KIF3B

protein-coding

kinesin family member 3B, the group of Kinesins

Gene summary

The protein encoded by this gene acts as a heterodimer with kinesin family member 3A to aid in chromosome movement during mitosis and meiosis. The encoded protein is a plus end-directed microtubule motor and can interact with the SMC3 subunit of the cohesin complex. In addition, the encoded protein may be involved in the intracellular movement of membranous organelles. This protein and kinesin family member 3A form the kinesin II subfamily of the kinesin superfamily. [provided by RefSeq, Jul 2008]

MANE transcript

NM_004798.4

Inheritance

AD, AR

ClinVar variants

P:2U:76B:7

Top phenotype

Retinitis pigmentosa 89

gnomAD constraint

pLI —, LoF o/e 0.26

Max pathogenic AF

—

Genomic locus

chr20:32,277,651-32,335,011

External References & Databases

Ensembl (ENSG00000101350)

Transcript & Mutation Effects

hg38 • Region Span ~57.4 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

retinitis pigmentosa 89STRONG

Inheritance Pattern: AD

Disease ID:MONDO:0030071

Submitter: Labcorp Genetics (formerly Invitae)

retinitis pigmentosa 89LIMITED

Inheritance Pattern: AD

Disease ID:MONDO:0030071

Submitter: Ambry Genetics

retinitis pigmentosa 89MODERATE

Inheritance Pattern: AD

Disease ID:MONDO:0030071

Submitter: PanelApp Australia

ciliopathyLIMITED

Inheritance Pattern: AD

Disease ID:MONDO:0005308

Submitter: G2P

ciliopathyMODERATE

Inheritance Pattern: AD

Disease ID:MONDO:0005308

Submitter: Franklin by Genoox

Two unrelated families with hallmark ciliopathy phenotypes. In the first family, the proband presents with hepatic fibrosis, retinitis pigmentosa, and postaxial polydactyly. The second family is a six-generation pedigree affected predominantly by retinitis pigmentosa. Both families were found to carry KIF3B mutation which was segregated with the disease. https://doi.org/10.1016/j.ajhg.2020.04.005

Clinical Genomic Database (CGD)

Retinitis pigmentosa 89AR

Manifestation: Audiologic/Otolaryngologic; Cardiovascular; Gastrointestinal; Musculoskeletal; Ophthalmologic; Renal

Intervention: Cardiovascular; Gastrointestinal

Rationale: 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

Refs: 32386558; 37399313

Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to KIF3B variants in ClinVar

7 Conditions Cataloged

not specifiedTotal: 65

Retinitis pigmentosa 89Total: 7

not providedTotal: 5

Retinal dystrophyTotal: 3

KIF3B-related disorderTotal: 2

Optic atrophyTotal: 1

OligospermiaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_004798.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	3 clinvar	1 clinvar	5
missense	2 clinvar		71 clinvar	2 clinvar		75
nonsense			2 clinvar			2
start loss						0
frameshift			1 clinvar	1 clinvar		2
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	2	0	76	6	1	85

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 9 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_004798.4	RefSeq	NP_004789.1	8	MANE Select
ENST00000375712.4	Ensembl	ENSP00000364864.3	8	MANE Select
ENST00000929131.1	Ensembl	ENSP00000599190.1	8	Standard
ENST00000929131.2	Ensembl	ENSP00000599190.1	8	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
kif3b	Danio rerio	Structure: retinal rod cell Quality: degenerate abnormal

Gene / Model

Organism

Observed Phenotype

kif3b

Danio rerio

Structure: retinal rod cell

Quality: degenerate

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Vesicle-mediated transport
Membrane Trafficking
Kinesins
Factors involved in megakaryocyte development and platelet production
Hemostasis

Biological Process

retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum
microtubule-based movement
mitotic spindle organization
mitotic centrosome separation
determination of left/right symmetry

Molecular Function

microtubule motor activity
protein binding
ATP binding
microtubule binding
ATP-dependent microtubule motor activity, plus-end-directed

Cellular Component

centrosome
cytosol
kinesin complex
plus-end kinesin complex
microtubule

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000375712
Coding exons: 8
Length: 57348
Individuals with no LoFs: 125721
Homozygous LoFs: 0
Heterozygous LoFs: 17
Defined: 125738
p: 0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	3.00	259	435	0.595	0.0000251	4908
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000063	0.000062	rare
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00027	0.00027	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000080	0.000079	rare
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.211

Intolerance Scores

LoFtool: 0.458
RVIS EVS: -0.67
RVIS percentile EVS: 15.76

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.921

Gene Damage Prediction

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