IFT70A

Summary

IFT70A (intraflagellar transport 70A, HGNC:25853) is a protein-coding gene on chromosome 2q31.2, encoding Intraflagellar transport protein 70A (Q86WT1). Required for polyglutamylation of axonemal tubulin.

Predicted to enable intraciliary transport particle B binding activity. Predicted to be involved in intraciliary transport. Predicted to be located in centrosome. Predicted to be part of intraciliary transport particle B. Predicted to be active in axonemal microtubule.

Source: NCBI Gene 92104 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 86 total
• MANE Select transcript: NM_152275

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:25853
Approved symbol	IFT70A
Name	intraflagellar transport 70A
Location	2q31.2
Locus type	gene with protein product
Status	Approved
Aliases	FLJ13946, FAP259, CFAP259
Ensembl gene	ENSG00000197557
Ensembl biotype	protein_coding
OMIM	620741
Entrez	92104

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000355689

RefSeq mRNA: 1 — MANE Select: NM_152275 NM_152275

CCDS: CCDS2276

Canonical transcript exons

ENST00000355689 — 1 exons

Exon	Start	End
ENSE00001406487	177612999	177618742

Expression profiles

Bgee: expression breadth ubiquitous, 198 present calls, max score 86.90.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 2.1253 / max 35.1846, expressed in 1236 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
32003	2.0748	1211
202483	0.0505	22

Top tissues by expression

288 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	86.90	gold quality
bronchial epithelial cell	CL:0002328	85.05	gold quality
endothelial cell	CL:0000115	82.02	silver quality
epithelium of bronchus	UBERON:0002031	80.20	gold quality
bronchus	UBERON:0002185	78.81	gold quality
choroid plexus epithelium	UBERON:0003911	78.08	gold quality
islet of Langerhans	UBERON:0000006	76.67	gold quality
ventricular zone	UBERON:0003053	75.51	gold quality
calcaneal tendon	UBERON:0003701	75.26	gold quality
corpus epididymis	UBERON:0004359	74.86	gold quality
testis	UBERON:0000473	73.21	gold quality
right uterine tube	UBERON:0001302	73.16	gold quality
right testis	UBERON:0004534	72.94	gold quality
left testis	UBERON:0004533	72.88	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	72.34	gold quality
stromal cell of endometrium	CL:0002255	71.58	gold quality
cortical plate	UBERON:0005343	71.13	gold quality
ganglionic eminence	UBERON:0004023	70.78	gold quality
mucosa of paranasal sinus	UBERON:0005030	70.58	silver quality
rectum	UBERON:0001052	69.90	gold quality
caput epididymis	UBERON:0004358	69.79	gold quality
adrenal tissue	UBERON:0018303	69.34	gold quality
smooth muscle tissue	UBERON:0001135	69.15	gold quality
pancreas	UBERON:0001264	68.95	gold quality
pigmented layer of retina	UBERON:0001782	68.92	gold quality
gall bladder	UBERON:0002110	68.90	gold quality
right adrenal gland cortex	UBERON:0035827	68.54	gold quality
right adrenal gland	UBERON:0001233	68.52	gold quality
fallopian tube	UBERON:0003889	67.34	gold quality
right lobe of thyroid gland	UBERON:0001119	66.96	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	3.85

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

150 targeting IFT70A, 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-3163	100.00	77.23	8605
HSA-MIR-98-3P	100.00	74.08	3907
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-LET-7A-3P	100.00	74.03	3932
HSA-LET-7B-3P	100.00	74.08	3913
HSA-LET-7F-1-3P	100.00	74.02	3928
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-4533	100.00	69.48	2758
HSA-MIR-4668-3P	100.00	68.74	2635
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-548AW	99.99	72.57	3559
HSA-MIR-4531	99.99	69.70	3181
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-548N	99.98	71.94	4170
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-548P	99.98	72.25	3784
HSA-LET-7F-2-3P	99.98	70.98	2588
HSA-MIR-1185-1-3P	99.98	71.04	2593
HSA-MIR-1185-2-3P	99.98	71.04	2593
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-548AN	99.97	70.91	2817
HSA-MIR-3658	99.96	73.87	4379
HSA-MIR-548AA	99.96	70.64	3753
HSA-MIR-548AP-3P	99.96	70.64	3753
HSA-MIR-548T-3P	99.96	70.64	3753
HSA-MIR-548AB	99.95	71.31	3488

Cross-species orthologs

7 orthologs

Organism	Symbol	Gene ID
danio_rerio	ift70	ENSDARG00000038024
mus_musculus	Ift70a1	ENSMUSG00000075271
mus_musculus	Ift70a2	ENSMUSG00000075272
mus_musculus	Ift70b	ENSMUSG00000075273
rattus_norvegicus	Ift70a2	ENSRNOG00000052519
drosophila_melanogaster	Ttc30	FBGN0032470
caenorhabditis_elegans	dyf-1	WBGENE00001117

Paralogs (1): IFT70B (ENSG00000196659)

Protein

Protein identifiers

Intraflagellar transport protein 70A — Q86WT1 (reviewed: Q86WT1)

Alternative names: Tetratricopeptide repeat protein 30A

All UniProt accessions (1): Q86WT1

UniProt curated annotations — full annotation on UniProt →

Function. Required for polyglutamylation of axonemal tubulin. Plays a role in anterograde intraflagellar transport (IFT), the process by which cilia precursors are transported from the base of the cilium to the site of their incorporation at the tip.

Subcellular location. Cell projection. Cilium.

Similarity. Belongs to the TTC30/dfy-1/fleer family.

RefSeq proteins (1): NP_689488* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR011990	TPR-like_helical_dom_sf	Homologous_superfamily
IPR019734	TPR_rpt	Repeat
IPR039941	TT30	Family

Pfam: PF13432

UniProt features (13 total): repeat 8, sequence variant 2, chain 1, sequence conflict 1, coiled-coil region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q86WT1-F1	93.09	0.87

Function

Pathways and Gene Ontology

Reactome pathways

3 pathways

ID	Pathway
R-HSA-5620924	Intraflagellar transport
R-HSA-1852241	Organelle biogenesis and maintenance
R-HSA-5617833	Cilium Assembly

MSigDB gene sets: 115 (showing top): BROWNE_HCMV_INFECTION_48HR_DN, GOBP_CILIUM_ORGANIZATION, MODULE_171, GOBP_CELL_PROJECTION_ORGANIZATION, CHIANG_LIVER_CANCER_SUBCLASS_CTNNB1_UP, GOCC_CYTOPLASMIC_REGION, TCCCRNNRTGC_UNKNOWN, GOCC_INTRACILIARY_TRANSPORT_PARTICLE_B, GOCC_INTRACILIARY_TRANSPORT_PARTICLE, GOCC_CYTOPLASMIC_MICROTUBULE, GOCC_CILIUM, WILCOX_RESPONSE_TO_PROGESTERONE_UP, MODULE_292, FEVR_CTNNB1_TARGETS_DN, GOBP_INTRACILIARY_TRANSPORT

GO Biological Process (2): intraciliary transport (GO:0042073), cell projection organization (GO:0030030)

GO Molecular Function (2): intraciliary transport particle B binding (GO:0120170), protein binding (GO:0005515)

GO Cellular Component (4): axonemal microtubule (GO:0005879), intraciliary transport particle B (GO:0030992), cilium (GO:0005929), cell projection (GO:0042995)

Reactome top-level categories

Rollup of top-2 pathways:

Category	Pathways
Assembly of the 9+0 primary cilium	1
Organelle biogenesis and maintenance	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
intraciliary transport particle	2
cilium	1
transport along microtubule	1
cilium organization	1
cellular component organization	1
protein-containing complex binding	1
binding	1
cytoplasmic microtubule	1
axoneme	1
protein-containing complex	1
membrane-bounded organelle	1
plasma membrane bounded cell projection	1
cellular anatomical structure	1

Protein interactions and networks

STRING

684 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
IFT70A	IFT74	Q96LB3	801
IFT70A	IFT46	Q9NQC8	709
IFT70A	IFT52	Q9Y366	707
IFT70A	IFT56	A0AVF1	704
IFT70A	IFT22	Q9H7X7	630
IFT70A	IFT88	Q13099	623
IFT70A	IFT81	Q8WYA0	605
IFT70A	IFT27	Q9BW83	595
IFT70A	LYG1	Q8N1E2	578
IFT70A	IFT57	Q9NWB7	567
IFT70A	IFT172	Q9UG01	549
IFT70A	IFT80	Q9P2H3	540
IFT70A	IFT140	Q96RY7	535
IFT70A	TTC29	Q8NA56	525
IFT70A	IFT54	Q8TDR0	514

IntAct

63 interactions, top by confidence:

A	B	Type	Score
IFT57	CORO1A	psi-mi:“MI:0914”(association)	0.790
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
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
IFT22	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
IFT74	IFT56	psi-mi:“MI:0914”(association)	0.510
IFT80	IFT56	psi-mi:“MI:0914”(association)	0.510

BioGRID (82): TTC30A (Affinity Capture-MS), TTC30A (Affinity Capture-MS), TTC30A (Affinity Capture-MS), TTC30A (Affinity Capture-MS), UBXN10 (Reconstituted Complex), TTC30A (Affinity Capture-MS), CLUAP1 (Affinity Capture-MS), IFT81 (Affinity Capture-MS), TRAF3IP1 (Affinity Capture-MS), IFT52 (Affinity Capture-MS), IFT88 (Affinity Capture-MS), IFT46 (Affinity Capture-MS), IFT80 (Affinity Capture-MS), IFT22 (Affinity Capture-MS), TTC30A (Affinity Capture-MS)

ESM2 similar proteins: A1L1K3, A2AKQ8, A2VE45, A4IHR1, A6H739, A7YE96, A8WE67, A8XBR9, B0WYS3, B2RYD6, B3M1B7, B3P0R4, B4GF49, B4HE12, B4JHK2, B4K4X6, B4M4L4, B4NKT1, B4PS83, B4QZ45, E9Q6P5, Q0HA38, Q13099, Q16JL4, Q16NZ8, Q296H8, Q29L58, Q4QQS2, Q4QR29, Q5RE52, Q5RFR8, Q61371, Q62018, Q6DEU9, Q6INU8, Q6PD62, Q7PRA4, Q7Z4L5, Q86TV6, Q86WT1

Diamond homologs: A2AKQ8, A2VE45, A4IHR1, A6H739, A7YE96, A8XBR9, B2RYD6, Q16JL4, Q29L58, Q4QQS2, Q6INU8, Q7PRA4, Q86WT1, Q8I7G4, Q8N4P2, Q99J38, Q9CY00, Q9VK41

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 36 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	107.9×	1e-24

GO biological processes:

GO term	Partners	Fold	FDR
intraciliary anterograde transport	14	413.9×	3e-34
intraciliary transport	10	187.2×	2e-19
negative regulation of keratinocyte proliferation	5	117.0×	2e-08
keratinocyte proliferation	5	96.8×	6e-08
non-motile cilium assembly	7	67.8×	4e-10
smoothened signaling pathway	10	60.4×	3e-14
heart looping	5	44.6×	3e-06
cilium assembly	15	36.8×	7e-19

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	80
Likely benign	6
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

151 predictions. Top by Δscore:

Variant	Effect	Δscore
2:177616759:T:C	donor_gain	1.0000
2:177616710:ATT:A	donor_gain	0.9800
2:177617053:A:AC	donor_gain	0.9700
2:177617119:T:TA	donor_gain	0.9300
2:177616710:A:AC	donor_gain	0.9100
2:177616776:C:A	donor_gain	0.9100
2:177616710:ATTC:A	donor_gain	0.8900
2:177616758:A:AC	donor_gain	0.8900
2:177616758:AT:A	donor_gain	0.8900
2:177613169:T:TC	acceptor_gain	0.8800
2:177615834:A:AC	acceptor_gain	0.8700
2:177615835:C:CC	acceptor_gain	0.8700
2:177616775:T:TA	donor_gain	0.8600
2:177616949:A:AC	donor_gain	0.8500
2:177616742:T:A	donor_gain	0.8300
2:177615830:TCA:T	acceptor_gain	0.7900
2:177617028:T:A	donor_gain	0.7700
2:177616704:C:CT	donor_gain	0.7600
2:177616705:T:TT	donor_gain	0.7600
2:177617122:T:TA	donor_gain	0.7400
2:177615836:T:C	acceptor_gain	0.7300
2:177616711:T:C	donor_gain	0.7200
2:177617018:A:C	donor_gain	0.7200
2:177613169:T:C	acceptor_gain	0.7100
2:177615253:T:TC	acceptor_gain	0.7100
2:177616738:G:C	donor_gain	0.6900
2:177617087:T:A	donor_gain	0.6800
2:177615240:ATTTC:A	acceptor_gain	0.6400
2:177617704:T:C	donor_gain	0.6400
2:177617024:AGTTT:A	donor_gain	0.6300

AlphaMissense

4366 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
2:177617191:A:G	L504P	0.998
2:177617308:G:T	A465D	0.998
2:177617725:A:G	L326P	0.998
2:177617935:A:G	L256P	0.997
2:177617016:A:C	F562L	0.996
2:177617016:A:T	F562L	0.996
2:177617018:A:G	F562L	0.996
2:177617270:C:G	A478P	0.996
2:177617411:C:G	A431P	0.996
2:177617674:A:G	L343P	0.996
2:177617822:C:G	A294P	0.996
2:177616955:A:G	W583R	0.995
2:177616955:A:T	W583R	0.995
2:177617193:A:C	N503K	0.995
2:177617193:A:T	N503K	0.995
2:177617245:A:T	V486D	0.995
2:177617309:C:G	A465P	0.995
2:177617324:A:G	W460R	0.995
2:177617324:A:T	W460R	0.995
2:177617579:C:G	A375P	0.995
2:177617776:A:G	L309P	0.995
2:177617833:A:G	L290P	0.995
2:177618344:C:G	A120P	0.994
2:177618540:G:C	C54W	0.994
2:177617299:A:G	L468P	0.993
2:177617684:C:G	A340P	0.993
2:177618118:G:T	A195D	0.993
2:177617612:C:G	A364P	0.992
2:177617672:C:G	A344P	0.992
2:177617686:G:T	A339E	0.992

dbSNP variants (sampled 300 via entrez): RS1000142232 (2:177613153 T>C), RS1000281001 (2:177613936 CACTT>C), RS1000367061 (2:177619110 G>A), RS1000745818 (2:177614518 T>C), RS1001158289 (2:177614142 T>C), RS1002351517 (2:177614604 T>C), RS1002832546 (2:177618042 G>A), RS1002907671 (2:177615897 T>C), RS1003186192 (2:177616408 C>G,T), RS1004265068 (2:177613898 A>G,T), RS1004315978 (2:177613665 A>G,T), RS1004392898 (2:177614206 T>C), RS1004618756 (2:177618712 G>A,T), RS1004729315 (2:177612844 TCA>T), RS1005249945 (2:177613175 A>C)

Disease associations

OMIM: gene MIM:620741 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

28 total (human), top 28 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, decreases methylation, increases expression	7
Tretinoin	decreases expression, increases expression	2
p-Chloromercuribenzoic Acid	affects cotreatment, decreases expression	2
aristolochic acid I	decreases expression	1
methylmercuric chloride	decreases expression	1
trichostatin A	increases expression	1
perfluorooctanoic acid	decreases expression	1
ferrous chloride	decreases expression	1
nickel sulfate	increases expression	1
pentanal	decreases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
abrine	decreases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
Vorinostat	increases expression	1
Acetaminophen	decreases expression	1
Atrazine	decreases expression	1
Benzo(a)pyrene	affects methylation	1
Cisplatin	increases expression	1
Methyl Methanesulfonate	increases expression	1
Oxygen	increases expression	1
Progesterone	increases expression	1
Tobacco Smoke Pollution	decreases expression	1
Urethane	decreases expression	1
Cyclosporine	decreases expression	1
Aflatoxin B1	decreases methylation	1
Aflatoxin M1	decreases expression	1
Gold Compounds	increases expression	1
Lactic Acid	decreases expression	1

Clinical trials (associated diseases)

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