KIF5B

kinesin family member 5B, the group of Kinesins

Basic information

Region (hg38): 10:32009015-32056425

Previous symbols: [ "KNS1" ]

Links

ENSG00000170759 ∙ NCBI:3799 ∙ OMIM:602809 ∙ HGNC:6324 ∙ Uniprot:P33176 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• disease (Moderate), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the KIF5B gene.

• 6 conditions (1 variants)
• Feeding difficulties;Intellectual disability;Severe muscular hypotonia;Fatigable weakness of swallowing muscles (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KIF5B 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
missense	2	1	42	3		48
nonsense			1			1
start loss						0
frameshift						0
inframe indel		1	1			2
splice donor/acceptor (+/-2bp)			2			2
splice region					1	1
non coding						0
Total	2	2	46	3	1

Variants in KIF5B

This is a list of pathogenic ClinVar variants found in the KIF5B region.

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

Position	Type	Phenotype	Significance	ClinVar
10-32015539-T-C			Uncertain significance (Apr 17, 2024)
10-32015558-C-T		not specified	Uncertain significance (Aug 12, 2021)
10-32015560-G-A		not specified	Uncertain significance (Jan 16, 2024)
10-32015608-C-T		not specified	Uncertain significance (Oct 12, 2022)
10-32017183-C-G		not specified	Uncertain significance (Dec 06, 2024)
10-32017293-C-T		not specified	Uncertain significance (Jul 26, 2024)
10-32017339-A-T			Uncertain significance (Oct 17, 2022)
10-32017352-C-A		not specified	Uncertain significance (Sep 20, 2023)
10-32018051-C-A			Uncertain significance (Jul 10, 2024)
10-32018069-T-C			Uncertain significance (May 14, 2024)
10-32018099-A-T		not specified	Uncertain significance (Feb 22, 2024)
10-32018121-G-A			Benign (Oct 10, 2018)
10-32019867-T-C		not specified	Uncertain significance (Oct 24, 2023)
10-32019912-T-C		Brain atrophy;Global developmental delay;Hypoplasia of the corpus callosum;Seizure;Attention deficit hyperactivity disorder	Likely pathogenic (Jan 10, 2016)
10-32021034-G-A		not specified	Uncertain significance (Jul 09, 2021)
10-32021058-A-G		not specified	Uncertain significance (May 31, 2023)
10-32021114-C-A		not specified	Uncertain significance (Dec 16, 2022)
10-32021118-T-C		not specified	Uncertain significance (May 27, 2022)
10-32021131-G-A			Uncertain significance (Dec 12, 2023)
10-32022139-C-AA			Uncertain significance (Apr 28, 2023)
10-32022229-T-G		not specified	Uncertain significance (Jul 14, 2023)
10-32022933-T-C			Uncertain significance (Sep 23, 2022)
10-32022996-A-G		not specified	Uncertain significance (May 27, 2022)
10-32023011-T-A			Uncertain significance (May 31, 2024)
10-32023018-T-C		not specified	Uncertain significance (May 25, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KIF5B	protein_coding	protein_coding	ENST00000302418	25	47422

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.994	0.00573	125708	0	40	125748	0.000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.06	306	498	0.615	0.0000255	6398
Missense in Polyphen		75	186.75	0.40162		2428
Synonymous	-0.381	171	165	1.04	0.00000794	1698
Loss of Function	5.94	10	59.4	0.168	0.00000328	728

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000269	0.000268
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.000232	0.000231
European (Non-Finnish)	0.000196	0.000193
Middle Eastern	0.00	0.00
South Asian	0.000132	0.000131
Other	0.000327	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Microtubule-dependent motor required for normal distribution of mitochondria and lysosomes. Can induce formation of neurite-like membrane protrusions in non-neuronal cells in a ZFYVE27-dependent manner (By similarity). Regulates centrosome and nuclear positioning during mitotic entry. During the G2 phase of the cell cycle in a BICD2-dependent manner, antagonizes dynein function and drives the separation of nuclei and centrosomes (PubMed:20386726). Required for anterograde axonal transportation of MAPK8IP3/JIP3 which is essential for MAPK8IP3/JIP3 function in axon elongation (By similarity). {ECO:0000250|UniProtKB:Q2PQA9, ECO:0000250|UniProtKB:Q61768, ECO:0000269|PubMed:20386726}.
• Pathway: Dopaminergic synapse - Homo sapiens (human);Endocytosis - Homo sapiens (human);Insulin Signaling;Signal Transduction;Vesicle-mediated transport;Membrane Trafficking;RHO GTPases activate KTN1;Kinesins;Factors involved in megakaryocyte development and platelet production;RHO GTPase Effectors;Signaling by Rho GTPases;Hemostasis;COPI-dependent Golgi-to-ER retrograde traffic;Golgi-to-ER retrograde transport;N-cadherin signaling events;Intra-Golgi and retrograde Golgi-to-ER traffic (Consensus)

Recessive Scores

• pRec: 0.117

Intolerance Scores

• loftool: 0.316
• rvis_EVS: -0.93
• rvis_percentile_EVS: 9.55

Haploinsufficiency Scores

• pHI: 0.573
• hipred: Y
• hipred_score: 0.648
• ghis: 0.624

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.636

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Kif5b
• Phenotype: growth/size/body region phenotype; endocrine/exocrine gland phenotype; homeostasis/metabolism phenotype; cellular phenotype; embryo phenotype; 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)

Zebrafish Information Network

• Gene name: kif5ba
• Affected structure: chondrocyte
• Phenotype tag: abnormal
• Phenotype quality: decreased occurrence

Gene ontology

• Biological process: microtubule-based movement;cytoplasm organization;hippocampus development;positive regulation of vesicle fusion;positive regulation of synaptic transmission, GABAergic;stress granule disassembly;positive regulation of insulin secretion involved in cellular response to glucose stimulus;regulation of membrane potential;positive regulation of potassium ion transport;vesicle transport along microtubule;centrosome localization;cellular response to interferon-gamma;plus-end-directed vesicle transport along microtubule;positive regulation of intracellular protein transport;anterograde axonal protein transport;positive regulation of protein localization to plasma membrane;positive regulation of voltage-gated sodium channel activity;anterograde neuronal dense core vesicle transport;retrograde neuronal dense core vesicle transport
• Cellular component: microtubule organizing center;cytosol;kinesin complex;microtubule;membrane;vesicle;ciliary rootlet;axonal growth cone;phagocytic vesicle;perinuclear region of cytoplasm;axon cytoplasm
• Molecular function: microtubule motor activity;protein binding;ATP binding;microtubule binding;JUN kinase binding;ATPase activity;identical protein binding;cadherin binding;microtubule lateral binding