KLC4

protein-coding

kinesin light chain 4, the group of Tetratricopeptide repeat domain containing

Gene summary

Predicted to enable kinesin binding activity. Predicted to be involved in microtubule-based movement. Predicted to be located in microtubule. Predicted to be part of kinesin complex. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

KNSL8

MANE transcript

NM_201521.3

Inheritance

ClinVar variants

P:3U:106

Top phenotype

Early-childhood-onset neurodegeneration with retinitis pigmentosa, sensorineural hearing loss, and demyelinating peripheral neuropathy

gnomAD constraint

pLI —, LoF o/e 0.33

Max pathogenic AF

—

Genomic locus

chr6:43,040,777-43,075,095

External References & Databases

Ensembl (ENSG00000137171)

Transcript & Mutation Effects

hg38 • Region Span ~34.3 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

early-childhood-onset neurodegeneration with retinitis pigmentosa, sensorineural hearing loss, and demyelinating peripheral neuropathyLIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0700288

Submitter: PanelApp Australia

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to KLC4 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 98

not providedTotal: 4

Early-childhood-onset neurodegeneration with retinitis pigmentosa, sensorineural hearing loss, and demyelinating peripheral neuropathyTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_201521.3. 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			98 clinvar			98
nonsense		2 clinvar	1 clinvar			3
start loss						0
frameshift	1 clinvar		1 clinvar			2
splice donor/acceptor (+/-2bp)			5 clinvar			5
Total	1	2	106	0	0	109

Highest pathogenic variant AF is 0.000015495823

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 90 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_201521.3	RefSeq	NP_958929.1	15	MANE Select
ENST00000347162.10	Ensembl	ENSP00000340221.5	15	MANE Select
NM_001289034.2	RefSeq	NP_001275963.1	15	Standard
NM_001289035.2	RefSeq	NP_001275964.1	14	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Salmonella infection - Homo sapiens (human)
Signal Transduction
Vesicle-mediated transport
Membrane Trafficking
RHO GTPases activate KTN1

Molecular Function

microtubule motor activity
protein binding

Cellular Component

cytoplasm
kinesin complex
microtubule

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000259708
Coding exons: 16
Length: 34323
Individuals with no LoFs: 125674
Homozygous LoFs: 0
Heterozygous LoFs: 74
Defined: 125748
p: 0.000294

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.893	340	390	0.873	0.0000239	4100
Missense (PolyPhen)		127	146.6	0.86628		1613
Synonymous	1.54	128	152	0.842	0.00000794	1301
Loss of Function	3.75	12	36.5	0.329	0.00000179	410

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.00012	0.00012	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00038	0.00038	rare
Finnish	0.00018	0.00018	rare
European (Non-Finnish)	0.00040	0.00040	rare
South Asian	0.00029	0.00029	rare
Other	0.00065	0.00065	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Kinesin is a microtubule-associated force-producing protein that may play a role in organelle transport. The light chain may function in coupling of cargo to the heavy chain or in the modulation of its ATPase activity (By similarity). {ECO:0000250}.;

Recessive Scores

pRec: 0.104

Intolerance Scores

LoFtool: 0.477
RVIS EVS: -0.26
RVIS percentile EVS: 34.93

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.940

Gene Damage Prediction

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