IFTAP

Summary

IFTAP (intraflagellar transport associated protein, HGNC:25142) is a protein-coding gene on chromosome 11p12, encoding Intraflagellar transport-associated protein (Q86VG3). Seems to play a role in ciliary BBSome localization, maybe through interaction with IFT-A complex.

This gene encodes a protein that was identified as a cellular interacting partner of non-structural protein 10 of the severe acute respiratory syndrome coronavirus (SARS-CoV). The encoded protein may function as a negative regulator of transcription. There is a pseudogene for this gene on chromosome 1. Alternative splicing results in multiple transcript variants.

Source: NCBI Gene 119710 — RefSeq curated summary.

At a glance

• GWAS associations: 6
• Clinical variants (ClinVar): 24 total
• MANE Select transcript: NM_138787

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:25142
Approved symbol	IFTAP
Name	intraflagellar transport associated protein
Location	11p12
Locus type	gene with protein product
Status	Approved
Aliases	FLJ38678, HEPIS, NWC
Ensembl gene	ENSG00000166352
Ensembl biotype	protein_coding
OMIM	619270
Entrez	119710

Gene structure

Transcript identifiers

Ensembl transcripts: 37 — 26 protein_coding, 8 nonsense_mediated_decay, 3 retained_intron

ENST00000334307, ENST00000347206, ENST00000446510, ENST00000524539, ENST00000527108, ENST00000528092, ENST00000530697, ENST00000531554, ENST00000532470, ENST00000534635, ENST00000617650, ENST00000676885, ENST00000676921, ENST00000676979, ENST00000677097, ENST00000677116, ENST00000677156, ENST00000677406, ENST00000677623, ENST00000677673, ENST00000677808, ENST00000678060, ENST00000678480, ENST00000678950, ENST00000679022, ENST00000679072, ENST00000679127, ENST00000864503, ENST00000864504, ENST00000967886, ENST00000967887, ENST00000967888, ENST00000967889, ENST00000967890, ENST00000967891, ENST00000967892, ENST00000967893

RefSeq mRNA: 7 — MANE Select: NM_138787 NM_001276722, NM_001276723, NM_001276724, NM_001276725, NM_001276726, NM_001276727, NM_138787

CCDS: CCDS60762, CCDS7904

Canonical transcript exons

ENST00000334307 — 6 exons

Exon	Start	End
ENSE00001333877	36633284	36633438
ENSE00002173836	36594502	36594592
ENSE00002175522	36659019	36659272
ENSE00003393668	36636051	36636117
ENSE00003552072	36610081	36610239
ENSE00003591777	36648016	36648155

Expression profiles

Bgee: expression breadth ubiquitous, 247 present calls, max score 95.92.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 15.6807 / max 642.6341, expressed in 1651 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
113917	15.0621	1648
113918	0.4777	264
113919	0.1180	33
113916	0.0229	6

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
left ventricle myocardium	UBERON:0006566	95.92	gold quality
bronchial epithelial cell	CL:0002328	95.18	gold quality
myocardium	UBERON:0002349	94.68	gold quality
left testis	UBERON:0004533	94.57	gold quality
cardiac muscle of right atrium	UBERON:0003379	94.49	gold quality
right testis	UBERON:0004534	94.13	gold quality
bronchus	UBERON:0002185	94.11	gold quality
right uterine tube	UBERON:0001302	93.87	gold quality
oocyte	CL:0000023	93.31	gold quality
testis	UBERON:0000473	93.27	gold quality
right lobe of thyroid gland	UBERON:0001119	93.26	gold quality
left lobe of thyroid gland	UBERON:0001120	93.19	gold quality
thyroid gland	UBERON:0002046	93.17	gold quality
hindlimb stylopod muscle	UBERON:0004252	93.05	gold quality
heart left ventricle	UBERON:0002084	93.02	gold quality
cardiac ventricle	UBERON:0002082	92.71	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	92.45	gold quality
right atrium auricular region	UBERON:0006631	92.25	gold quality
cortical plate	UBERON:0005343	92.23	gold quality
cardiac atrium	UBERON:0002081	92.04	gold quality
heart	UBERON:0000948	91.82	gold quality
ganglionic eminence	UBERON:0004023	91.82	gold quality
mucosa of paranasal sinus	UBERON:0005030	91.62	gold quality
apex of heart	UBERON:0002098	91.57	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	91.47	gold quality
pigmented layer of retina	UBERON:0001782	91.36	gold quality
ventricular zone	UBERON:0003053	91.30	gold quality
muscle of leg	UBERON:0001383	91.25	gold quality
gastrocnemius	UBERON:0001388	91.23	gold quality
sperm	CL:0000019	90.61	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-MTAB-7606	no	63.41
E-CURD-112	no	2.68
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

5 targeting IFTAP, 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-8485	100.00	77.57	4731
HSA-MIR-3692-3P	99.98	70.27	2139
HSA-MIR-409-3P	99.50	66.33	1192
HSA-MIR-548B-3P	99.38	67.26	1000
HSA-MIR-4511	98.32	67.97	1500

Literature-anchored findings (GeneRIF, showing 2)

• identification of HEPIS as a protein that binds nsp10 of SARS-CoV (PMID:16157265)
• The C11ORF74, interacts with the IFT-A complex via the IFT122 subunit and is accumulated at the distal tip in the absence of an IFT-A subunit IFT139, suggesting that at least a fraction of C11ORF74 molecules can be transported towards the ciliary tip by associating with the IFT-A complex, although its majority might be out of cilia at steady state. (PMID:30476139)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Iftap	ENSMUSG00000027165
rattus_norvegicus	Iftap	ENSRNOG00000037567

Protein

Protein identifiers

Intraflagellar transport-associated protein — Q86VG3 (reviewed: Q86VG3)

Alternative names: Protein HEPIS

All UniProt accessions (11): A0A7I2V427, A0A7I2V4A0, A0A7I2V4J5, A0A7I2V5I0, A0A7I2V5I8, A0A7I2V5V2, A0A7I2YQT1, B4DYW4, Q86VG3, E9PJ48, E9PPH4

UniProt curated annotations — full annotation on UniProt →

Function. Seems to play a role in ciliary BBSome localization, maybe through interaction with IFT-A complex.

Subunit / interactions. Interacts with IFT122; the interaction associates IFTAP with IFT-A complex.

Isoforms (2)

UniProt ID	Names	Canonical?
Q86VG3-1	1	yes
Q86VG3-2	2

RefSeq proteins (7): NP_001263651, NP_001263652, NP_001263653, NP_001263654, NP_001263655, NP_001263656, NP_620142* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR040028	IFTAP	Family

Pfam: PF17722

UniProt features (3 total): chain 1, modified residue 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q86VG3-F1	66.65	0.16

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): 59

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 150 (showing top): GOBP_SINGLE_FERTILIZATION, STARK_PREFRONTAL_CORTEX_22Q11_DELETION_DN, AACYNNNNTTCCS_UNKNOWN, GOBP_MALE_GAMETE_GENERATION, GGAMTNNNNNTCCY_UNKNOWN, SENGUPTA_NASOPHARYNGEAL_CARCINOMA_DN, MILI_PSEUDOPODIA_HAPTOTAXIS_UP, GOBP_ACROSOME_REACTION, GOBP_DEVELOPMENTAL_PROCESS_INVOLVED_IN_REPRODUCTION, ZHANG_BREAST_CANCER_PROGENITORS_UP, GOBP_FERTILIZATION, MODULE_48, MODULE_95, IVANOVA_HEMATOPOIESIS_EARLY_PROGENITOR, STAT1_01

GO Biological Process (3): spermatogenesis (GO:0007283), acrosome reaction (GO:0007340), fertilization (GO:0009566)

GO Molecular Function (2): intraciliary transport particle A binding (GO:0120160), protein binding (GO:0005515)

GO Cellular Component (2): cytosol (GO:0005829), 9+0 non-motile cilium (GO:0097731)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
reproductive process	2
developmental process involved in reproduction	1
male gamete generation	1
membrane fusion involved in acrosome reaction	1
single fertilization	1
acrosomal vesicle exocytosis	1
sexual reproduction	1
protein-containing complex binding	1
binding	1
cytoplasm	1
cellular anatomical structure	1
non-motile cilium	1

Protein interactions and networks

STRING

412 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
IFTAP	IFT122	Q9HBG6	739
IFTAP	IFT43	Q96FT9	643
IFTAP	OR52R1	Q8NGF1	582
IFTAP	WDR19	Q8NEZ3	541
IFTAP	C14orf119	Q9NWQ9	448
IFTAP	C11orf91	Q3C1V1	434
IFTAP	RCSD1	Q6JBY9	391
IFTAP	CNBD2	Q96M20	377
IFTAP	ZNF397	Q8NF99	375
IFTAP	DYNLRB1	Q9NP97	372
IFTAP	TCP11L1	Q9NUJ3	370
IFTAP	GTF2IRD1	Q9UHL9	362
IFTAP	PRPSAP2	O60256	360
IFTAP	LRFN1	Q9P244	358
IFTAP	GARIN4	Q8IYT1	358

IntAct

22 interactions, top by confidence:

A	B	Type	Score
IFT43	TULP3	psi-mi:“MI:0914”(association)	0.790
IFTAP	PLK1	psi-mi:“MI:0914”(association)	0.640
IFTAP	WDR19	psi-mi:“MI:0914”(association)	0.530
IFTAP	BTF3	psi-mi:“MI:0915”(physical association)	0.510
IFTAP	MFHAS1	psi-mi:“MI:0407”(direct interaction)	0.440
IFTAP		psi-mi:“MI:0915”(physical association)	0.370
IFTAP	bipA	psi-mi:“MI:0915”(physical association)	0.370
IFTAP	SFRS5	psi-mi:“MI:0915”(physical association)	0.370
IFTAP	POLR2A	psi-mi:“MI:0915”(physical association)	0.370
SLC10A1	IFTAP	psi-mi:“MI:0915”(physical association)	0.370
IFTAP	SMARCC2	psi-mi:“MI:0915”(physical association)	0.370
IFTAP	PPP1CC	psi-mi:“MI:0915”(physical association)	0.370
IFT43	TULP3	psi-mi:“MI:0914”(association)	0.350
IFTAP	GNPAT	psi-mi:“MI:0914”(association)	0.350
IFT43	TLE1	psi-mi:“MI:0914”(association)	0.350

BioGRID (45): WDR35 (Affinity Capture-MS), IFT140 (Affinity Capture-MS), WDR19 (Affinity Capture-MS), IFT122 (Affinity Capture-MS), PLK1 (Affinity Capture-MS), IFT43 (Affinity Capture-MS), UBE2S (Affinity Capture-MS), C11orf74 (Affinity Capture-MS), WDR35 (Affinity Capture-MS), WDR19 (Affinity Capture-MS), IFT140 (Affinity Capture-MS), IFT122 (Affinity Capture-MS), PLK1 (Affinity Capture-MS), UBE2S (Affinity Capture-MS), C11orf74 (Reconstituted Complex)

ESM2 similar proteins: A0A1B0GTZ2, A0A1B0GVH6, A1DL98, A2RRY8, A3RM20, A4UHQ4, A6ZMG4, B0BK70, B3LLZ8, B6LI37, C7GWA2, C8ZEW0, O55527, O74982, P04861, P04862, P14253, P40167, P69738, Q04438, Q06616, Q0GBX8, Q1T763, Q2YDE5, Q3TTJ4, Q3URK1, Q3ZBP0, Q4R309, Q561K4, Q5R498, Q5SQS8, Q6PI97, Q6PKN7, Q6X1D3, Q86UF4, Q86VG3, Q8IZS5, Q8N9R6, Q8TAL5, Q8WWF3

Diamond homologs: Q3ZBP0, Q86VG3, Q9CQI4

SIGNOR signaling

2 interactions.

A	Effect	B	Mechanism
IFTAP	“down-regulates activity”	BTF3	binding
“Non-structural protein 10”	unknown	IFTAP	binding

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	7
Likely benign	2
Benign	2

Top pathogenic / likely-pathogenic (0)

SpliceAI

1585 predictions. Top by Δscore:

Variant	Effect	Δscore
11:36633282:A:AG	acceptor_gain	1.0000
11:36633282:AGAG:A	acceptor_gain	1.0000
11:36633283:G:GG	acceptor_gain	1.0000
11:36633283:GA:G	acceptor_gain	1.0000
11:36633283:GAGG:G	acceptor_gain	1.0000
11:36648167:GGAAT:G	donor_gain	1.0000
11:36648168:G:T	donor_gain	1.0000
11:36659008:A:AG	acceptor_gain	1.0000
11:36659015:ATAG:A	acceptor_loss	1.0000
11:36659016:T:G	acceptor_gain	1.0000
11:36659016:TAGA:T	acceptor_loss	1.0000
11:36659017:A:AG	acceptor_gain	1.0000
11:36659017:A:AT	acceptor_loss	1.0000
11:36659018:G:GG	acceptor_gain	1.0000
11:36659018:GA:G	acceptor_gain	1.0000
11:36594774:G:GT	donor_gain	0.9900
11:36594913:G:GT	donor_gain	0.9900
11:36598097:CCTA:C	donor_loss	0.9900
11:36598099:TACC:T	donor_loss	0.9900
11:36598101:CCTG:C	donor_loss	0.9900
11:36610075:TTGCA:T	acceptor_loss	0.9900
11:36610076:TGCA:T	acceptor_loss	0.9900
11:36610077:GCA:G	acceptor_loss	0.9900
11:36610078:CA:C	acceptor_loss	0.9900
11:36610079:A:AG	acceptor_gain	0.9900
11:36610079:AGAT:A	acceptor_loss	0.9900
11:36610080:G:GA	acceptor_gain	0.9900
11:36610080:G:GC	acceptor_loss	0.9900
11:36610080:GAT:G	acceptor_gain	0.9900
11:36610080:GATA:G	acceptor_gain	0.9900

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000026201 (11:36631884 G>A), RS1000081251 (11:36648882 C>T), RS1000104905 (11:36602349 A>C,G), RS1000257013 (11:36641919 G>T), RS1000286519 (11:36642430 G>A), RS1000409879 (11:36618788 T>C), RS1000441646 (11:36632052 G>C), RS1000478527 (11:36635924 A>G), RS1000558040 (11:36654489 A>G), RS1000616544 (11:36595746 A>T), RS1000707417 (11:36597896 C>G,T), RS1000775627 (11:36648678 T>A), RS1000785938 (11:36635552 T>G), RS1000816170 (11:36604781 A>G), RS1000862385 (11:36618526 G>A)

Disease associations

OMIM: gene MIM:619270 | disease phenotypes: MIM:601457, MIM:603554

GenCC curated gene-disease

Mondo (2): severe combined immunodeficiency, autosomal recessive, T cell-negative, B cell-negative, NK cell-positive (MONDO:0011086), Omenn syndrome (MONDO:0011338)

Orphanet (2): Severe combined immunodeficiency due to complete RAG1/2 deficiency (Orphanet:331206), Omenn syndrome (Orphanet:39041)

HPO phenotypes

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

GWAS associations

6 associations (top):

Study	Trait	p-value
GCST001034_2	Cutaneous nevi	2.000000e-06
GCST003944_17	Hepcidin/ferritin ratio	2.000000e-06
GCST005588_1	Idiopathic dilated cardiomyopathy	3.000000e-06
GCST006484_12	Type 2 diabetes	2.000000e-06
GCST008526_9	Coffee consumption	6.000000e-07
GCST011836_4	Cervical high-risk human papilloma virus infection (persistent)	7.000000e-07

EFO canonical traits (4, from GWAS)

EFO ID	Trait name
EFO:0000625	nevus
EFO:0007901	hepcidin:ferritin ratio
EFO:0009094	idiopathic dilated cardiomyopathy
EFO:0006781	coffee consumption measurement

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
C563311	Severe Combined Immunodeficiency, Autosomal Recessive, T Cell-Negative, B Cell-Negative, NK Cell-Positive (supp.)

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
sodium arsenite	decreases expression, affects cotreatment, increases abundance, increases expression	3
Air Pollutants	decreases expression, increases abundance, increases expression	2
Particulate Matter	decreases reaction, increases expression, decreases expression, increases abundance	2
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamide	increases expression	1
dicrotophos	decreases expression	1
arsenite	affects binding, increases reaction	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
manganese chloride	affects cotreatment, increases abundance, increases expression	1
abrine	decreases expression	1
2-methyl-2H-pyrazole-3-carboxylic acid (2-methyl-4-o-tolylazophenyl)amide	decreases reaction, increases expression	1
jinfukang	affects cotreatment, increases expression	1
Sunitinib	decreases expression	1
Vorinostat	increases expression	1
Acetaminophen	decreases expression	1
Arsenic	affects cotreatment, increases abundance, increases expression	1
Vehicle Emissions	decreases reaction, increases expression	1
Benzo(a)pyrene	decreases methylation, increases methylation	1
Cisplatin	affects cotreatment, increases expression	1
Doxorubicin	decreases expression	1
Estradiol	decreases expression	1
Manganese	affects cotreatment, increases abundance, increases expression	1
Smoke	increases abundance, increases expression	1
Tobacco Smoke Pollution	decreases expression	1
Urethane	decreases expression	1
Valproic Acid	decreases methylation, increases expression	1
Aflatoxin B1	decreases methylation	1
Cadmium Chloride	decreases expression	1
Copper Sulfate	decreases expression	1

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT07284641	PHASE2	RECRUITING	Hematopoietic Stem Cell Transplantation (HSCT) for Common Variable Immunodeficiency (CVID) and Other Autoimmune Manifestations of Primary Immune Regulatory Disorders (PIRD)
NCT01186913	Not specified	ENROLLING_BY_INVITATION	Natural History Study of SCID Disorders
NCT01346150	Not specified	UNKNOWN	Patients Treated for SCID (1968-Present)