KLC3

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

Basic information

Region (hg38): 19:45333433-45351520

Links

ENSG00000104892 ∙ NCBI:147700 ∙ OMIM:601334 ∙ HGNC:20717 ∙ Uniprot:Q6P597 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the KLC3 gene.

• Inborn genetic diseases (39 variants)
• Xeroderma pigmentosum, group D (10 variants)
• not provided (4 variants)
• Xeroderma pigmentosum (1 variants)
• Cerebrooculofacioskeletal syndrome 2;Trichothiodystrophy 1, photosensitive;Xeroderma pigmentosum, group D (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KLC3 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1		1
missense			37	1		38
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			8	3	1	12
Total	0	0	45	5	1

Variants in KLC3

This is a list of pathogenic ClinVar variants found in the KLC3 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
19-45345558-C-T		not specified	Uncertain significance (Aug 10, 2021)
19-45345579-T-C		not specified	Uncertain significance (Dec 19, 2022)
19-45345647-G-A		not specified	Uncertain significance (Nov 17, 2023)
19-45345654-G-A		not specified	Uncertain significance (Aug 10, 2023)
19-45345698-G-A		not specified	Uncertain significance (Sep 23, 2023)
19-45345699-C-T		not specified	Uncertain significance (Dec 02, 2022)
19-45345711-C-T		not specified	Uncertain significance (Apr 20, 2023)
19-45345719-G-A		not specified	Uncertain significance (Jan 26, 2022)
19-45345791-G-A		not specified	Uncertain significance (Mar 04, 2024)
19-45346551-T-C		not specified	Uncertain significance (Jul 14, 2022)
19-45346616-C-T		not specified	Uncertain significance (Nov 18, 2022)
19-45346643-C-T		not specified	Uncertain significance (Jan 04, 2022)
19-45346679-G-A		not specified	Uncertain significance (Jan 04, 2022)
19-45346712-G-A		not specified	Uncertain significance (Jan 23, 2023)
19-45346714-G-T		not specified	Uncertain significance (Feb 27, 2023)
19-45346717-G-T		not specified	Uncertain significance (Oct 12, 2022)
19-45346727-G-C		not specified	Uncertain significance (Jun 26, 2023)
19-45346755-A-C		not specified	Uncertain significance (Oct 06, 2022)
19-45346761-C-T		not specified	Uncertain significance (Oct 20, 2023)
19-45347465-C-T		not specified	Uncertain significance (Jun 07, 2023)
19-45347484-C-T		not specified	Uncertain significance (Jun 16, 2023)
19-45347497-C-A		not specified	Uncertain significance (Feb 05, 2024)
19-45347952-G-A		not specified	Uncertain significance (Mar 07, 2024)
19-45348003-C-T		not specified	Uncertain significance (Sep 22, 2023)
19-45348004-G-A		not specified	Uncertain significance (Jan 16, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KLC3	protein_coding	protein_coding	ENST00000391946	12	18087

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.86e-18	0.00526	125119	2	483	125604	0.00193

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.37	388	319	1.22	0.0000216	3119
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00259	0.00251
Ashkenazi Jewish	0.00517	0.00507
East Asian	0.0100	0.00972
Finnish	0.000332	0.000324
European (Non-Finnish)	0.000988	0.000941
Middle Eastern	0.0100	0.00972
South Asian	0.00251	0.00245
Other	0.00285	0.00278

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Kinesin is a microtubule-associated force-producing protein that may play a role in organelle transport.
• Pathway: Salmonella infection - Homo sapiens (human);Signal Transduction;Vesicle-mediated transport;Membrane Trafficking;RHO GTPases activate KTN1;Kinesins;Factors involved in megakaryocyte development and platelet production;RHO GTPase Effectors;Signaling by Rho GTPases;Hemostasis;COPI-dependent Golgi-to-ER retrograde traffic;Golgi-to-ER retrograde transport;Intra-Golgi and retrograde Golgi-to-ER traffic (Consensus)

Recessive Scores

• pRec: 0.135

Haploinsufficiency Scores

• pHI: 0.156
• hipred: N
• hipred_score: 0.266
• ghis: 0.629

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.617

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Klc3

Gene ontology

• Biological process: axo-dendritic transport
• Cellular component: cytoplasm;kinesin complex;microtubule;motile cilium;ciliary rootlet;neuron projection
• Molecular function: microtubule motor activity;protein binding;microtubule binding;kinesin binding