KLC1

kinesin light chain 1, the group of Tetratricopeptide repeat domain containing

Basic information

Region (hg38): 14:103561895-103714249

Previous symbols: [ "KNS2" ]

Links

ENSG00000126214 ∙ NCBI:3831 ∙ OMIM:600025 ∙ HGNC:6387 ∙ Uniprot:Q07866 ∙ 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 KLC1 gene.

• Inborn genetic diseases (37 variants)
• not provided (6 variants)
• not specified (3 variants)
• Ovarian cancer (3 variants)
• Melanoma, cutaneous malignant, susceptibility to, 6 (1 variants)
• Familial cancer of breast (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KLC1 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			16			16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			23	1	7	31
Total	0	0	39	1	8

Variants in KLC1

This is a list of pathogenic ClinVar variants found in the KLC1 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-103561922-G-C		Inborn genetic diseases	Uncertain significance (Dec 15, 2023)
14-103561923-G-A		Inborn genetic diseases	Uncertain significance (May 25, 2022)
14-103561946-G-A		Inborn genetic diseases	Uncertain significance (Oct 12, 2022)
14-103562004-G-A		Inborn genetic diseases	Uncertain significance (Dec 21, 2023)
14-103562786-C-A			Benign (Jun 14, 2018)
14-103562805-G-A			Likely benign (Jul 07, 2018)
14-103562851-C-CCCG			Benign (Jul 10, 2018)
14-103562909-G-A			Benign (Jun 23, 2018)
14-103562952-G-T		not specified	Benign (Nov 14, 2016)
14-103562968-G-A		COA8-related disorder	Likely benign (Sep 06, 2022)
14-103562970-C-G		Inborn genetic diseases	Uncertain significance (Nov 02, 2023)
14-103562970-C-T		Inborn genetic diseases	Uncertain significance (Sep 14, 2022)
14-103562974-C-T			Likely benign (Nov 01, 2022)
14-103562976-C-A			Uncertain significance (Apr 17, 2022)
14-103562986-C-T			Likely benign (Aug 23, 2022)
14-103562987-A-AG		Mitochondrial complex IV deficiency, nuclear type 1 • Mitochondrial complex 4 deficiency, nuclear type 17 • Inborn genetic diseases	Conflicting classifications of pathogenicity (Oct 12, 2022)
14-103562991-G-A			Uncertain significance (Jan 15, 2022)
14-103562993-C-T		Inborn genetic diseases	Uncertain significance (Mar 21, 2022)
14-103562995-T-G			Likely benign (Jan 02, 2024)
14-103563002-A-G		Inborn genetic diseases	Uncertain significance (Jan 08, 2024)
14-103563003-T-C		Inborn genetic diseases	Uncertain significance (Sep 26, 2023)
14-103563003-T-G		Inborn genetic diseases	Uncertain significance (Dec 07, 2023)
14-103563009-T-C		not specified	Benign (Jan 26, 2024)
14-103563014-C-A		COA8-related disorder	Likely benign (May 20, 2019)
14-103563021-G-A			Uncertain significance (Jul 12, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KLC1	protein_coding	protein_coding	ENST00000452929	14	139656

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.371	0.629	125731	0	17	125748	0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.22	189	361	0.523	0.0000216	4083
Missense in Polyphen		40	129.36	0.30922		1345
Synonymous	-0.0887	144	143	1.01	0.00000949	1119
Loss of Function	4.27	8	35.4	0.226	0.00000178	435

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000619	0.0000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000891	0.0000879
Middle Eastern	0.0000619	0.0000544
South Asian	0.000133	0.000131
Other	0.000171	0.000163

dbNSFP

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.
• 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;Arf6 trafficking events;Intra-Golgi and retrograde Golgi-to-ER traffic (Consensus)

Recessive Scores

• pRec: 0.154

Intolerance Scores

• loftool: 0.690
• rvis_EVS: -0.49
• rvis_percentile_EVS: 22.36

Haploinsufficiency Scores

• pHI: 0.221
• hipred: N
• hipred_score: 0.466
• ghis: 0.590

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.539

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Klc1
• Phenotype: cellular phenotype; homeostasis/metabolism phenotype; growth/size/body region phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: intracellular protein transport;retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum;microtubule-based movement;viral process;antigen processing and presentation of exogenous peptide antigen via MHC class II;protein localization to synapse;stress granule disassembly
• Cellular component: cytosol;kinesin complex;microtubule;membrane;growth cone;cytoplasmic vesicle;neuronal cell body
• Molecular function: motor activity;microtubule motor activity;protein binding;tubulin binding