IFT22

Summary

IFT22 (intraflagellar transport 22, HGNC:21895) is a protein-coding gene on chromosome 7q22.1, encoding Intraflagellar transport protein 22 homolog (Q9H7X7). Small GTPase-like component of the intraflagellar transport (IFT) complex B.

Predicted to enable GTPase activity. Predicted to be involved in intracellular protein transport. Part of intraciliary transport particle B.

Source: NCBI Gene 64792 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 36 total
• MANE Select transcript: NM_022777

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:21895
Approved symbol	IFT22
Name	intraflagellar transport 22
Location	7q22.1
Locus type	gene with protein product
Status	Approved
Aliases	FLJ14117, FLJ13225, DKFZp761N0823, FAP9, CFAP9
Ensembl gene	ENSG00000128581
Ensembl biotype	protein_coding
OMIM	620505
Entrez	64792

Gene structure

Transcript identifiers

Ensembl transcripts: 11 — 5 protein_coding, 3 retained_intron, 2 nonsense_mediated_decay, 1 protein_coding_CDS_not_defined

ENST00000315322, ENST00000422177, ENST00000430911, ENST00000437644, ENST00000440362, ENST00000468833, ENST00000485695, ENST00000495166, ENST00000498704, ENST00000517481, ENST00000621899

RefSeq mRNA: 6 — MANE Select: NM_022777 NM_001130820, NM_001130821, NM_001130822, NM_001287525, NM_001287526, NM_022777

CCDS: CCDS47670, CCDS47671, CCDS5719

Canonical transcript exons

ENST00000315322 — 5 exons

Exon	Start	End
ENSE00001809756	101310914	101315282
ENSE00001909958	101321671	101321812
ENSE00003490265	101318124	101318213
ENSE00003603155	101316340	101316542
ENSE00003631224	101318956	101319032

Expression profiles

Bgee: expression breadth ubiquitous, 273 present calls, max score 98.36.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 20.5783 / max 223.7382, expressed in 1735 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
85332	20.5783	1735

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
bronchial epithelial cell	CL:0002328	98.36	gold quality
left testis	UBERON:0004533	97.06	gold quality
right testis	UBERON:0004534	96.73	gold quality
adult organism	UBERON:0007023	96.46	gold quality
mucosa of paranasal sinus	UBERON:0005030	96.45	gold quality
sperm	CL:0000019	96.08	gold quality
right uterine tube	UBERON:0001302	95.98	gold quality
male germ cell	CL:0000015	95.46	gold quality
testis	UBERON:0000473	95.30	gold quality
epithelium of bronchus	UBERON:0002031	94.49	gold quality
bronchus	UBERON:0002185	94.29	gold quality
caput epididymis	UBERON:0004358	94.24	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	94.22	gold quality
corpus epididymis	UBERON:0004359	93.27	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	93.12	gold quality
prefrontal cortex	UBERON:0000451	92.93	gold quality
anterior cingulate cortex	UBERON:0009835	92.56	gold quality
cingulate cortex	UBERON:0003027	92.55	gold quality
nucleus accumbens	UBERON:0001882	92.31	gold quality
ventricular zone	UBERON:0003053	92.20	gold quality
amygdala	UBERON:0001876	92.09	gold quality
epithelium of nasopharynx	UBERON:0001951	92.05	gold quality
nasopharynx	UBERON:0001728	92.03	gold quality
pituitary gland	UBERON:0000007	91.95	gold quality
adenohypophysis	UBERON:0002196	91.93	gold quality
caudate nucleus	UBERON:0001873	91.85	gold quality
cortical plate	UBERON:0005343	91.53	gold quality
putamen	UBERON:0001874	91.12	gold quality
islet of Langerhans	UBERON:0000006	90.91	gold quality
neocortex	UBERON:0001950	90.89	gold quality

Single-cell (SCXA)

Detected in 6 experiment(s), a significant marker in 4.

Experiment	Marker?	Max mean expression
E-HCAD-1	yes	25.85
E-CURD-114	yes	11.77
E-MTAB-9388	yes	8.02
E-CURD-135	no	708.02
E-MTAB-6678	no	3.38
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

69 targeting IFT22, 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-4776-3P	100.00	68.73	1340
HSA-MIR-4510	100.00	66.60	2050
HSA-MIR-6127	100.00	66.76	2188
HSA-MIR-6129	100.00	66.46	2080
HSA-MIR-6130	100.00	66.69	2012
HSA-MIR-6133	100.00	66.48	2064
HSA-MIR-1193	100.00	65.93	529
HSA-MIR-4482-3P	99.98	72.50	3147
HSA-MIR-6888-3P	99.97	65.95	1170
HSA-MIR-6778-3P	99.96	67.29	2693
HSA-MIR-302E	99.96	70.74	2669
HSA-MIR-9983-3P	99.94	71.48	3631
HSA-MIR-335-3P	99.93	73.36	4958
HSA-MIR-129-5P	99.88	70.26	3273
HSA-MIR-579-3P	99.86	71.66	3628
HSA-MIR-664B-3P	99.84	71.65	3590
HSA-MIR-548AJ-5P	99.78	71.12	3085
HSA-MIR-548F-5P	99.78	71.02	3093
HSA-MIR-548G-5P	99.78	71.12	3085
HSA-MIR-548X-5P	99.78	71.12	3085
HSA-MIR-3680-3P	99.75	72.51	3095
HSA-MIR-4524A-3P	99.72	66.85	2406
HSA-MIR-6134	99.63	65.68	1537
HSA-MIR-4743-3P	99.62	68.12	2095
HSA-MIR-4516	99.61	67.78	3390
HSA-MIR-6832-5P	99.58	64.82	1132
HSA-MIR-3123	99.47	67.15	2693
HSA-MIR-372-5P	99.41	69.11	2299
HSA-MIR-302A-5P	99.39	68.21	1913
HSA-MIR-504-3P	99.30	67.18	1745

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
danio_rerio	ift22	ENSDARG00000020822
mus_musculus	Ift22	ENSMUSG00000007987

Protein

Protein identifiers

Intraflagellar transport protein 22 homolog — Q9H7X7 (reviewed: Q9H7X7)

Alternative names: Rab-like protein 5

All UniProt accessions (2): Q9H7X7, F8WDY0

UniProt curated annotations — full annotation on UniProt →

Function. Small GTPase-like component of the intraflagellar transport (IFT) complex B.

Subunit / interactions. Component of the IFT complex B, at least composed of IFT20, IFT22, IFT25, IFT27, IFT46, IFT52, TRAF3IP1/IFT54, IFT57, IFT74, IFT80, IFT81, and IFT88. Interacts with IFT88. Interacts with CFAP61.

Subcellular location. Cell projection. Cilium.

Similarity. Belongs to the small GTPase superfamily. Rab family.

Isoforms (3)

UniProt ID	Names	Canonical?
Q9H7X7-1	1	yes
Q9H7X7-2	2
Q9H7X7-3	3

RefSeq proteins (6): NP_001124292, NP_001124293, NP_001124294, NP_001274454, NP_001274455, NP_073614* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR027417	P-loop_NTPase	Homologous_superfamily

Pfam: PF08477

UniProt features (7 total): binding site 3, splice variant 2, chain 1, modified residue 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9H7X7-F1	92.12	0.76

Functional residue map

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

Ligand- & substrate-binding residues (3): 10–17; 63–67; 123–126

Post-translational modifications (1): 137

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-5620924	Intraflagellar transport

MSigDB gene sets: 136 (showing top): GOBP_INTRACELLULAR_PROTEIN_TRANSPORT, GOCC_MICROTUBULE_ORGANIZING_CENTER, GOBP_CILIUM_ORGANIZATION, GOCC_CENTROSOME, GOBP_ORGANELLE_ASSEMBLY, RFX1_02, GOBP_CELL_PROJECTION_ORGANIZATION, TGGAAA_NFAT_Q4_01, GOCC_CILIARY_TIP, GOCC_INTRACILIARY_TRANSPORT_PARTICLE_B, GOCC_INTRACILIARY_TRANSPORT_PARTICLE, GOCC_CILIUM, GOMF_GTPASE_ACTIVITY, GOMF_HYDROLASE_ACTIVITY_ACTING_ON_ACID_ANHYDRIDES, DODD_NASOPHARYNGEAL_CARCINOMA_DN

GO Biological Process (3): intracellular protein transport (GO:0006886), intraciliary anterograde transport (GO:0035720), cilium assembly (GO:0060271)

GO Molecular Function (3): GTPase activity (GO:0003924), GTP binding (GO:0005525), nucleotide binding (GO:0000166)

GO Cellular Component (7): centrosome (GO:0005813), cilium (GO:0005929), endomembrane system (GO:0012505), intraciliary transport particle A (GO:0030991), intraciliary transport particle B (GO:0030992), ciliary tip (GO:0097542), cell projection (GO:0042995)

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
Assembly of the 9+0 primary cilium	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
intraciliary transport particle	3
cellular anatomical structure	3
protein-containing complex	2
intracellular protein localization	1
protein transport	1
intracellular transport	1
intraciliary transport	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
ribonucleoside triphosphate phosphatase activity	1
guanyl ribonucleotide binding	1
purine ribonucleoside triphosphate binding	1
nucleoside phosphate binding	1
heterocyclic compound binding	1
centriole	1
microtubule organizing center	1
membrane-bounded organelle	1
plasma membrane bounded cell projection	1
vacuole	1
plasma membrane	1
cilium	1

Protein interactions and networks

STRING

1390 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
IFT22	IFT27	Q9BW83	996
IFT22	IFT74	Q96LB3	994
IFT22	IFT25	Q9Y547	993
IFT22	IFT46	Q9NQC8	992
IFT22	IFT81	Q8WYA0	990
IFT22	IFT52	Q9Y366	989
IFT22	IFT70B	Q8N4P2	983
IFT22	IFT54	Q8TDR0	976
IFT22	IFT57	Q9NWB7	959
IFT22	IFT20	Q8IY31	945
IFT22	IFT88	Q13099	916
IFT22	IFT56	A0AVF1	905
IFT22	IFT172	Q9UG01	888
IFT22	IFT38	Q96AJ1	882
IFT22	IFT80	Q9P2H3	849

IntAct

74 interactions, top by confidence:

A	B	Type	Score
IFT56	IFT70A	psi-mi:“MI:0914”(association)	0.790
IFT70A	IFT56	psi-mi:“MI:0914”(association)	0.790
IFT70B	IFT56	psi-mi:“MI:0914”(association)	0.790
IFT27	IFT56	psi-mi:“MI:0914”(association)	0.690
IFT25	IFT56	psi-mi:“MI:0914”(association)	0.690
IFT22	IFT56	psi-mi:“MI:0914”(association)	0.640
IFT46	IFT56	psi-mi:“MI:0914”(association)	0.640
IFT88	IFT56	psi-mi:“MI:0914”(association)	0.640
IFT57	IFT56	psi-mi:“MI:0914”(association)	0.640
IFT172	IFT56	psi-mi:“MI:0914”(association)	0.590
ARL13B	STK25	psi-mi:“MI:0914”(association)	0.530
ODAD3	CCDC22	psi-mi:“MI:0914”(association)	0.530
JPH4	ZSWIM8	psi-mi:“MI:0914”(association)	0.530

BioGRID (78): IFT22 (Affinity Capture-MS), IFT22 (Affinity Capture-MS), IFT22 (Affinity Capture-MS), IFT22 (Affinity Capture-MS), IFT22 (Proximity Label-MS), IFT22 (Proximity Label-MS), IFT22 (Affinity Capture-MS), IFT22 (Affinity Capture-MS), IFT22 (Affinity Capture-MS), IFT22 (Affinity Capture-MS), IFT22 (Affinity Capture-MS), IFT22 (Affinity Capture-MS), IFT22 (Affinity Capture-MS), IFT22 (Affinity Capture-MS), IFT22 (Affinity Capture-MS)

ESM2 similar proteins: A2AGL3, A4FUD6, A4IHM6, B0LPN4, E9PZQ0, O35626, O94844, P16960, P51157, P51158, Q12829, Q15413, Q32LJ6, Q32NS2, Q3SWY9, Q3SX43, Q4R4K5, Q5E9J4, Q5F361, Q5FVD6, Q5FVJ7, Q5HYI8, Q5M8K8, Q5R8I6, Q5RCC1, Q5RFI2, Q5XGS8, Q5ZKR4, Q63486, Q66JN8, Q6GPS4, Q6NRC7, Q6TNS7, Q7L523, Q7SXV1, Q7ZUV0, Q80X95, Q8BHL5, Q8K0F1, Q91V93

Diamond homologs: A8HME3, O77683, P52198, P61587, P61588, Q381A3, Q4R4K5, Q567Y6, Q5E9J4, Q5FVJ7, Q5M8K8, Q5R9F4, Q6SA80, Q9DAI2, Q9H7X7, Q9QYM5, Q10133, Q54KM9, P06780

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 53 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
Intraflagellar transport	14	82.5×	2e-22

GO biological processes:

GO term	Partners	Fold	FDR
intraciliary anterograde transport	13	240.2×	2e-27
intraciliary transport	11	128.7×	3e-19
negative regulation of keratinocyte proliferation	5	73.1×	4e-07
keratinocyte proliferation	5	60.5×	1e-06
non-motile cilium assembly	8	48.4×	4e-10
smoothened signaling pathway	10	37.8×	1e-11
heart looping	5	27.9×	5e-05
cilium assembly	16	24.5×	2e-16

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	32
Likely benign	3
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

621 predictions. Top by Δscore:

Variant	Effect	Δscore
7:101315281:CGCT:C	acceptor_gain	1.0000
7:101315284:T:C	acceptor_gain	1.0000
7:101315284:T:TC	acceptor_gain	1.0000
7:101316333:T:A	donor_gain	1.0000
7:101316338:A:AC	donor_gain	1.0000
7:101316339:C:CC	donor_gain	1.0000
7:101316339:CA:C	donor_gain	1.0000
7:101316353:T:TA	donor_gain	1.0000
7:101316399:CA:C	donor_gain	1.0000
7:101316408:T:TA	donor_gain	1.0000
7:101316460:T:TA	donor_gain	1.0000
7:101316538:CAAAC:C	acceptor_gain	1.0000
7:101316539:AAAC:A	acceptor_gain	1.0000
7:101316540:AAC:A	acceptor_gain	1.0000
7:101316541:AC:A	acceptor_gain	1.0000
7:101316542:CC:C	acceptor_gain	1.0000
7:101316542:CCTG:C	acceptor_loss	1.0000
7:101316543:C:CA	acceptor_loss	1.0000
7:101316543:C:CC	acceptor_gain	1.0000
7:101318122:A:AC	donor_gain	1.0000
7:101318123:C:CC	donor_gain	1.0000
7:101318126:A:AC	donor_gain	1.0000
7:101318126:AGCAT:A	donor_gain	1.0000
7:101318127:G:C	donor_gain	1.0000
7:101321666:CTTA:C	donor_loss	1.0000
7:101321667:TTA:T	donor_loss	1.0000
7:101321668:TAC:T	donor_loss	1.0000
7:101321669:A:AC	donor_gain	1.0000
7:101321669:A:C	donor_loss	1.0000
7:101321669:AC:A	donor_gain	1.0000

AlphaMissense

1241 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
7:101318146:A:G	W62R	0.999
7:101318146:A:T	W62R	0.999
7:101321682:C:G	G10R	0.999
7:101321682:C:T	G10R	0.999
7:101318144:C:A	W62C	0.998
7:101318144:C:G	W62C	0.998
7:101319022:G:A	T17I	0.998
7:101321682:C:A	G10W	0.998
7:101318143:C:G	D63H	0.997
7:101318956:C:A	R39M	0.997
7:101319025:T:A	K16I	0.997
7:101321681:C:T	G10E	0.997
7:101318211:A:G	I40T	0.996
7:101318213:C:A	R39S	0.996
7:101318213:C:G	R39S	0.996
7:101318956:C:G	R39T	0.996
7:101316501:C:T	G83E	0.995
7:101318142:T:G	D63A	0.995
7:101318148:A:G	L61P	0.995
7:101318208:A:G	L41P	0.995
7:101319013:G:T	A20D	0.995
7:101319014:C:G	A20P	0.995
7:101319028:C:T	G15E	0.995
7:101318142:T:C	D63G	0.994
7:101318145:C:G	W62S	0.994
7:101318962:C:T	G37E	0.994
7:101318142:T:A	D63V	0.993
7:101319028:C:A	G15V	0.993
7:101318963:C:G	G37R	0.992
7:101318963:C:T	G37R	0.992

dbSNP variants (sampled 300 via entrez): RS1000320641 (7:101314479 A>G), RS1000394365 (7:101314772 C>G), RS1000400338 (7:101319221 G>C), RS1000618668 (7:101310701 A>G), RS1000628953 (7:101313620 C>G,T), RS1000951520 (7:101310461 C>A,G), RS1001149101 (7:101323164 A>C), RS1001178605 (7:101323521 C>T), RS1001576927 (7:101321552 G>A,C), RS1001605748 (7:101312126 G>A), RS1001633696 (7:101312334 C>G), RS1001975993 (7:101322864 A>C), RS1002219875 (7:101311775 G>A), RS1002365710 (7:101317299 C>T), RS1002396764 (7:101317560 G>A)

Disease associations

OMIM: gene MIM:620505 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST007843_12	Rheumatoid arthritis	8.000000e-09

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	increases expression, affects expression, affects cotreatment	6
Smoke	increases abundance, increases expression, decreases expression	2
Tobacco Smoke Pollution	decreases expression	2
beta-lapachone	decreases expression	1
arsenite	affects binding, increases reaction	1
zinc chromate	decreases expression, increases abundance	1
chromium hexavalent ion	decreases expression, increases abundance	1
Air Pollutants	increases abundance, increases expression	1
Arsenic	affects methylation	1
Vehicle Emissions	increases abundance, increases expression	1
Carbamazepine	affects expression	1
Demecolcine	increases expression	1
Estradiol	decreases expression	1
Ethyl Methanesulfonate	increases expression	1
Formaldehyde	increases expression	1
Hydralazine	affects cotreatment, increases expression	1
Methyl Methanesulfonate	increases expression	1
Rotenone	decreases expression	1
Thiram	decreases expression	1
Cyclosporine	increases expression	1
Antirheumatic Agents	increases expression	1
Cadmium Chloride	decreases expression	1
Copper Sulfate	decreases expression	1
Vitamin K 3	affects expression	1
Particulate Matter	increases abundance, increases expression	1

Clinical trials (associated diseases)

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