KLC3

protein-coding

kinesin light chain 3, the group of Tetratricopeptide repeat domain containing

Gene summary

This gene encodes a member of the kinesin light chain gene family. Kinesins are molecular motors involved in the transport of cargo along microtubules, and are composed of two kinesin heavy chain (KHC) and two kinesin light chain (KLC) molecules. KLCs are thought to typically be involved in binding cargo and regulating kinesin activity. In the rat, a protein similar to this gene product is expressed in post-meiotic spermatids, where it associates with structural components of sperm tails and mitochondria. [provided by RefSeq, Jul 2008]

MANE transcript

NM_177417.3

Inheritance

—

ClinVar variants

U:144B:10

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.98

Max pathogenic AF

—

Genomic locus

chr19:45,333,434-45,351,520

External References & Databases

Ensembl (ENSG00000104892)

Transcript & Mutation Effects

hg38 • Region Span ~18.1 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 KLC3 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 133

not providedTotal: 10

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_177417.3. 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			2 clinvar	8 clinvar		10
missense			137 clinvar	2 clinvar		139
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			5 clinvar			5
Total	0	0	144	10	0	154

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 21 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_177417.3	RefSeq	NP_803136.2	12	MANE Select
ENST00000391946.7	Ensembl	ENSP00000375810.2	12	MANE Select
ENST00000470402.1	Ensembl	ENSP00000436019.1	12	Standard
ENST00000470402.2	Ensembl	ENSP00000436019.1	12	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

Biological Process

axo-dendritic transport

Molecular Function

microtubule motor activity
protein binding
microtubule binding
kinesin binding

Cellular Component

cytoplasm
kinesin complex
microtubule
motile cilium
ciliary rootlet

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000391946
Coding exons: 12
Length: 18087
Individuals with no LoFs: 125119
Homozygous LoFs: 2
Heterozygous LoFs: 483
Defined: 125604
p: 0.00193

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-1.37	388	319	1.22	0.0000216	3119
Missense (PolyPhen)		120	104.51	1.1483		1087
Synonymous	-2.72	174	134	1.30	0.00000871	1037
Loss of Function	0.0747	27	27.4	0.985	0.00000155	285

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0014	0.0014	notable
Latino/Admixed American	0.0011	0.00084	notable
Ashkenazi Jewish	0.0052	0.0051	notable
East Asian	0.010	0.0097	notable
Finnish	0.00033	0.00032	rare
European (Non-Finnish)	0.00099	0.00094	rare
South Asian	0.0025	0.0025	notable
Other	0.0029	0.0028	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Kinesin is a microtubule-associated force-producing protein that may play a role in organelle transport.;

Recessive Scores

pRec: 0.135

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.617

Gene Damage Prediction

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