IFT70B

Summary

IFT70B (intraflagellar transport 70B, HGNC:26425) is a protein-coding gene on chromosome 2q31.2, encoding Intraflagellar transport protein 70B (Q8N4P2). Required for polyglutamylation of axonemal tubulin.

Predicted to enable intraciliary transport particle B binding activity. Predicted to be involved in intraciliary transport. Part of intraciliary transport particle B.

Source: NCBI Gene 150737 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 106 total
• MANE Select transcript: NM_152517

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26425
Approved symbol	IFT70B
Name	intraflagellar transport 70B
Location	2q31.2
Locus type	gene with protein product
Status	Approved
Aliases	FLJ30990, fleer
Ensembl gene	ENSG00000196659
Ensembl biotype	protein_coding
OMIM	620742
Entrez	150737

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000408939

RefSeq mRNA: 1 — MANE Select: NM_152517 NM_152517

CCDS: CCDS42784

Canonical transcript exons

ENST00000408939 — 1 exons

Exon	Start	End
ENSE00001570879	177548998	177552796

Expression profiles

Bgee: expression breadth ubiquitous, 200 present calls, max score 94.26.

FANTOM5 (CAGE): breadth broad, TPM avg 1.3078 / max 15.0808, expressed in 840 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
32002	1.3078	840

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
bronchial epithelial cell	CL:0002328	94.26	gold quality
bronchus	UBERON:0002185	91.87	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	80.89	gold quality
mucosa of paranasal sinus	UBERON:0005030	80.89	gold quality
caput epididymis	UBERON:0004358	80.41	gold quality
corpus epididymis	UBERON:0004359	79.39	gold quality
right uterine tube	UBERON:0001302	78.95	gold quality
islet of Langerhans	UBERON:0000006	76.84	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	75.22	gold quality
ventricular zone	UBERON:0003053	74.60	gold quality
stromal cell of endometrium	CL:0002255	72.46	gold quality
calcaneal tendon	UBERON:0003701	72.44	gold quality
smooth muscle tissue	UBERON:0001135	71.66	gold quality
adrenal tissue	UBERON:0018303	71.58	gold quality
cauda epididymis	UBERON:0004360	71.39	gold quality
rectum	UBERON:0001052	71.21	gold quality
right testis	UBERON:0004534	69.82	gold quality
pancreas	UBERON:0001264	69.76	gold quality
germinal epithelium of ovary	UBERON:0001304	69.65	gold quality
testis	UBERON:0000473	69.44	gold quality
right adrenal gland cortex	UBERON:0035827	69.43	gold quality
ganglionic eminence	UBERON:0004023	69.32	gold quality
epithelium of nasopharynx	UBERON:0001951	69.17	gold quality
palpebral conjunctiva	UBERON:0001812	68.98	gold quality
left testis	UBERON:0004533	68.95	gold quality
fallopian tube	UBERON:0003889	68.77	gold quality
mucosa of transverse colon	UBERON:0004991	68.63	gold quality
right adrenal gland	UBERON:0001233	68.62	gold quality
endometrium	UBERON:0001295	68.38	gold quality
gall bladder	UBERON:0002110	68.13	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	3.63

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

63 targeting IFT70B, 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-29A-3P	100.00	73.11	1835
HSA-MIR-29B-3P	100.00	73.18	1833
HSA-MIR-29C-3P	100.00	73.15	1833
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-574-5P	100.00	66.01	989
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-12136	99.98	72.81	5713
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-5688	99.96	73.23	4504
HSA-MIR-767-5P	99.95	70.85	993
HSA-LET-7C-3P	99.95	73.42	2862
HSA-MIR-545-3P	99.95	70.74	2783
HSA-MIR-651-3P	99.94	73.48	5177
HSA-MIR-335-3P	99.93	73.36	4958
HSA-MIR-7-1-3P	99.91	71.53	4384
HSA-MIR-7-2-3P	99.91	71.40	4394
HSA-MIR-345-3P	99.89	70.23	1421
HSA-MIR-5682	99.89	72.56	1005
HSA-MIR-4496	99.88	68.89	2236
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-4658	99.77	64.94	514
HSA-MIR-6790-5P	99.77	65.24	505

Literature-anchored findings (GeneRIF, showing 1)

• A rare TTC30B variant is identified as a candidate for synpolydactyly in a Chinese pedigree. (PMID:31306809)

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): IFT70A (ENSG00000197557)

Protein

Protein identifiers

Intraflagellar transport protein 70B — Q8N4P2 (reviewed: Q8N4P2)

Alternative names: Tetratricopeptide repeat protein 30B

All UniProt accessions (1): Q8N4P2

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.

Subunit / interactions. Interacts with the IFT B complex components IFT27, IFT46, IFT74, IFT52, IFT57, IFT80, IFT81 and IFT88. Interacts with KIF17.

Subcellular location. Cell projection. Cilium.

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

RefSeq proteins (1): NP_689730* (*=MANE)

Domains & families (InterPro)

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

UniProt features (17 total): repeat 8, sequence conflict 4, sequence variant 2, chain 1, coiled-coil region 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8N4P2-F1	93.04	0.86

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: 125 (showing top): TERAMOTO_OPN_TARGETS_CLUSTER_4, GOBP_CILIUM_ORGANIZATION, GOBP_ORGANELLE_ASSEMBLY, ZHOU_INFLAMMATORY_RESPONSE_LIVE_DN, GOBP_CELL_PROJECTION_ORGANIZATION, GOCC_CYTOPLASMIC_REGION, TAATTA_CHX10_01, GOCC_CILIARY_TIP, TCCCRNNRTGC_UNKNOWN, GOCC_INTRACILIARY_TRANSPORT_PARTICLE_B, GOCC_INTRACILIARY_TRANSPORT_PARTICLE, GOCC_CYTOPLASMIC_MICROTUBULE, GOCC_CILIUM, FEVR_CTNNB1_TARGETS_DN, GOBP_INTRACILIARY_TRANSPORT

GO Biological Process (4): intraciliary anterograde transport (GO:0035720), intraciliary transport (GO:0042073), cilium assembly (GO:0060271), cell projection organization (GO:0030030)

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

GO Cellular Component (6): axonemal microtubule (GO:0005879), cilium (GO:0005929), 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-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	3
cilium	2
cilium organization	2
protein-containing complex	2
cellular anatomical structure	2
intraciliary transport	1
transport along microtubule	1
axoneme assembly	1
intraciliary transport involved in cilium assembly	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
cellular component organization	1
protein-containing complex binding	1
binding	1
cytoplasmic microtubule	1
axoneme	1
membrane-bounded organelle	1
plasma membrane bounded cell projection	1

Protein interactions and networks

STRING

738 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
IFT70B	IFT46	Q9NQC8	997
IFT70B	IFT52	Q9Y366	997
IFT70B	IFT88	Q13099	995
IFT70B	IFT27	Q9BW83	995
IFT70B	IFT25	Q9Y547	991
IFT70B	IFT74	Q96LB3	990
IFT70B	IFT81	Q8WYA0	986
IFT70B	IFT22	Q9H7X7	983
IFT70B	IFT56	A0AVF1	966
IFT70B	IFT54	Q8TDR0	961
IFT70B	IFT80	Q9P2H3	947
IFT70B	IFT57	Q9NWB7	937
IFT70B	IFT172	Q9UG01	878
IFT70B	IFT38	Q96AJ1	842
IFT70B	IFT20	Q8IY31	823

IntAct

74 interactions, top by confidence:

A	B	Type	Score
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
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
IFT70B	B9D2	psi-mi:“MI:0407”(direct interaction)	0.530
IFT70B	Ift52	psi-mi:“MI:0407”(direct interaction)	0.530
Ift52	IFT70B	psi-mi:“MI:0915”(physical association)	0.530
B9D2	IFT70B	psi-mi:“MI:0915”(physical association)	0.530
IFT74	IFT56	psi-mi:“MI:0914”(association)	0.510
IFT80	IFT56	psi-mi:“MI:0914”(association)	0.510
INVS	IFT70B	psi-mi:“MI:0915”(physical association)	0.400
ANKRD55	YWHAG	psi-mi:“MI:0914”(association)	0.350

BioGRID (94): TTC30B (Affinity Capture-MS), TTC30B (Affinity Capture-MS), UBXN10 (Reconstituted Complex), TTC30B (Affinity Capture-MS), IFT52 (Affinity Capture-MS), CLUAP1 (Affinity Capture-MS), IFT46 (Affinity Capture-MS), IFT81 (Affinity Capture-MS), IFT88 (Affinity Capture-MS), IFT80 (Affinity Capture-MS), IFT74 (Affinity Capture-MS), IFT22 (Affinity Capture-MS), TRAF3IP1 (Affinity Capture-MS), IFT20 (Affinity Capture-MS), IFT172 (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 47 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	100.2×	5e-24
Organelle biogenesis and maintenance	5	11.8×	2e-03

GO biological processes:

GO term	Partners	Fold	FDR
intraciliary anterograde transport	13	281.2×	1e-28
intraciliary transport	9	123.3×	2e-15
negative regulation of keratinocyte proliferation	5	85.6×	1e-07
keratinocyte proliferation	5	70.9×	3e-07
non-motile cilium assembly	7	49.6×	5e-09
smoothened signaling pathway	10	44.2×	1e-12
cilium assembly	15	26.9×	4e-16
kidney development	5	17.1×	3e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	85
Likely benign	18
Benign	2

Top pathogenic / likely-pathogenic (0)

SpliceAI

28 predictions. Top by Δscore:

Variant	Effect	Δscore
2:177552354:TC:T	donor_gain	0.7700
2:177552355:C:CT	donor_gain	0.7600
2:177552356:T:TT	donor_gain	0.7600
2:177552351:TGCTC:T	donor_gain	0.6800
2:177552394:A:AC	donor_gain	0.5200
2:177552395:C:CC	donor_gain	0.5200
2:177552263:CTCCT:C	acceptor_gain	0.4700
2:177552264:TCCTT:T	acceptor_gain	0.4700
2:177552391:TG:T	donor_gain	0.4500
2:177552396:T:C	donor_gain	0.4500
2:177552353:CT:C	donor_gain	0.3400
2:177552360:A:T	donor_gain	0.3400
2:177552266:CT:C	acceptor_gain	0.3200
2:177552267:TT:T	acceptor_gain	0.3200
2:177550838:T:A	donor_gain	0.3100
2:177552728:C:A	donor_gain	0.2900
2:177552337:C:A	donor_gain	0.2800
2:177551230:T:C	acceptor_gain	0.2600
2:177552239:G:GT	acceptor_gain	0.2600
2:177552324:T:A	donor_gain	0.2500
2:177552350:CTGCT:C	donor_gain	0.2500
2:177548999:T:C	acceptor_gain	0.2400
2:177552267:T:C	acceptor_gain	0.2300
2:177552365:CCTGG:C	donor_gain	0.2300
2:177551234:C:CT	acceptor_gain	0.2200
2:177552367:TGG:T	donor_gain	0.2200
2:177552265:CCT:C	acceptor_gain	0.2100
2:177552613:G:C	donor_gain	0.2000

AlphaMissense

4377 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
2:177551078:A:C	F562L	1.000
2:177551078:A:T	F562L	1.000
2:177551080:A:G	F562L	1.000
2:177551017:A:G	W583R	0.999
2:177551017:A:T	W583R	0.999
2:177551076:C:T	G563D	0.999
2:177551077:C:G	G563R	0.999
2:177551112:C:T	G551E	0.999
2:177551113:C:G	G551R	0.999
2:177551113:C:T	G551R	0.999
2:177551253:A:G	L504P	0.999
2:177551307:A:T	V486D	0.999
2:177551370:G:T	A465D	0.999
2:177550827:A:T	V646D	0.998
2:177551054:G:C	S570R	0.998
2:177551054:G:T	S570R	0.998
2:177551056:T:G	S570R	0.998
2:177551067:C:G	R566P	0.998
2:177551106:A:G	L553P	0.998
2:177551112:C:A	G551V	0.998
2:177551259:G:T	A502D	0.998
2:177551997:A:G	L256P	0.998
2:177551076:C:A	G563V	0.997
2:177551079:A:C	F562C	0.997
2:177551104:A:C	Y554D	0.997
2:177551104:A:G	Y554H	0.997
2:177551386:A:G	W460R	0.997
2:177551386:A:T	W460R	0.997
2:177551461:A:G	W435R	0.997
2:177551461:A:T	W435R	0.997

dbSNP variants (sampled 300 via entrez): RS1000808997 (2:177549037 G>A), RS1000881245 (2:177548709 T>C), RS1001136824 (2:177549861 T>C), RS1001920974 (2:177549252 G>A), RS1002293118 (2:177549922 T>C), RS1002702055 (2:177549417 G>A,T), RS1003706742 (2:177554169 T>C), RS1005764182 (2:177554745 G>A), RS1006045990 (2:177550245 C>A,T), RS1006119457 (2:177550029 A>G), RS1006133295 (2:177553475 A>C,G), RS1006554559 (2:177553277 G>A,C), RS1007044134 (2:177554575 T>G), RS1007165768 (2:177550696 C>G), RS1007239396 (2:177550366 G>A,C,T)

Disease associations

OMIM: gene MIM:620742 | disease phenotypes:

GenCC curated gene-disease

Mondo (1): synpolydactyly (MONDO:0021651)

Orphanet (1): Syndactyly type 2 (Orphanet:93403)

HPO phenotypes

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

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST004250_38	Alanine aminotransferase (ALT) levels after remission induction therapy in actute lymphoblastic leukemia (ALL)	4.000000e-06

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0007965	response to combination chemotherapy

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
C538153	Syndactyly, type 2 (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Tetrachlorodibenzodioxin	increases expression	2
Tobacco Smoke Pollution	decreases expression	2
Valproic Acid	decreases methylation, increases expression	2
Cyclosporine	decreases expression	2
aristolochic acid I	decreases expression	1
GSK-J4	decreases expression	1
methylmercuric chloride	decreases expression	1
bisphenol A	affects cotreatment, increases expression	1
methylparaben	decreases expression	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
potassium chromate(VI)	decreases expression, affects cotreatment	1
epigallocatechin gallate	affects cotreatment, decreases expression	1
avobenzone	decreases expression	1
pentabromodiphenyl ether	decreases expression	1
clothianidin	decreases expression	1
abrine	decreases expression	1
jinfukang	affects cotreatment, increases expression	1
Sunitinib	decreases expression	1
Vorinostat	increases expression	1
Acetaminophen	decreases expression	1
Benzo(a)pyrene	increases methylation	1
Cisplatin	affects cotreatment, increases expression	1
Dexamethasone	affects cotreatment, increases expression	1
Dimethyl Sulfoxide	increases expression	1
Ethyl Methanesulfonate	increases expression	1
Formaldehyde	decreases expression	1
Indomethacin	affects cotreatment, increases expression	1
Melphalan	decreases expression	1
Methyl Methanesulfonate	increases expression	1
Potassium Chloride	decreases response to substance, decreases expression	1

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT04564430	PHASE4	UNKNOWN	Clonidine for Tourniquet-related Pain in Children
NCT02507206	PHASE2	COMPLETED	A D1 Agonist For Working Memory
NCT02524899	PHASE2	COMPLETED	CRT-Guanfacine for SPD
NCT02149823	PHASE1	TERMINATED	Examining Dose-Related Effects of Oxytocin on Social Cognition Across Populations
NCT02040688	Not specified	UNKNOWN	Sensory Integration (Processing) Disorder Among Children With Behavioral Insomnia and Children With Feeding Disorder