KIF3A
protein-codingkinesin family member 3A, the group of Kinesins
Gene summary
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. Implicated in allergic disease and asthma. Biomarker of asthma and silicosis. [provided by Alliance of Genome Resources, Jun 2026]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~45.0 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to KIF3A variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001300791.2. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 1 | ||||
| missense | 49 | 1 | 50 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 4 | 4 | ||||
| Total | 0 | 0 | 53 | 2 | 0 | 55 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001287720.1 | 19 | MANE Select | |
| Ensembl | ENSP00000385808.1 | 19 | MANE Select | |
| RefSeq | NP_001287721.1 | 18 | Standard | |
| RefSeq | NP_008985.3 | 17 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| kif3a | Danio rerio | Structure: retinal rod cell Quality: decreased amount abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Hedgehog signaling pathway - Homo sapiens (human)
- Hedgehog Signaling Pathway
- Endochondral Ossification
- Insulin Signaling
- Signal Transduction
Biological Process
- retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum
- organelle organization
- microtubule-based movement
- axon guidance
- anterograde axonal transport
Molecular Function
- microtubule motor activity
- protein binding
- ATP binding
- microtubule binding
- ATP-dependent microtubule motor activity, plus-end-directed
Cellular Component
- centrosome
- centriole
- cytosol
- kinesin complex
- microtubule
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000378746
- Coding exons
- 17
- Length
- 45011
- Individuals with no LoFs
- 125737
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 11
- Defined
- 125748
- p
- 0.0000437
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 3.09 | 209 | 378 | 0.553 | 0.0000198 | 4614 |
| Missense (PolyPhen) | 42 | 122.07 | 0.34405 | 1449 | ||
| Synonymous | 1.09 | 104 | 119 | 0.873 | 0.00000573 | 1263 |
| Loss of Function | 4.68 | 7 | 38.2 | 0.183 | 0.00000192 | 505 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000062 | 0.000062 | rare |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0.000099 | 0.000099 | rare |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000081 | 0.000079 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- 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 recruitement of DCTN1 to the centriole. Also required for ciliary basal feet formation and microtubule anchoring to mother centriole. {ECO:0000250|UniProtKB:P28741}.;
Recessive Scores
- pRec
- 0.248
Intolerance Scores
- LoFtool
- 0.179
- RVIS EVS
- -0.63
- RVIS percentile EVS
- 17.03
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.897
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | High |
| Cancer | High | Medium | High |