KIF3B

kinesin family member 3B, the group of Kinesins

Basic information

Region (hg38): 20:32277651-32335011

Links

ENSG00000101350 ∙ NCBI:9371 ∙ OMIM:603754 ∙ HGNC:6320 ∙ Uniprot:O15066 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• ciliopathy (Moderate), mode of inheritance: AD
• retinitis pigmentosa 89 (Limited), mode of inheritance: AD
• retinitis pigmentosa 89 (Strong), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Retinitis pigmentosa 89	AR	Cardiovascular; Gastrointestinal	Among other features, the condition can include cardiac valvular anomalies, and early identificaiton may enable interventions; The condition can involve gastrointestinal anomalies, including leading to esophageal varices and other sequelae, and awareness may allow early identification and management	Audiologic/Otolaryngologic; Cardiovascular; Gastrointestinal; Musculoskeletal; Ophthalmologic; Renal	32386558; 37399313

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the KIF3B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KIF3B 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				1	1	2
missense			26			26
nonsense						0
start loss						0
frameshift				1		1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	26	2	1

Variants in KIF3B

This is a list of pathogenic ClinVar variants found in the KIF3B region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
20-32277706-CCCG-C		Retinal dystrophy	Uncertain significance (Jan 01, 2022)
20-32277706-CCCGCCGCCGCCG-C		Retinal dystrophy	Uncertain significance (Jan 01, 2022)
20-32277706-C-CCCG		Optic atrophy	Likely benign (Jan 01, 2023)
20-32309826-C-T		not specified	Uncertain significance (Nov 09, 2022)
20-32309834-G-C		not specified	Uncertain significance (Apr 10, 2023)
20-32309923-C-A		not specified	Uncertain significance (Mar 07, 2024)
20-32309923-C-T		not specified	Uncertain significance (Mar 31, 2023)
20-32309928-C-T		not specified	Uncertain significance (May 24, 2024)
20-32309937-C-T		not specified	Uncertain significance (Jun 12, 2023)
20-32309973-A-T		not specified	Uncertain significance (Jul 23, 2024)
20-32310106-G-A		not specified • Optic atrophy	Uncertain significance (Jul 22, 2024)
20-32310234-C-T		not specified	Uncertain significance (Nov 18, 2024)
20-32310250-A-G		not specified	Uncertain significance (Sep 26, 2024)
20-32310290-C-G		not specified	Uncertain significance (May 28, 2024)
20-32310297-G-T		not specified	Uncertain significance (Oct 24, 2024)
20-32310312-C-G		not specified	Uncertain significance (May 28, 2024)
20-32310328-C-T		not specified	Uncertain significance (Dec 15, 2023)
20-32310364-T-C		not specified	Uncertain significance (Oct 05, 2023)
20-32310399-A-G		KIF3B-related disorder	Uncertain significance (Mar 29, 2023)
20-32310434-C-G		Retinal dystrophy	Uncertain significance (Jan 01, 2022)
20-32310456-G-A		not specified	Uncertain significance (Oct 03, 2022)
20-32310502-A-G		not specified	Uncertain significance (Apr 26, 2024)
20-32310525-G-C		Retinitis pigmentosa 89	Pathogenic (Jul 16, 2020)
20-32310529-G-A		not specified	Uncertain significance (Jan 24, 2024)
20-32310595-C-T		not specified	Uncertain significance (Apr 21, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KIF3B	protein_coding	protein_coding	ENST00000375712	8	57348

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0842	0.916	125721	0	17	125738	0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.00	259	435	0.595	0.0000251	4908
Missense in Polyphen		48	119.68	0.40108		1344
Synonymous	0.148	161	163	0.985	0.00000928	1440
Loss of Function	4.06	9	34.9	0.258	0.00000220	392

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000916	0.0000905
Ashkenazi Jewish	0.00	0.00
East Asian	0.000272	0.000272
Finnish	0.00	0.00
European (Non-Finnish)	0.0000800	0.0000791
Middle Eastern	0.000272	0.000272
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in tethering the chromosomes to the spindle pole and in chromosome movement. Microtubule-based anterograde translocator for membranous organelles. Plus end-directed microtubule sliding activity in vitro (By similarity). {ECO:0000250}.
• Pathway: Vesicle-mediated transport;Membrane Trafficking;Kinesins;Factors involved in megakaryocyte development and platelet production;Hemostasis;COPI-dependent Golgi-to-ER retrograde traffic;Golgi-to-ER retrograde transport;Translocation of GLUT4 to the plasma membrane;Intra-Golgi and retrograde Golgi-to-ER traffic;Intraflagellar transport;Cilium Assembly;Organelle biogenesis and maintenance (Consensus)

Recessive Scores

• pRec: 0.211

Intolerance Scores

• loftool: 0.458
• rvis_EVS: -0.67
• rvis_percentile_EVS: 15.76

Haploinsufficiency Scores

• pHI: 0.381
• hipred: Y
• hipred_score: 0.601
• ghis: 0.609

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.921

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Kif3b
• Phenotype: embryo phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms 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); hematopoietic system 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); 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); skeleton phenotype; growth/size/body region phenotype; cellular phenotype

Zebrafish Information Network

• Gene name: kif3b
• Affected structure: retinal rod cell
• Phenotype tag: abnormal
• Phenotype quality: degenerate

Gene ontology

• Biological process: retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum;microtubule-based movement;mitotic spindle organization;mitotic centrosome separation;determination of left/right symmetry;anterograde axonal transport;antigen processing and presentation of exogenous peptide antigen via MHC class II;positive regulation of cytokinesis;intraciliary transport involved in cilium assembly;plus-end-directed vesicle transport along microtubule;mitotic spindle assembly
• Cellular component: centrosome;cytosol;kinesin complex;plus-end kinesin complex;microtubule;spindle microtubule;cilium;microtubule cytoskeleton;membrane;kinesin II complex;midbody;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;Rho GTPase binding;intraciliary transport particle B binding