KIF3A

Chr 5

kinesin family member 3A

Also known as: FLA10, KLP-20

NCBI Gene: 11127ENSG00000131437UniProt: Q9Y496

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. [provided by Alliance of Genome Resources, Jul 2025]

67
ClinVar variants
14
Pathogenic / LP
0.90
pLI score
0
Active trials
Clinical Summary— KIF3A
⚡
Population Constraint (gnomAD)
Moderately constrained gene (pLI 0.90) — some intolerance to loss-of-function variants.
📋
ClinVar Variants
14 Pathogenic / Likely Pathogenic· 47 VUS of 67 total submissions

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Dual constrained — LoF & missense intolerant
LoF Constraint?LOEUF (Loss-of-function Observed/Expected Upper bound Fraction) is the upper bound of the 90% CI for LoF OE — the preferred gnomAD v4 metric. Lower = more intolerant to LoF. LOEUF < 0.35 = highly constrained.
0.34LOEUF
pLI 0.898
Z-score 4.68
OE 0.18 (0.10–0.34)
Highly constrained

Highly LoF-intolerant (top ~10% of genes)

Missense Constraint?Missense Z-score: standard deviations fewer missense variants observed vs. expected. Z > 3.09 (p < 0.001) = gene does not tolerate missense variation. OE missense < 0.6 is also considered constrained.
3.09Z-score
OE missense 0.55 (0.49–0.62)
209 obs / 378.2 exp
Constrained

Highly missense-constrained (top ~0.1%)

Observed / Expected Ratios?Shaded band = 90% confidence interval. Vertical tick = point estimate. Grey threshold line = gnomAD constraint cutoff for that variant class.
LoF OE?Ratio of observed to expected LoF variants. Upper CI bound (LOEUF) ≤ 0.35 = strong LoF constraint signal.0.18 (0.10–0.34)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.0.55 (0.49–0.62)
0≤0.61.4
Synonymous OE?Control metric — synonymous variants are largely neutral and expected near OE = 1.0. Significant deviation may indicate annotation issues.0.87
0≤1.21.6
LoF obs/exp: 7 / 38.2Missense obs/exp: 209 / 378.2Syn Z: 1.09

ClinVar Variant Classifications

67 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic13
Likely Pathogenic1
VUS47
Likely Benign6
13
Pathogenic
1
Likely Pathogenic
47
VUS
6
Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
13
0
13
Likely Pathogenic
0
0
1
0
1
VUS
0
45
2
0
47
Likely Benign
0
1
4
1
6
Benign
0
0
0
0
0
Total04620167

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

KIF3A · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

OMIM — Genotype-Phenotype Relationships

1 OMIM entry

OMIM
Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
Inhibitory mechanism of KIF3A gene on nasopharyngeal carcinoma stem cells.
Liu R et al.·Cell Mol Biol (Noisy-le-grand)
2023Functional
Primary cilia as a targetable node between biliary injury, senescence and regeneration in liver transplantation.
Esser H et al.·J Hepatol
2024
Cyclin-dependent kinase 4 drives cystic kidney disease in the absence of mTORC1 signaling activity.
Grahammer F et al.·Kidney Int
2024
Regulatory role of primary cilia in oral and maxillofacial development and disease.
Liu Z et al.·Tissue Cell
2024Review
The cilium: a cellular antenna with an influence on obesity risk.
Mariman EC et al.·Br J Nutr
2016Review
Mutations in the Kinesin-2 Motor KIF3B Cause an Autosomal-Dominant Ciliopathy.
Cogné B et al.·Am J Hum Genet
2020
Identification and dynamic transcription of KIF3A homologue gene in spermiogenesis of Octopus tankahkeei.
Wang W et al.·Comp Biochem Physiol A Mol Integr Physiol
2010
Loss of Glis2/NPHP7 causes kidney epithelial cell senescence and suppresses cyst growth in the Kif3a mouse model of cystic kidney disease.
Lu D et al.·Kidney Int
2016Functional
Identification of two early life eczema and non-eczema phenotypes with high risk for asthma development.
Johansson E et al.·Clin Exp Allergy
2019Clinical trial
Gardner's syndrome (familial adenomatous polyposis): a cilia-related disorder.
Gómez García EB et al.·Lancet Oncol
2009Review
Top 10 resultsSearch PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →

External Resources

Links to major genomics databases and tools