KIF3A

Summary

KIF3A (kinesin family member 3A, HGNC:6319) is a protein-coding gene on chromosome 5q31.1, encoding Kinesin-like protein KIF3A (Q9Y496). Microtubule-based anterograde translocator for membranous organelles.

Enables protein phosphatase binding activity; small GTPase binding activity; and spectrin binding activity. Involved in protein localization to cell junction and protein transport. Located in centriole; centrosome; and spindle microtubule. Part of kinesin II complex. Biomarker of silicosis.

Source: NCBI Gene 11127 — RefSeq curated summary.

At a glance

• GWAS associations: 20
• Clinical variants (ClinVar): 73 total
• Druggable target: yes
• MANE Select transcript: NM_001300791

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:6319
Approved symbol	KIF3A
Name	kinesin family member 3A
Location	5q31.1
Locus type	gene with protein product
Status	Approved
Aliases	FLA10, KLP-20
Ensembl gene	ENSG00000131437
Ensembl biotype	protein_coding
OMIM	604683
Entrez	11127

Gene structure

Transcript identifiers

Ensembl transcripts: 11 — 9 protein_coding, 2 protein_coding_CDS_not_defined

ENST00000378735, ENST00000378746, ENST00000403231, ENST00000428744, ENST00000450441, ENST00000487055, ENST00000488471, ENST00000618515, ENST00000875777, ENST00000928467, ENST00000928468

RefSeq mRNA: 3 — MANE Select: NM_001300791 NM_001300791, NM_001300792, NM_007054

CCDS: CCDS34235, CCDS75295, CCDS75296

Canonical transcript exons

ENST00000403231 — 19 exons

Exon	Start	End
ENSE00000899329	132699171	132699295
ENSE00000899330	132700216	132700284
ENSE00000899332	132700647	132700700
ENSE00000899340	132703463	132703619
ENSE00000899341	132710959	132711057
ENSE00000899342	132715757	132715931
ENSE00000899343	132716245	132716442
ENSE00000899344	132716845	132716984
ENSE00000899345	132720609	132720714
ENSE00000899347	132726354	132726498
ENSE00001551763	132692631	132696682
ENSE00001562378	132708907	132708978
ENSE00002445575	132706451	132706459
ENSE00002445604	132734205	132734478
ENSE00002500727	132737414	132737546
ENSE00003586161	132702558	132702668
ENSE00003587109	132702087	132702212
ENSE00003678716	132702885	132703065
ENSE00003789387	132726128	132726212

Expression profiles

Bgee: expression breadth ubiquitous, 264 present calls, max score 99.17.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 27.6893 / max 2009.5060, expressed in 1746 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
63349	23.9943	1729
63348	3.6315	1157
63347	0.0635	21

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
Brodmann (1909) area 23	UBERON:0013554	99.17	gold quality
endothelial cell	CL:0000115	97.72	gold quality
middle temporal gyrus	UBERON:0002771	97.42	gold quality
secondary oocyte	CL:0000655	96.10	gold quality
pons	UBERON:0000988	96.09	gold quality
buccal mucosa cell	CL:0002336	95.61	gold quality
entorhinal cortex	UBERON:0002728	95.45	gold quality
postcentral gyrus	UBERON:0002581	95.13	gold quality
superior vestibular nucleus	UBERON:0007227	95.02	gold quality
parietal lobe	UBERON:0001872	95.01	gold quality
sural nerve	UBERON:0015488	94.74	gold quality
cortical plate	UBERON:0005343	94.73	gold quality
primary visual cortex	UBERON:0002436	94.72	gold quality
superior frontal gyrus	UBERON:0002661	94.68	gold quality
lateral nuclear group of thalamus	UBERON:0002736	94.55	gold quality
substantia nigra pars compacta	UBERON:0001965	93.78	gold quality
occipital lobe	UBERON:0002021	93.69	gold quality
substantia nigra pars reticulata	UBERON:0001966	93.07	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	92.63	gold quality
prefrontal cortex	UBERON:0000451	92.57	gold quality
dorsal root ganglion	UBERON:0000044	92.54	gold quality
bronchial epithelial cell	CL:0002328	92.15	gold quality
oocyte	CL:0000023	91.90	gold quality
corpus callosum	UBERON:0002336	91.39	gold quality
calcaneal tendon	UBERON:0003701	91.06	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	90.62	gold quality
frontal cortex	UBERON:0001870	90.46	gold quality
cerebral cortex	UBERON:0000956	90.40	gold quality
neocortex	UBERON:0001950	90.18	gold quality
ventral tegmental area	UBERON:0002691	90.13	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-HCAD-5	yes	46.27
E-GEOD-134144	yes	27.96
E-ANND-3	yes	11.12

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

204 targeting KIF3A, 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-3613-3P	100.00	76.36	7965
HSA-MIR-4262	100.00	73.26	3931
HSA-MIR-4673	100.00	66.64	1490
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-5692A	100.00	74.40	6850
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-98-3P	100.00	74.08	3907
HSA-MIR-3924	100.00	72.09	2394
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-4747-5P	100.00	67.90	2681
HSA-MIR-5196-5P	100.00	67.98	2761
HSA-MIR-4795-3P	100.00	74.62	4024
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-4455	100.00	65.48	1587
HSA-MIR-6748-5P	100.00	65.81	1057
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-181A-5P	99.99	72.96	2995
HSA-MIR-181B-5P	99.99	72.97	2996
HSA-MIR-181C-5P	99.99	72.95	2996
HSA-MIR-181D-5P	99.99	73.04	2997
HSA-MIR-196A-1-3P	99.99	72.15	2772
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-4645-5P	99.98	65.81	1284
HSA-MIR-19A-3P	99.98	75.33	2762

Literature-anchored findings (GeneRIF, showing 36)

• both motor domains of KIF3A/B coordinate for processive motility and move at different speeds (PMID:15345558)
• Required for the normal steady-state localization of late endosomes/lysosomes but not early endosomes or recycling endosomes. (PMID:16262723)
• Interaction of KIF3A/3B with KAP3 may be important for the proper progression of mitosis. (PMID:16298999)
• We detected ALS-specific down-regulation of KIF1Bbeta and novel KIF3Abeta, two isoforms we show to be enriched in the brain, and also of SOD1, a key enzyme linked to familial ALS (PMID:17418584)
• Rip11/FIP5-kinesin-II complex plays a key role in the routing of internalized receptors through the perinuclear recycling endosomes. (PMID:18957512)
• Protein phosphatase Dusp26 associates with KIF3 motor and promotes N-cadherin-mediated cell-cell adhesion. (PMID:19043453)
• This study thus reports on transportation of KSHV viral complexes on microtubules by KIF3A (PMID:19282970)
• KIF3, cilia, and nodal flow have roles in left-right determination [review] (PMID:20066075)
• Variants carried by the haplotypes of SLC22A4, SLC22A5 and KIF3A region potentially contribute to tuberculosis susceptibility among the Thai population. (PMID:20485362)
• Our findings suggest that the KIF3A gene and/or its polymorphisms might have a susceptibility effect on aspirin-intolerant asthma (AIA). (PMID:20922562)
• KIF3A is a novel candidate gene for childhood asthma (PMID:21912604)
• Association of KIF3A, but not OVOL1 and ACTL9, with atopic eczema in Italian patients (PMID:23278845)
• in addition to its ciliogenic roles, Kif3a recruits p150(Glued) to the subdistal appendages of mother centrioles, critical for centrosomes to function as microtubule-organizing centres. (PMID:23386061)
• POPX2 affects trafficking by determining the phosphorylation status of KIF3A at serine 690. (PMID:24338362)
• Findings support the notion that upregulation of KIF3a is causal of aberrant activation of Wnt signaling in advanced prostate cancer through the KIF3a-DVL2-beta-catenin axis. (PMID:24413182)
• These data suggest that GLI interactions with KIF3A-KIF3B-KAP3 complexes are essential for proper GLI transcriptional activity. (PMID:25588831)
• Ablation of this phosphorylation abolished herpes simplex virus 1 US3-mediated downregulation of CD1d expression, suggesting that phosphorylation of KIF3A is the primary mechanism of viral suppression of CD1d expression. (PMID:25878107)
• KIF3A and OVOL1 are involved in the development of Atopic dermatitis in the Chinese pediatric population. (PMID:26127003)
• High KIF3A expression is associated with glioblastoma. (PMID:26760767)
• Inhibition of kif3a in the human dental follicle cells (hDFCs) and human dental pulp cells (hDPCs) is disrupted primary cilia formation and/or function, and it was shown that kif3a is important in the differentiation of hDFCs and hDPCs through the Wnt pathway. (PMID:27432616)
• A correlation between KIF3A loss and a poorer NSCLC prognosis as well as beta-catenin and cyclin D1 upregulation further suggests that KIF3A suppresses Wnt/beta-catenin signalling and tumourigenesis in NSCLC (PMID:27596264)
• the association of KIF3A is with asthma + eczema. The presence of AR comorbidity did not increase the genetic association of KIF3A with asthma or even with asthma + eczema. Thus, asthma + eczema constitutes a distinct asthmatic phenotype characterized by an association with KIF3A SNPs, which is not strengthened by AR. (PMID:28238750)
• PLCD1 acts as a tumour suppressor, by KIF3A-mediated suppression of ERK1/2/beta-catenin/MMP7 signalling, at least in part, in breast cancer. (PMID:28423710)
• The rate of transport is set by an equilibrium between a faster state, where only kinesin family member 17 protein (KIF17) motors move the train, and a slower state, where at least one kinesin family member 3A/B protein (KIF3AB) motor on the train remains active in transport. (PMID:28761002)
• p0071 is required for directional vesicle movement and secretion of different KIF3-transported carriers, thereby regulating the transport of intracellular membrane vesicles along microtubules. (PMID:28808088)
• KIF3A plays an important role in epithelium apoptosis and bronchial inflammation in asthma (PMID:29156524)
• Study demonstrates that human ICK (intestinal cell kinase) that authors herein call CAPK (ciliopathy-associated protein kinase) interacts with human KIF3A and phosphorylates a conserved site Thr672 both in vitro and in vivo. Long, unstructured, non-catalytic carboxyl-terminal domain (CTD) of CAPK is required for this interaction with and phosphorylation of KIF3A (PMID:31277411)
• Silencing of KIF3A suppressed TNBC cell proliferation by repressing the Rb-E2F signaling pathway and inhibited migration and invasion by repressing epithelial-mesenchymal transition. The tumor size was smaller and the number of lung metastatic nodules was lower in KIF3A depletion MDA-MB-231 cell xenograft mice than in the negative control group. In addition, KIF3A overexpression correlated with chemoresistance. (PMID:32011034)
• Disease-associated KIF3A variants alter gene methylation and expression impacting skin barrier and atopic dermatitis risk. (PMID:32796837)
• Skin depletion of Kif3a resembles the pediatric atopic dermatitis transcriptome profile. (PMID:34964466)
• Coordination of two kinesin superfamily motor proteins, KIF3A and KIF13A, is essential for pericellular matrix degradation by membrane-type 1 matrix metalloproteinase (MT1-MMP) in cancer cells. (PMID:35122963)
• lncRNA MIR600HG induces the proliferation and invasion of colorectal cancer cells via regulating miR-144-3p/KIF3A. (PMID:35378445)
• Kinesin family member 3A induces related diseases via wingless-related integration site/beta-catenin signaling pathway. (PMID:36594221)
• Inhibitory mechanism of KIF3A gene on nasopharyngeal carcinoma stem cells. (PMID:37715417)
• CircRAPGEF5 sponges miR-582-3p and targets KIF3A to regulate bladder cancer cell proliferation, migration and invasion. (PMID:38489970)
• The heterotrimeric kinesin-2 family member KIF3A directly binds to disabled-1 (Dab1). (PMID:38919020)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	kif3a	ENSDARG00000087538
mus_musculus	Kif3a	ENSMUSG00000018395
rattus_norvegicus	Kif3a	ENSRNOG00000007515
drosophila_melanogaster	Klp64D	FBGN0004380
caenorhabditis_elegans		WBGENE00002230

Paralogs (41): KIF1B (ENSG00000054523), KIF26A (ENSG00000066735), KIF2A (ENSG00000068796), KIF22 (ENSG00000079616), KIF3C (ENSG00000084731), KIF9 (ENSG00000088727), KIF16B (ENSG00000089177), KIF4A (ENSG00000090889), KIF3B (ENSG00000101350), KIF20A (ENSG00000112984), KIF21B (ENSG00000116852), KIF17 (ENSG00000117245), KIF14 (ENSG00000118193), KIF18A (ENSG00000121621), KIF25 (ENSG00000125337), KIF1C (ENSG00000129250), KIF1A (ENSG00000130294), KIF12 (ENSG00000136883), KIF13A (ENSG00000137177), KIF23 (ENSG00000137807), KIF11 (ENSG00000138160), CENPE (ENSG00000138778), KIF21A (ENSG00000139116), KIFC3 (ENSG00000140859), KIF2B (ENSG00000141200), KIF2C (ENSG00000142945), KIF5A (ENSG00000155980), KIF26B (ENSG00000162849), KIF15 (ENSG00000163808), KIF6 (ENSG00000164627), KIF27 (ENSG00000165115), KIF7 (ENSG00000166813), KIFC2 (ENSG00000167702), KIF5C (ENSG00000168280), KIF5B (ENSG00000170759), KIF18B (ENSG00000186185), KIF24 (ENSG00000186638), KIF19 (ENSG00000196169), KIF13B (ENSG00000197892), KIF4B (ENSG00000226650)

Protein

Protein identifiers

Kinesin-like protein KIF3A — Q9Y496 (reviewed: Q9Y496)

Alternative names: Microtubule plus end-directed kinesin motor 3A

All UniProt accessions (6): A0A087X011, C9J9X2, E9PES4, Q9Y496, H7C2F6, J3KPF9

UniProt curated annotations — full annotation on UniProt →

Function. Microtubule-based anterograde translocator for membranous organelles. Plus end-directed microtubule sliding activity in vitro. Plays a role in primary cilia formation. Plays a role in centriole cohesion and subdistal appendage organization and function. Regulates the formation of the subdistal appendage via recruitment of DCTN1 to the centriole. Also required for ciliary basal feet formation and microtubule anchoring to mother centriole.

Subunit / interactions. Heterodimer of KIF3A and KIF3B. Interacts with CIMAP3. Interacts with CLN3. Interacts with DCTN1. Interacts with FLCN. Interacts with AP3B1.

Subcellular location. Cytoplasm. Cytoskeleton. Cell projection. Cilium. Microtubule organizing center. Centrosome. Centriole.

Similarity. Belongs to the TRAFAC class myosin-kinesin ATPase superfamily. Kinesin family. Kinesin II subfamily.

RefSeq proteins (3): NP_001287720, NP_001287721, NP_008985 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001752	Kinesin_motor_dom	Domain
IPR019821	Kinesin_motor_CS	Conserved_site
IPR027417	P-loop_NTPase	Homologous_superfamily
IPR027640	Kinesin-like_fam	Family
IPR036961	Kinesin_motor_dom_sf	Homologous_superfamily

Pfam: PF00225

UniProt features (16 total): sequence conflict 5, region of interest 3, compositionally biased region 2, chain 1, domain 1, sequence variant 1, coiled-coil region 1, binding site 1, modified residue 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9Y496-F1	75.65	0.20

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 (1): 100–107

Post-translational modifications (1): 687

Function

Pathways and Gene Ontology

Reactome pathways

20 pathways

ID	Pathway
R-HSA-1445148	Translocation of SLC2A4 (GLUT4) to the plasma membrane
R-HSA-2132295	MHC class II antigen presentation
R-HSA-5610787	Hedgehog ‘off’ state
R-HSA-5620924	Intraflagellar transport
R-HSA-5635838	Activation of SMO
R-HSA-6811434	COPI-dependent Golgi-to-ER retrograde traffic
R-HSA-983189	Kinesins
R-HSA-109582	Hemostasis
R-HSA-1280218	Adaptive Immune System
R-HSA-162582	Signal Transduction
R-HSA-168256	Immune System
R-HSA-1852241	Organelle biogenesis and maintenance
R-HSA-199991	Membrane Trafficking
R-HSA-5358351	Signaling by Hedgehog
R-HSA-5617833	Cilium Assembly
R-HSA-5632684	Hedgehog ‘on’ state
R-HSA-5653656	Vesicle-mediated transport
R-HSA-6811442	Intra-Golgi and retrograde Golgi-to-ER traffic
R-HSA-8856688	Golgi-to-ER retrograde transport
R-HSA-983231	Factors involved in megakaryocyte development and platelet production

MSigDB gene sets: 294 (showing top): MULLIGHAN_NPM1_SIGNATURE_3_UP, GOBP_AXO_DENDRITIC_TRANSPORT, TGCGCANK_UNKNOWN, GOBP_VESICLE_LOCALIZATION, REACTOME_ADAPTIVE_IMMUNE_SYSTEM, GOBP_MICROTUBULE_ANCHORING, GOCC_KINESIN_COMPLEX, REACTOME_MEMBRANE_TRAFFICKING, GOBP_ORGANELLE_TRANSPORT_ALONG_MICROTUBULE, GOMF_GTPASE_BINDING, GOCC_MICROTUBULE_ORGANIZING_CENTER, MODULE_66, GTGCCTT_MIR506, GOBP_VESICLE_CYTOSKELETAL_TRAFFICKING, GOBP_CILIUM_ORGANIZATION

GO Biological Process (16): organelle organization (GO:0006996), anterograde axonal transport (GO:0008089), centriole-centriole cohesion (GO:0010457), protein transport (GO:0015031), microtubule anchoring at centrosome (GO:0034454), cilium assembly (GO:0060271), plus-end-directed vesicle transport along microtubule (GO:0072383), protein localization to cell junction (GO:1902414), microtubule-based movement (GO:0007018), transport along microtubule (GO:0010970), cell projection organization (GO:0030030), response to silicon dioxide (GO:0034021), positive regulation of receptor-mediated endocytosis (GO:0048260), positive regulation of intracellular protein transport (GO:0090316), positive regulation of axo-dendritic protein transport (GO:1905128), positive regulation of establishment or maintenance of cell polarity regulating cell shape (GO:2000771)

GO Molecular Function (14): microtubule motor activity (GO:0003777), ATP binding (GO:0005524), microtubule binding (GO:0008017), plus-end-directed microtubule motor activity (GO:0008574), ATP hydrolysis activity (GO:0016887), protein phosphatase binding (GO:0019903), spectrin binding (GO:0030507), small GTPase binding (GO:0031267), nucleotide binding (GO:0000166), cytoskeletal motor activity (GO:0003774), protein binding (GO:0005515), cytoskeletal protein binding (GO:0008092), kinesin binding (GO:0019894), protein-containing complex binding (GO:0044877)

GO Cellular Component (18): cytoplasm (GO:0005737), centrosome (GO:0005813), centriole (GO:0005814), cytosol (GO:0005829), kinesin complex (GO:0005871), microtubule (GO:0005874), cilium (GO:0005929), microtubule cytoskeleton (GO:0015630), kinesin II complex (GO:0016939), extracellular exosome (GO:0070062), ciliary tip (GO:0097542), axon cytoplasm (GO:1904115), cytoskeleton (GO:0005856), spindle microtubule (GO:0005876), axoneme (GO:0005930), cell projection (GO:0042995), neuronal cell body (GO:0043025), ribbon synapse (GO:0097470)

Reactome top-level categories

Rollup of top-13 pathways:

Category	Pathways
Membrane Trafficking	2
Signaling by Hedgehog	2
Adaptive Immune System	1
Assembly of the 9+0 primary cilium	1
Hedgehog ‘on’ state	1
Golgi-to-ER retrograde transport	1
Factors involved in megakaryocyte development and platelet production	1
Immune System	1
Vesicle-mediated transport	1
Signal Transduction	1
Organelle biogenesis and maintenance	1
Intra-Golgi and retrograde Golgi-to-ER traffic	1
Hemostasis	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	5
cellular component organization	2
intracellular protein localization	2
ATP-dependent activity	2
cytoskeletal protein binding	2
binding	2
microtubule organizing center	2
intracellular membraneless organelle	2
cytoskeleton	2
microtubule	2
axonal transport	1
axon cytoplasm	1
centrosome cycle	1
cell cycle process	1
transport	1
establishment of protein localization	1
microtubule anchoring at microtubule organizing center	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
vesicle transport along microtubule	1
plus-end-directed organelle transport along microtubule	1
microtubule-based process	1
microtubule-based movement	1
cytoskeleton-dependent intracellular transport	1
microtubule-based transport	1
response to oxygen-containing compound	1
receptor-mediated endocytosis	1
positive regulation of endocytosis	1
regulation of receptor-mediated endocytosis	1
intracellular protein transport	1
positive regulation of intracellular transport	1
regulation of intracellular protein transport	1
positive regulation of protein transport	1
positive regulation of intracellular protein transport	1

Protein interactions and networks

STRING

2324 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
KIF3A	KIFAP3	Q92845	998
KIF3A	KIF3B	O15066	984
KIF3A	SMO	Q99835	983
KIF3A	IFT88	Q13099	978
KIF3A	KIF3C	O14782	907
KIF3A	ARRB1	P49407	903
KIF3A	IFT172	Q9UG01	900
KIF3A	ARRB2	P32121	892
KIF3A	SAG	P10523	867
KIF3A	PKD2	Q13563	858
KIF3A	TTC21B	Q7Z4L5	829
KIF3A	MAP3K10	Q02779	826
KIF3A	SUFU	Q9UMX1	802
KIF3A	SHH	Q15465	786
KIF3A	ARL13B	Q3SXY8	773

IntAct

121 interactions, top by confidence:

A	B	Type	Score
KIF3A	KIFAP3	psi-mi:“MI:0403”(colocalization)	0.910
KIFAP3	KIF3A	psi-mi:“MI:0915”(physical association)	0.910
KIFAP3	KIF3B	psi-mi:“MI:0914”(association)	0.900
MED4	MED19	psi-mi:“MI:2364”(proximity)	0.900
KIF3B	KIFAP3	psi-mi:“MI:0914”(association)	0.900
KIFAP3	KIF3B	psi-mi:“MI:0915”(physical association)	0.900
KIF3A	KIF3B	psi-mi:“MI:0914”(association)	0.840
EXOC3	EXOC5	psi-mi:“MI:0914”(association)	0.790
KIF3A	KIF3C	psi-mi:“MI:0914”(association)	0.730
KIFAP3	KIF3C	psi-mi:“MI:0914”(association)	0.640
AP3B1	KIF3A	psi-mi:“MI:0407”(direct interaction)	0.600
KIF3A	AP3B1	psi-mi:“MI:0407”(direct interaction)	0.600
KIF3A	AP3B1	psi-mi:“MI:0915”(physical association)	0.600
AP3B1	KIF3A	psi-mi:“MI:0915”(physical association)	0.600
NUF2	SPC24	psi-mi:“MI:0914”(association)	0.530
STN1	SMCO3	psi-mi:“MI:0914”(association)	0.530
KIFBP	KIF3C	psi-mi:“MI:0914”(association)	0.530
TNFRSF8	DAPK3	psi-mi:“MI:0914”(association)	0.530
HENMT1	SNX2	psi-mi:“MI:0914”(association)	0.530
KIF3B	PSMC5	psi-mi:“MI:0914”(association)	0.510

BioGRID (199): KIF3A (Affinity Capture-MS), KIF3A (Affinity Capture-MS), KIF3A (Affinity Capture-MS), KIF3A (Affinity Capture-MS), KIF3A (Co-fractionation), KIF3A (Affinity Capture-MS), KIF3A (Reconstituted Complex), KIF3A (Proximity Label-MS), KIF3A (Proximity Label-MS), RAN (Affinity Capture-MS), KIF3B (Affinity Capture-MS), DHX34 (Affinity Capture-MS), KIF3A (Affinity Capture-MS), KIF3A (Affinity Capture-MS), KIF3A (Affinity Capture-MS)

ESM2 similar proteins: A0JN40, A8BB91, A8BKD1, B1AVY7, B9F2Y7, F1M4A4, F1M5N7, F1QN54, F4K0J3, G5EGS3, O14782, O15066, O35066, O55165, O60333, O75037, O88658, P28741, P33173, P33176, P34540, P35978, P46867, P46871, P46872, P46873, Q10E64, Q12756, Q29DY1, Q2PQA9, Q4R628, Q5JKW1, Q5R4H3, Q5R706, Q60575, Q61768, Q61771, Q6YUL8, Q7Z4S6, Q86Z98

Diamond homologs: A0A068FIK2, A0JN40, A1ZAJ2, A8BB91, A8BKD1, B1AVY7, B7EJ91, B7ZNG0, B9F2Y7, B9GE13, F1M4A4, F1M5N7, F1QN54, F4IIS5, F4J1U4, F4K0J3, G5EGS3, O14343, O14782, O15066, O23826, O35066, O35071, O35787, O43896, O45935, O55165, O60282, O60333, O75037, O88658, O95239, P17210, P21613, P23678, P28738, P28741, P33173, P33174, P33175

SIGNOR signaling

6 interactions.

A	Effect	B	Mechanism
ARRB2	up-regulates	KIF3A	binding
ARRB1	up-regulates	KIF3A	binding
KIF3A	up-regulates	“Plus-end directed sliding movement”
KIF3A	up-regulates	“Minus-end directed microtubule movement”
AP3B1	“up-regulates activity”	KIF3A	binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 121 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.

GO biological processes:

GO term	Partners	Fold	FDR
microtubule-based movement	5	13.4×	9e-03
non-motile cilium assembly	5	13.2×	9e-03
mitotic spindle organization	5	12.3×	1e-02
cilium assembly	9	6.0×	9e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	45
Likely benign	5
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2744 predictions. Top by Δscore:

Variant	Effect	Δscore
5:132699167:TTACC:T	donor_loss	1.0000
5:132699169:A:AC	donor_gain	1.0000
5:132699169:A:AG	donor_loss	1.0000
5:132699170:C:CC	donor_gain	1.0000
5:132699170:CCTT:C	donor_gain	1.0000
5:132699170:CCTTC:C	donor_loss	1.0000
5:132699292:AGGG:A	acceptor_gain	1.0000
5:132699293:GGG:G	acceptor_gain	1.0000
5:132699294:GG:G	acceptor_gain	1.0000
5:132699295:GCT:G	acceptor_loss	1.0000
5:132699296:C:CC	acceptor_gain	1.0000
5:132699297:T:A	acceptor_loss	1.0000
5:132699300:G:C	acceptor_gain	1.0000
5:132699300:G:GC	acceptor_gain	1.0000
5:132700215:CAT:C	donor_gain	1.0000
5:132700645:A:AC	donor_gain	1.0000
5:132700646:C:CT	donor_gain	1.0000
5:132700646:CTAG:C	donor_gain	1.0000
5:132702077:T:TA	donor_gain	1.0000
5:132702081:TTTTA:T	donor_loss	1.0000
5:132702082:TTTAC:T	donor_loss	1.0000
5:132702083:TTACC:T	donor_loss	1.0000
5:132702084:TAC:T	donor_loss	1.0000
5:132702085:ACCT:A	donor_loss	1.0000
5:132702086:CCTGA:C	donor_loss	1.0000
5:132702208:GCCAT:G	acceptor_gain	1.0000
5:132702209:CCAT:C	acceptor_gain	1.0000
5:132702209:CCATC:C	acceptor_gain	1.0000
5:132702210:CAT:C	acceptor_gain	1.0000
5:132702210:CATC:C	acceptor_gain	1.0000

AlphaMissense

4817 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
5:132700265:C:T	G626E	1.000
5:132700655:A:G	W617R	1.000
5:132700655:A:T	W617R	1.000
5:132702569:C:G	A556P	1.000
5:132702577:A:G	L553P	1.000
5:132702620:C:G	A539P	1.000
5:132702953:A:G	S500P	1.000
5:132715852:A:C	I345S	1.000
5:132715852:A:T	I345N	1.000
5:132715857:C:A	K343N	1.000
5:132715857:C:G	K343N	1.000
5:132715859:T:C	K343E	1.000
5:132715861:G:T	A342D	1.000
5:132715862:C:G	A342P	1.000
5:132715864:C:G	R341P	1.000
5:132715865:G:T	R341S	1.000
5:132715870:G:T	A339D	1.000
5:132715871:C:G	A339P	1.000
5:132715873:T:C	Y338C	1.000
5:132715874:A:G	Y338H	1.000
5:132715876:C:G	R337P	1.000
5:132715879:A:G	L336S	1.000
5:132715882:G:T	T335K	1.000
5:132715927:G:T	A320E	1.000
5:132716259:A:G	S314P	1.000
5:132716264:C:A	G312V	1.000
5:132716264:C:T	G312E	1.000
5:132716265:C:G	G312R	1.000
5:132716265:C:T	G312R	1.000
5:132716267:C:A	G311V	1.000

dbSNP variants (sampled 300 via entrez): RS1000050397 (5:132691484 T>C), RS1000067175 (5:132718122 T>C), RS1000072739 (5:132710814 A>C,G), RS1000088881 (5:132699178 C>T), RS1000144320 (5:132698824 G>A,C), RS1000258761 (5:132733713 T>C), RS1000265307 (5:132726280 A>C,G), RS1000339311 (5:132726065 C>T), RS1000352929 (5:132703826 G>A), RS1000417025 (5:132717691 T>C,G), RS1000477622 (5:132722192 T>C), RS1000565886 (5:132689968 C>T), RS1000601136 (5:132727838 A>G), RS1000674505 (5:132727635 G>A), RS1000718011 (5:132727876 C>A)

Disease associations

OMIM: gene MIM:604683 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

20 associations (top):

Study	Trait	p-value
GCST001363_3	Atopic dermatitis	4.000000e-08
GCST001709_5	Atopic dermatitis	2.000000e-06
GCST002737_2	Atopic dermatitis	5.000000e-09
GCST003180_4	Atopic march	5.000000e-08
GCST003184_27	Atopic dermatitis	1.000000e-10
GCST004862_229	Itch intensity from mosquito bite adjusted by bite size	1.000000e-08
GCST004863_107	Mosquito bite size	3.000000e-07
GCST007564_19	Asthma or allergic disease (pleiotropy)	2.000000e-10
GCST007995_20	Asthma (childhood onset)	3.000000e-22
GCST008916_112	Asthma	2.000000e-11
GCST008916_34	Asthma	2.000000e-09
GCST008916_48	Asthma	1.000000e-11
GCST008916_99	Asthma	6.000000e-32
GCST009798_39	Asthma	5.000000e-29
GCST009798_75	Asthma	9.000000e-24
GCST010002_38	Refractive error	3.000000e-10
GCST010984_17	Allergic disease (asthma, hay fever and/or eczema) (multivariate analysis)	2.000000e-10
GCST010985_4	Allergic disease (asthma, hay fever and/or eczema) (age of onset)	2.000000e-10
GCST90002381_389	Eosinophil count	1.000000e-18
GCST90002382_122	Eosinophil percentage of white cells	1.000000e-10

EFO canonical traits (6, from GWAS)

EFO ID	Trait name
EFO:0007755	atopic march
EFO:0008377	mosquito bite reaction itch intensity measurement
EFO:0008378	mosquito bite reaction size measurement
EFO:0004847	age at onset
EFO:0004842	eosinophil count
EFO:0007991	eosinophil percentage of leukocytes

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL5544 (SINGLE PROTEIN)

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
trichostatin A	increases expression, affects expression	2
Hydrogen Peroxide	increases expression, affects expression	2
Valproic Acid	increases expression	2
triphenyl phosphate	affects expression	1
bisphenol A	increases methylation	1
arsenic disulfide	decreases expression	1
CD 437	decreases expression	1
3-(4’-hydroxy-3’-adamantylbiphenyl-4-yl)acrylic acid	decreases expression	1
abrine	decreases expression	1
(+)-JQ1 compound	increases expression	1
Sunitinib	increases expression	1
Arsenic Trioxide	increases expression	1
Vorinostat	decreases expression	1
Acetaminophen	increases expression	1
Air Pollutants	decreases expression, increases abundance	1
Aspirin	increases expression, affects response to substance	1
Benzo(a)pyrene	affects methylation	1
Cyclophosphamide	affects cotreatment, affects response to substance	1
Demecolcine	increases expression	1
Dimethyl Sulfoxide	decreases expression	1
Doxorubicin	affects cotreatment, affects response to substance	1
Fluorouracil	affects cotreatment, affects response to substance	1
Mercuric Chloride	decreases expression	1
Polychlorinated Biphenyls	affects expression	1
Quercetin	decreases expression	1
Rotenone	decreases expression	1
Urethane	increases expression	1
Vanadates	decreases expression	1
Cyclosporine	increases expression	1
Aflatoxin M1	decreases expression	1

ChEMBL screening assays

1 unique, capped per target: 1 binding

Representative assays (with source publication via chembl_document):

Assay ID	Type	Description	Source paper
CHEMBL1020051	Binding	Inhibition of cloned human Kif3A	Kinesin spindle protein (KSP) inhibitors. 9. Discovery of (2S)-4-(2,5-difluorophenyl)-n-[(3R,4S)-3-fluoro-1-methylpiperidin-4-yl]-2-(hydroxymethyl)-N-methyl-2-phenyl-2,5-dihydro-1H-pyrrole-1-carboxamide (MK-0731) for the treatment of taxane-refractory cancer. — J Med Chem

Clinical trials (associated diseases)

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