KIF24

protein-coding

kinesin family member 24, the group of Small nucleolar RNA protein coding host genes|Kinesins|Sterile alpha motif domain containing

Gene summary

This gene encodes a member of the kinesin superfamily of microtubule-based motor proteins which are involved in the intracellular transport of membranous organelles, protein complexes, and mRNAs. They also play critical roles in mitosis, morphogenesis, and signal transduction. The encoded protein contains an N-terminal sterile alpha motif (SAM) domain and an ATP-binding kinesin motor domain. It binds centriolar coiled coil protein 110 and centrosomal protein 97 and localizes to the mother centriole to regulate ciliogenesis by controlling microtubule polymerization. [provided by RefSeq, Mar 2017]

Previous symbols:

C9orf48

MANE transcript

NM_194313.4

Inheritance

—

ClinVar variants

P:1U:182B:28

Top phenotype

EBV-positive nodal T- and NK-cell lymphoma

gnomAD constraint

pLI —, LoF o/e 0.67

Max pathogenic AF

—

Genomic locus

chr9:34,252,380-34,329,268

External References & Databases

Ensembl (ENSG00000186638)

Transcript & Mutation Effects

hg38 • Region Span ~76.9 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

schizophreniaNO_KNOWN

Inheritance Pattern: Unknown

Disease ID:MONDO:0005090

Submitter: Labcorp Genetics (formerly Invitae)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to KIF24 variants in ClinVar

4 Conditions Cataloged

not specifiedTotal: 186

not providedTotal: 15

EBV-positive nodal T- and NK-cell lymphomaTotal: 1

Asphyxiating thoracic dystrophy 3Total: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_194313.4. 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	4 clinvar	3 clinvar	8
missense	1 clinvar		176 clinvar	15 clinvar	5 clinvar	197
nonsense			3 clinvar			3
start loss						0
frameshift					1 clinvar	1
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	1	0	182	19	9	211

Highest pathogenic variant AF is 0.00032035713

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 22 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_194313.4	RefSeq	NP_919289.2	12	MANE Select
ENST00000402558.7	Ensembl	ENSP00000384433.1	12	MANE Select
ENST00000379174.7	Ensembl	ENSP00000368472.3	9	Standard
ENST00000379174.8	Ensembl	ENSP00000368472.3	9	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Anchoring of the basal body to the plasma membrane
Cilium Assembly
Organelle biogenesis and maintenance

Biological Process

microtubule-based movement
microtubule depolymerization
cilium assembly
ciliary basal body-plasma membrane docking

Molecular Function

microtubule motor activity
protein binding
ATP binding
microtubule binding
ATPase activity

Cellular Component

centriole
cytosol
kinesin complex
microtubule
protein-containing complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000379166
Coding exons: 12
Length: 76820
Individuals with no LoFs: 124696
Homozygous LoFs: 13
Heterozygous LoFs: 884
Defined: 125593
p: 0.00358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.712	675	729	0.926	0.0000382	8946
Missense (PolyPhen)		196	198.1	0.98942		2517
Synonymous	0.0119	277	277	0.999	0.0000147	2727
Loss of Function	2.23	35	52.4	0.668	0.00000280	635

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0012	0.0012	notable
Latino/Admixed American	0.019	0.018	notable
Ashkenazi Jewish	0.00020	0.00020	rare
East Asian	0.0018	0.0018	notable
Finnish	0.00037	0.00037	rare
European (Non-Finnish)	0.0014	0.0014	notable
South Asian	0.00082	0.00082	rare
Other	0.0032	0.0031	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Microtubule-dependent motor protein that acts as a negative regulator of ciliogenesis by mediating recruitment of CCP110 to mother centriole in cycling cells, leading to restrict nucleation of cilia at centrioles. Mediates depolymerization of microtubules of centriolar origin, possibly to suppress aberrant cilia formation (PubMed:21620453). Following activation by NEK2 involved in disassembly of primary cilium during G2/M phase but does not disassemble fully formed ciliary axonemes. As cilium assembly and disassembly is proposed to coexist in a dynamic equilibrium may suppress nascent cilium assembly and, potentially, ciliar re-assembly in cells that have already disassembled their cilia ensuring the completion of cilium removal in the later stages of the cell cycle (PubMed:26290419). {ECO:0000269|PubMed:21620453}.;

Intolerance Scores

LoFtool: 0.959
RVIS EVS: 0.55
RVIS percentile EVS: 81.23

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Indispensability pred.: N
Indispensability score: 0.428

Gene Damage Prediction

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