associated protein 54 |
| Location | 12q23.1 |
| Locus type | gene with protein product |
| Status | Approved |
| Aliases | FLJ31514, FLJ44112 |
| Ensembl gene | ENSG00000188596 |
| Ensembl biotype | protein_coding |
| OMIM | 621121 |
| Entrez | 144535 |
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
| Exon | Start | End |
|---|---|---|
| ENSE00001098718 | 96538384 | 96538518 |
| ENSE00001098720 | 96506928 | 96507099 |
| ENSE00001098722 | 96534062 | 96534227 |
| ENSE00001098723 | 96500834 | 96500939 |
| ENSE00001098725 | 96512986 | 96513044 |
| ENSE00001098727 | 96533792 | 96533973 |
| ENSE00001098728 | 96522088 | 96522189 |
| ENSE00001098729 | 96503886 | 96504029 |
| ENSE00001098730 | 96535515 | 96535600 |
| ENSE00001098732 | 96521857 | 96521970 |
| ENSE00001098734 | 96527246 | 96527444 |
| ENSE00001098735 | 96518928 | 96519071 |
| ENSE00002140299 | 96644178 | 96644408 |
| ENSE00002142968 | 96765077 | 96765218 |
| ENSE00002146946 | 96489577 | 96489926 |
| ENSE00002151484 | 96630551 | 96630651 |
| ENSE00002155585 | 96811736 | 96811842 |
| ENSE00002160590 | 96786675 | 96786898 |
| ENSE00002188627 | 96817775 | 96817913 |
| ENSE00002194862 | 96829014 | 96829088 |
| ENSE00002196247 | 96875118 | 96875555 |
| ENSE00002200497 | 96784717 | 96784890 |
| ENSE00002200837 | 96792329 | 96792499 |
| ENSE00002201548 | 96860819 | 96860952 |
| ENSE00003460474 | 96625718 | 96625807 |
| ENSE00003461296 | 96693722 | 96693808 |
| ENSE00003463199 | 96647875 | 96648017 |
| ENSE00003464173 | 96764151 | 96764249 |
| ENSE00003471196 | 96684648 | 96684735 |
| ENSE00003472558 | 96679600 | 96679752 |
| ENSE00003478953 | 96739956 | 96740061 |
| ENSE00003483408 | 96658211 | 96658346 |
| ENSE00003484633 | 96540837 | 96540987 |
| ENSE00003485607 | 96663830 | 96663932 |
| ENSE00003512781 | 96623767 | 96623881 |
| ENSE00003522931 | 96704743 | 96704796 |
| ENSE00003538196 | 96554182 | 96554310 |
| ENSE00003541931 | 96744020 | 96744146 |
| ENSE00003561555 | 96630093 | 96630204 |
| ENSE00003569114 | 96720405 | 96720565 |
| ENSE00003579120 | 96547902 | 96547978 |
| ENSE00003581135 | 96699971 | 96700093 |
| ENSE00003593394 | 96685029 | 96685238 |
| ENSE00003599529 | 96743402 | 96743559 |
| ENSE00003600731 | 96756458 | 96756563 |
| ENSE00003601158 | 96688916 | 96688982 |
| ENSE00003601791 | 96743731 | 96743910 |
| ENSE00003605267 | 96753743 | 96753898 |
| ENSE00003614268 | 96708608 | 96708803 |
| ENSE00003614688 | 96757495 | 96757588 |
| ENSE00003623803 | 96718443 | 96718522 |
| ENSE00003626370 | 96651588 | 96651815 |
| ENSE00003638770 | 96626813 | 96626939 |
| ENSE00003650021 | 96657882 | 96658105 |
| ENSE00003665991 | 96742439 | 96742586 |
| ENSE00003674785 | 96649891 | 96650072 |
| ENSE00003689202 | 96691128 | 96691310 |
| ENSE00003702855 | 96621590 | 96621721 |
| ENSE00003702979 | 96594291 | 96594446 |
| ENSE00003703817 | 96576585 | 96576761 |
| ENSE00003704769 | 96580920 | 96581105 |
| ENSE00003706091 | 96589427 | 96589563 |
| ENSE00003706629 | 96580597 | 96580689 |
| ENSE00003706678 | 96598645 | 96598767 |
| ENSE00003707936 | 96554676 | 96554802 |
| ENSE00003709863 | 96564644 | 96564765 |
| ENSE00003710012 | 96592490 | 96592637 |
| ENSE00003710776 | 96564468 | 96564554 |
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 ID | TPM avg | Samples expressed |
|---|---|---|
| 127485 | 1.4739 | 620 |
Top tissues by expression
245 total, by Bgee expression score (0-100, higher = more expressed):
| Tissue | Anatomy ID | Expression score | Quality |
|---|---|---|---|
| male germ line stem cell (sensu Vertebrata) in testis | CL:0000089 ∩ UBERON:0000473 | 89.66 | gold quality |
| right uterine tube | UBERON:0001302 | 87.39 | gold quality |
| colonic epithelium | UBERON:0000397 | 80.55 | gold quality |
| primordial germ cell in gonad | CL:0000670 ∩ UBERON:0000991 | 80.10 | gold quality |
| olfactory segment of nasal mucosa | UBERON:0005386 | 78.20 | gold quality |
| bone marrow cell | CL:0002092 | 76.28 | gold quality |
| ventricular zone | UBERON:0003053 | 75.65 | gold quality |
| bronchial epithelial cell | CL:0002328 | 74.50 | gold quality |
| bronchus | UBERON:0002185 | 72.97 | gold quality |
| oviduct epithelium | UBERON:0004804 | 72.05 | gold quality |
| fallopian tube | UBERON:0003889 | 69.65 | gold quality |
| adenohypophysis | UBERON:0002196 | 67.77 | gold quality |
| buccal mucosa cell | CL:0002336 | 67.54 | silver quality |
| pituitary gland | UBERON:0000007 | 66.00 | gold quality |
| testis | UBERON:0000473 | 65.85 | gold quality |
| ganglionic eminence | UBERON:0004023 | 65.20 | gold quality |
| right testis | UBERON:0004534 | 64.30 | gold quality |
| left testis | UBERON:0004533 | 64.25 | gold quality |
| tonsil | UBERON:0002372 | 63.98 | gold quality |
| left uterine tube | UBERON:0001303 | 63.89 | gold quality |
| calcaneal tendon | UBERON:0003701 | 62.92 | gold quality |
| corpus callosum | UBERON:0002336 | 62.91 | gold quality |
| stromal cell of endometrium | CL:0002255 | 62.86 | gold quality |
| body of uterus | UBERON:0009853 | 62.79 | gold quality |
| thyroid gland | UBERON:0002046 | 62.40 | gold quality |
| lower esophagus muscularis layer | UBERON:0035833 | 62.39 | gold quality |
| lower esophagus | UBERON:0013473 | 62.34 | gold quality |
| left lobe of thyroid gland | UBERON:0001120 | 61.74 | gold quality |
| right lung | UBERON:0002167 | 61.71 | gold quality |
| right lobe of thyroid gland | UBERON:0001119 | 60.85 | gold quality |
Single-cell (SCXA)
Detected in 8 experiment(s), a significant marker in 5.
| Experiment | Marker? | Max mean expression |
|---|---|---|
| E-GEOD-180759 | yes | 3295.68 |
| E-GEOD-81547 | yes | 131.46 |
| E-MTAB-5061 | yes | 13.91 |
| E-ANND-3 | yes | 11.11 |
| E-HCAD-35 | yes | 7.09 |
| E-ENAD-20 | no | 105.77 |
| E-MTAB-9067 | no | 3.63 |
| E-GEOD-137537 | no | 3.38 |
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):
| miRNA | Max score | Avg score | miRNA target_count |
|---|---|---|---|
| HSA-MIR-518D-5P | 100.00 | 67.51 | 979 |
| HSA-MIR-518E-5P | 100.00 | 67.66 | 954 |
| HSA-MIR-518F-5P | 100.00 | 67.51 | 979 |
| HSA-MIR-519A-5P | 100.00 | 67.66 | 954 |
| HSA-MIR-519B-5P | 100.00 | 67.66 | 954 |
| HSA-MIR-519C-5P | 100.00 | 67.66 | 954 |
| HSA-MIR-520C-5P | 100.00 | 67.51 | 979 |
| HSA-MIR-522-5P | 100.00 | 67.66 | 954 |
| HSA-MIR-523-5P | 100.00 | 67.66 | 954 |
| HSA-MIR-526A-5P | 100.00 | 67.51 | 979 |
| HSA-MIR-520G-5P | 99.99 | 66.76 | 658 |
| HSA-MIR-1229-3P | 99.97 | 66.49 | 906 |
| HSA-MIR-627-3P | 99.90 | 71.42 | 3316 |
| HSA-MIR-2681-5P | 99.75 | 67.64 | 1655 |
| HSA-MIR-580-3P | 99.67 | 69.23 | 1841 |
| HSA-MIR-4328 | 99.57 | 71.06 | 4094 |
| HSA-MIR-18A-3P | 99.56 | 65.68 | 1092 |
| HSA-MIR-4696 | 99.48 | 67.48 | 1040 |
| HSA-MIR-330-3P | 99.41 | 69.95 | 2521 |
| HSA-MIR-4784 | 99.15 | 67.41 | 1733 |
| HSA-MIR-7160-5P | 99.11 | 67.17 | 2207 |
| HSA-MIR-622 | 98.99 | 66.48 | 1050 |
| HSA-MIR-3150B-3P | 98.81 | 67.21 | 1728 |
| HSA-MIR-6755-3P | 98.61 | 66.90 | 834 |
| HSA-MIR-7158-3P | 98.46 | 66.45 | 728 |
| HSA-MIR-138-1-3P | 98.25 | 67.89 | 867 |
| HSA-MIR-4638-3P | 97.90 | 65.75 | 905 |
| HSA-MIR-6511A-3P | 97.60 | 66.61 | 713 |
| HSA-MIR-6511B-3P | 97.60 | 66.61 | 713 |
| HSA-MIR-320E | 97.49 | 65.96 | 865 |
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
| Organism | Symbol | Gene ID |
|---|---|---|
| mus_musculus | Cfap54 | ENSMUSG00000020014 |
| rattus_norvegicus | Cfap54 | ENSRNOG00000024494 |
Protein
Protein identifiers
Cilia- and flagella-associated protein 54 — Q96N23 (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 ID | Names | Canonical? |
|---|---|---|
| Q96N23-1 | 1 | yes |
| Q96N23-2 | 2 |
RefSeq proteins (2): NP_001293013, NP_001354814 (=MANE)
Domains & families (InterPro)
| ID | Name | Type |
|---|---|---|
| IPR027912 | CFAP54 | Family |
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:
| Category | Terms |
|---|---|
| cellular anatomical structure | 5 |
| developmental process involved in reproduction | 2 |
| epithelial cilium movement involved in extracellular fluid movement | 2 |
| male gamete generation | 1 |
| establishment of localization | 1 |
| cellular localization | 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 |
| cilium movement | 1 |
| cell motility | 1 |
| cilium-dependent cell motility | 1 |
| nervous system process | 1 |
| respiratory system process | 1 |
| spermatid development | 1 |
| flagellated sperm motility | 1 |
| motile cilium assembly | 1 |
| cellular component organization | 1 |
| cellular developmental process | 1 |
| cytoskeleton | 1 |
| microtubule | 1 |
| ciliary plasm | 1 |
| intracellular anatomical structure | 1 |
| intracellular membraneless organelle | 1 |
| intraciliary transport particle | 1 |
| membrane-bounded organelle | 1 |
| plasma membrane bounded cell projection | 1 |
Protein interactions and networks
STRING
1023 interactions, top by confidence (×1000):
| Protein A | Protein B | Partner UniProt | Score |
|---|---|---|---|
| CFAP54 | SPEF2 | Q9C093 | 707 |
| CFAP54 | C1D | Q13901 | 587 |
| CFAP54 | CFAP221 | Q4G0U5 | 571 |
| CFAP54 | CALML6 | Q8TD86 | 484 |
| CFAP54 | CALML3 | P27482 | 484 |
| CFAP54 | CALML5 | Q9NZT1 | 484 |
| CFAP54 | CALML4 | Q96GE6 | 484 |
| CFAP54 | CALM1 | P02593 | 482 |
| CFAP54 | SPAG6 | O75602 | 479 |
| CFAP54 | HYDIN | Q4G0P3 | 479 |
| CFAP54 | GALNT18 | Q6P9A2 | 439 |
| CFAP54 | RCL1 | Q9Y2P8 | 438 |
| CFAP54 | PMIS2 | A0A1W2PS18 | 434 |
| CFAP54 | CFAP52 | Q8N1V2 | 421 |
| CFAP54 | R3HDM2 | Q9Y2K5 | 413 |
IntAct
4 interactions, top by confidence:
| A | B | Type | Score |
|---|---|---|---|
| CFAP54 | NPM1 | psi-mi:“MI:0915”(physical association) | 0.400 |
| CFAP54 | AP2B1 | psi-mi:“MI:0915”(physical association) | 0.400 |
| CFAP54 | TSPY2 | psi-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):
| Classification | Count (floor) |
|---|---|
| Pathogenic | 9 |
| Likely pathogenic | 2 |
| Uncertain significance | 2 |
| Likely benign | 6 |
| Benign | 0 |
Top pathogenic / likely-pathogenic (11)
| Variant ID | HGVS | Classification |
|---|---|---|
| 3767880 | NM_001306084.2(CFAP54):c.3317del (p.Phe1106fs) | Pathogenic |
| 3767881 | NM_001306084.2(CFAP54):c.878G>A (p.Arg293His) | Pathogenic |
| 3767882 | NM_001306084.2(CFAP54):c.955C>T (p.Arg319Cys) | Pathogenic |
| 3767883 | NM_001306084.2(CFAP54):c.937G>A (p.Gly313Arg) | Pathogenic |
| 3767884 | NM_001306084.2(CFAP54):c.4885C>T (p.Arg1629Cys) | Pathogenic |
| 3768007 | CFAP54, DEL/INS NT2649 | Pathogenic |
| 3768008 | CFAP54, 18-BP INS, NT7312 | Pathogenic |
| 3768009 | CFAP54, GLU1371ALA | Pathogenic |
| 3768010 | CFAP54, PRO2187SER | Pathogenic |
| 3778415 | NM_001306084.2(CFAP54):c.4713_4716del (p.Phe1571fs) | Likely pathogenic |
| 4526608 | NM_001306084.2(CFAP54):c.8644_8645del (p.Leu2882fs) | Likely pathogenic |
SpliceAI
11568 predictions. Top by Δscore:
| Variant | Effect | Δscore |
|---|---|---|
| 12:96489923:GTTG:G | donor_gain | 1.0000 |
| 12:96489926:GGTA:G | donor_loss | 1.0000 |
| 12:96489927:G:GG | donor_gain | 1.0000 |
| 12:96489928:T:A | donor_loss | 1.0000 |
| 12:96500936:GAAA:G | donor_gain | 1.0000 |
| 12:96500937:AAAGT:A | donor_loss | 1.0000 |
| 12:96500938:AAGTA:A | donor_loss | 1.0000 |
| 12:96500939:AGT:A | donor_loss | 1.0000 |
| 12:96500940:G:C | donor_loss | 1.0000 |
| 12:96500940:G:GG | donor_gain | 1.0000 |
| 12:96500941:T:G | donor_loss | 1.0000 |
| 12:96503879:GTTTC:G | acceptor_loss | 1.0000 |
| 12:96503880:TTTCA:T | acceptor_loss | 1.0000 |
| 12:96503881:TTCA:T | acceptor_loss | 1.0000 |
| 12:96503882:TCA:T | acceptor_loss | 1.0000 |
| 12:96503883:CAGG:C | acceptor_loss | 1.0000 |
| 12:96503884:A:C | acceptor_loss | 1.0000 |
| 12:96503964:G:GT | donor_gain | 1.0000 |
| 12:96504001:GCTT:G | donor_gain | 1.0000 |
| 12:96504030:G:GG | donor_gain | 1.0000 |
| 12:96506926:A:AG | acceptor_gain | 1.0000 |
| 12:96506927:G:GG | acceptor_gain | 1.0000 |
| 12:96527384:G:GT | donor_gain | 1.0000 |
| 12:96527428:A:T | donor_gain | 1.0000 |
| 12:96527440:GA:G | donor_gain | 1.0000 |
| 12:96527441:A:AG | donor_gain | 1.0000 |
| 12:96527441:A:G | donor_gain | 1.0000 |
| 12:96527445:G:GG | donor_gain | 1.0000 |
| 12:96533790:A:AG | acceptor_gain | 1.0000 |
| 12:96533791:G:GG | acceptor_gain | 1.0000 |
AlphaMissense
20344 scored. Top likely-pathogenic:
| Variant | Protein change | am_pathogenicity |
|---|---|---|
| 12:96626839:T:C | F1335L | 0.997 |
| 12:96626841:T:A | F1335L | 0.997 |
| 12:96626841:T:G | F1335L | 0.997 |
| 12:96792452:T:A | W2935R | 0.997 |
| 12:96792452:T:C | W2935R | 0.997 |
| 12:96651612:T:A | W1633R | 0.996 |
| 12:96651612:T:C | W1633R | 0.996 |
| 12:96685045:T:A | W1941R | 0.996 |
| 12:96685045:T:C | W1941R | 0.996 |
| 12:96625772:T:A | V1314D | 0.995 |
| 12:96658059:T:A | W1760R | 0.995 |
| 12:96658059:T:C | W1760R | 0.995 |
| 12:96757515:T:C | L2656P | 0.995 |
| 12:96784827:T:A | W2798R | 0.995 |
| 12:96784827:T:C | W2798R | 0.995 |
| 12:96580986:G:C | A986P | 0.994 |
| 12:96626840:T:C | F1335S | 0.994 |
| 12:96644299:T:A | W1480R | 0.994 |
| 12:96644299:T:C | W1480R | 0.994 |
| 12:96651601:G:C | R1629P | 0.994 |
| 12:96594339:A:C | S1137R | 0.993 |
| 12:96594341:C:A | S1137R | 0.993 |
| 12:96594341:C:G | S1137R | 0.993 |
| 12:96658264:T:C | L1793P | 0.993 |
| 12:96651595:C:A | A1627D | 0.992 |
| 12:96651622:T:C | L1636P | 0.992 |
| 12:96756538:A:C | S2641R | 0.992 |
| 12:96756540:C:A | S2641R | 0.992 |
| 12:96756540:C:G | S2641R | 0.992 |
| 12:96786780:T:C | L2854P | 0.992 |
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.
| Disease | Classification | Inheritance |
|---|---|---|
| ciliary dyskinesia, primary, 54 | Strong | AR |
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):
| HPO | Term |
|---|---|
| HP:0000007 | Autosomal recessive inheritance |
| HP:0000798 | Oligozoospermia |
| HP:0002090 | Pneumonia |
| HP:0002099 | Asthma |
| HP:0002110 | Bronchiectasis |
| HP:0002837 | Recurrent bronchitis |
| HP:0003251 | Male infertility |
| HP:0011462 | Young adult onset |
| HP:0011463 | Childhood onset |
| HP:0012207 | Reduced sperm motility |
| HP:0025708 | Early young adult onset |
| HP:0031245 | Productive cough |
| HP:0032558 | Absent sperm flagella |
| HP:0032559 | Short sperm flagella |
| HP:0032560 | Coiled sperm flagella |
| HP:0033393 | Irregularly shaped sperm tail |
| HP:0033524 | Abnormal sperm axoneme morphology |
| HP:0034011 | Reduced progressive sperm motility |
| HP:0034811 | Bent sperm flagella |
| HP:0100750 | Atelectasis |
| HP:6000135 | Low semen volume |
GWAS associations
6 associations (top):
| Study | Trait | p-value |
|---|---|---|
| GCST000837_3 | Weight | 4.000000e-06 |
| GCST005050_6 | Obstructive sleep apnea during REM sleep (apnea hypopnea index) | 6.000000e-07 |
| GCST007231_5 | Tuberculosis | 3.000000e-06 |
| GCST007637_21 | Diffusing capacity of carbon monoxide | 2.000000e-06 |
| GCST009222_4 | Corpus callosum posterior volume | 7.000000e-06 |
| GCST009391_187 | Metabolite levels | 2.000000e-06 |
EFO canonical traits (4, from GWAS)
| EFO ID | Trait name |
|---|---|
| EFO:0004338 | body weight |
| EFO:0008455 | sleep apnea measurement during REM sleep |
| EFO:0009369 | diffusing capacity of the lung for carbon monoxide |
| EFO:0010482 | gamma-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.
| Chemical | Actions (top 5) | PubMed papers |
|---|---|---|
| Smoke | decreases expression, increases abundance, increases expression | 2 |
| FR900359 | increases phosphorylation | 1 |
| sodium arsenite | decreases expression | 1 |
| 2-palmitoylglycerol | increases expression | 1 |
| Air Pollutants | increases expression, increases abundance | 1 |
| Arsenic | affects methylation | 1 |
| Caffeine | increases phosphorylation | 1 |
| Tobacco Smoke Pollution | affects expression | 1 |
| Aflatoxin B1 | decreases methylation | 1 |
Clinical trials (associated diseases)
0 trials via MONDO — disease-level, not drug-specific.
Related Atlas pages
- Associated diseases: ciliary dyskinesia, primary, 54
- Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): ciliary dyskinesia, primary, 54, spermatogenic failure 98, tuberculosis