KIF3A

kinesin family member 3A, the group of Kinesins

Basic information

Region (hg38): 5:132692627-132737638

Links

ENSG00000131437 ∙ NCBI:11127 ∙ OMIM:604683 ∙ HGNC:6319 ∙ Uniprot:Q9Y496 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the KIF3A gene.

• Inborn genetic diseases (11 variants)

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			10	1		11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	1	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)
5-132702143-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)
5-132734337-T-C		not specified	Uncertain significance (Aug 02, 2023)

GnomAD

Source: gnomAD

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: dbNSFP

• 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