KIF9

protein-coding

kinesin family member 9, the group of Kinesins

Gene summary

Enables identical protein binding activity. Involved in extracellular matrix disassembly; organelle disassembly; and regulation of podosome assembly. Located in microtubule; podosome; and vesicle. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_182902.4

Inheritance

—

ClinVar variants

U:118B:6

Top phenotype

Primary ciliary dyskinesia

gnomAD constraint

pLI —, LoF o/e 0.87

Max pathogenic AF

—

Genomic locus

chr3:47,227,998-47,283,451

External References & Databases

Ensembl (ENSG00000088727)

Transcript & Mutation Effects

hg38 • Region Span ~55.5 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to KIF9 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 116

Primary ciliary dyskinesiaTotal: 2

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_182902.4. 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		1
missense			115 clinvar	5 clinvar		120
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	118	6	0	124

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 55 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_182902.4	RefSeq	NP_878905.2	20	MANE Select
ENST00000684063.1	Ensembl	ENSP00000507186.1	20	MANE Select
NM_001134878.3	RefSeq	NP_001128350.1	20	Standard
NM_001377474.1	RefSeq	NP_001364403.1	19	Standard

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

microtubule-based movement
extracellular matrix disassembly
regulation of podosome assembly
organelle disassembly

Molecular Function

microtubule motor activity
protein binding
ATP binding
microtubule binding
ATPase activity

Cellular Component

podosome
cytoplasm
kinesin complex
microtubule
vesicle

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000335044
Coding exons: 20
Length: 55426
Individuals with no LoFs: 125588
Homozygous LoFs: 0
Heterozygous LoFs: 160
Defined: 125748
p: 0.000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.576	418	452	0.924	0.0000252	5218
Missense (PolyPhen)		108	129.76	0.83233		1522
Synonymous	0.826	158	172	0.920	0.00000944	1476
Loss of Function	0.805	36	41.6	0.865	0.00000195	511

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00055	0.00055	rare
Latino/Admixed American	0.0014	0.0014	notable
Ashkenazi Jewish	0.00020	0.00020	rare
East Asian	0.0021	0.0021	notable
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00040	0.00040	rare
South Asian	0.00040	0.00039	rare
Other	0.00065	0.00065	rare

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.975
RVIS EVS: 0.2
RVIS percentile EVS: 67.46

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.357

Gene Damage Prediction

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