KIF3C
protein-codingkinesin family member 3C, the group of Kinesins
Gene summary
Predicted to enable ATP hydrolysis activity; microtubule binding activity; and microtubule motor activity. Predicted to be involved in microtubule-based movement. Predicted to be located in microtubule cytoskeleton; neuronal cell body; and neuronal ribonucleoprotein granule. Predicted to be part of kinesin complex. Predicted to be active in cytoplasm and microtubule. [provided by Alliance of Genome Resources, Jul 2025]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~56.2 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 KIF3C variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_002254.8. 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 | 101 | 2 | 103 | |||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 2 | 2 | ||||
| splice donor/acceptor (+/-2bp) | 3 | 3 | ||||
| Total | 0 | 0 | 107 | 3 | 0 | 110 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_002245.4 | 8 | MANE Select | |
| Ensembl | ENSP00000264712.3 | 8 | MANE Select | |
| Ensembl | ENSP00000385030.1 | 8 | Standard | |
| Ensembl | ENSP00000385030.1 | 8 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| kif3cb | Danio rerio | Structure: photoreceptor outer segment layer Quality: decreased variability of size abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Vesicle-mediated transport
- Membrane Trafficking
- Kinesins
- Factors involved in megakaryocyte development and platelet production
- Hemostasis
Biological Process
- retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum
- microtubule-based movement
- antigen processing and presentation of exogenous peptide antigen via MHC class II
- intraciliary transport involved in cilium assembly
- organelle transport along microtubule
Molecular Function
- motor activity
- microtubule motor activity
- ATP binding
- microtubule binding
- ATPase activity
Cellular Component
- cytosol
- kinesin complex
- microtubule
- cilium
- ciliary tip
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000264712
- Coding exons
- 8
- Length
- 56148
- Individuals with no LoFs
- 125743
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 5
- Defined
- 125748
- p
- 0.0000199
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 2.36 | 358 | 508 | 0.705 | 0.0000326 | 5213 |
| Missense (PolyPhen) | 97 | 184.93 | 0.52451 | 1956 | ||
| Synonymous | 1.31 | 186 | 210 | 0.885 | 0.0000135 | 1598 |
| Loss of Function | 4.58 | 4 | 31.9 | 0.125 | 0.00000178 | 348 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0.00010 | 0.000099 | rare |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000035 | 0.000035 | 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. {ECO:0000250}.;
Recessive Scores
- pRec
- 0.109
Intolerance Scores
- LoFtool
- 0.254
- RVIS EVS
- -0.75
- RVIS percentile EVS
- 13.67
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.674
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |