KIF3A
kinesin family member 3A, the group of Kinesins
Basic information
Region (hg38): 5:132692628-132737638
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the KIF3A gene is commonly pathogenic or not.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 13 | 14 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 2 | 2 | ||||
| non coding | 1 | |||||
| Total | 0 | 0 | 13 | 2 | 0 |
Variants in KIF3A
This is a list of pathogenic ClinVar variants found in the KIF3A region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 5-132696677-C-T | not specified | Uncertain significance (Feb 10, 2022) | ||
| 5-132700697-T-C | not specified | Uncertain significance (Sep 17, 2021) | ||
| 5-132702097-C-T | not specified | Likely benign (Nov 15, 2021) | ||
| 5-132702122-G-T | not specified | Uncertain significance (Apr 04, 2024) | ||
| 5-132702138-C-A | not specified | Uncertain significance (May 08, 2024) | ||
| 5-132702143-G-A | not specified | Uncertain significance (Apr 07, 2023) | ||
| 5-132702967-T-G | not specified | Uncertain significance (Mar 27, 2023) | ||
| 5-132703040-T-C | not specified | Uncertain significance (Mar 01, 2023) | ||
| 5-132703042-T-C | not specified | Uncertain significance (Jan 03, 2024) | ||
| 5-132703073-T-A | KIF3A-related disorder | Likely benign (Oct 23, 2020) | ||
| 5-132703484-T-A | not specified | Uncertain significance (Sep 27, 2021) | ||
| 5-132708898-A-G | KIF3A-related disorder | Likely benign (Nov 23, 2020) | ||
| 5-132715826-C-A | not specified | Uncertain significance (Dec 02, 2022) | ||
| 5-132716337-C-T | not specified | Uncertain significance (Oct 05, 2023) | ||
| 5-132716886-T-A | not specified | Uncertain significance (Sep 06, 2022) | ||
| 5-132716917-T-C | not specified | Uncertain significance (Apr 11, 2023) | ||
| 5-132720716-T-TA | KIF3A-related disorder | Likely benign (Nov 23, 2020) | ||
| 5-132726142-T-C | not specified | Uncertain significance (Jan 09, 2024) | ||
| 5-132726369-G-A | not specified | Uncertain significance (May 09, 2024) | ||
| 5-132726483-T-C | not specified | Uncertain significance (Jun 18, 2024) | ||
| 5-132734337-T-C | not specified | Uncertain significance (Aug 02, 2023) | ||
| 5-132734411-T-C | not specified | Uncertain significance (Mar 26, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| KIF3A | protein_coding | protein_coding | ENST00000378746 | 17 | 45011 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.898 | 0.102 | 125737 | 0 | 11 | 125748 | 0.0000437 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 3.09 | 209 | 378 | 0.553 | 0.0000198 | 4614 |
| Missense in 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 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000615 | 0.0000615 |
| Ashkenazi Jewish | 0.0000994 | 0.0000992 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000814 | 0.0000791 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
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}.;
- Pathway
- Hedgehog signaling pathway - Homo sapiens (human);Hedgehog Signaling Pathway;Endochondral Ossification;Insulin Signaling;Signal Transduction;Vesicle-mediated transport;Membrane Trafficking;Kinesins;Factors involved in megakaryocyte development and platelet production;Activation of SMO;Hedgehog;Hedgehog ,on, state;Signaling by Hedgehog;Hemostasis;COPI-dependent Golgi-to-ER retrograde traffic;Golgi-to-ER retrograde transport;Translocation of GLUT4 to the plasma membrane;Hedgehog signaling events mediated by Gli proteins;Intra-Golgi and retrograde Golgi-to-ER traffic;Intraflagellar transport;Cilium Assembly;Organelle biogenesis and maintenance
(Consensus)
Recessive Scores
- pRec
- 0.248
Intolerance Scores
- loftool
- 0.179
- rvis_EVS
- -0.63
- rvis_percentile_EVS
- 17.03
Haploinsufficiency Scores
- pHI
- 0.543
- hipred
- Y
- hipred_score
- 0.786
- ghis
- 0.653
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.897
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | High |
| Cancer | High | Medium | High |
Mouse Genome Informatics
- Gene name
- Kif3a
- Phenotype
- respiratory system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); embryo phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); vision/eye phenotype; digestive/alimentary phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); limbs/digits/tail phenotype; renal/urinary system phenotype; skeleton phenotype; homeostasis/metabolism phenotype; cellular phenotype; growth/size/body region phenotype; craniofacial phenotype;
Zebrafish Information Network
- Gene name
- kif3a
- Affected structure
- retinal rod cell
- Phenotype tag
- abnormal
- Phenotype quality
- decreased amount
Gene ontology
- Biological process
- retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum;organelle organization;microtubule-based movement;axon guidance;anterograde axonal transport;centriole-centriole cohesion;protein transport;antigen processing and presentation of exogenous peptide antigen via MHC class II;microtubule anchoring at centrosome;intraciliary transport involved in cilium assembly;cilium assembly;plus-end-directed vesicle transport along microtubule;protein localization to cell junction
- Cellular component
- centrosome;centriole;cytosol;kinesin complex;microtubule;spindle microtubule;cilium;microtubule cytoskeleton;kinesin II complex;extracellular exosome;ciliary tip;axon cytoplasm
- Molecular function
- microtubule motor activity;protein binding;ATP binding;microtubule binding;ATP-dependent microtubule motor activity, plus-end-directed;ATPase activity;Rab GTPase binding;protein phosphatase binding;spectrin binding