KLC4

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

Basic information

Region (hg38): 6:43040776-43075095

Previous symbols: [ "KNSL8" ]

Links

ENSG00000137171 ∙ NCBI:89953 ∙ ∙ HGNC:21624 ∙ Uniprot:Q9NSK0 ∙ 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 KLC4 gene.

• Inborn genetic diseases (28 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KLC4 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						0
missense			26			26
nonsense		1				1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			2		1	3
Total	0	1	28	0	1

Highest pathogenic variant AF is 0.00000657

Variants in KLC4

This is a list of pathogenic ClinVar variants found in the KLC4 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-43040924-T-C		Inborn genetic diseases	Uncertain significance (Oct 14, 2023)
6-43040942-A-G		Inborn genetic diseases	Uncertain significance (Jul 11, 2023)
6-43040952-C-T		Inborn genetic diseases	Uncertain significance (Dec 21, 2023)
6-43040953-G-A		CUL7-related disorder	Benign/Likely benign (Jan 15, 2024)
6-43040956-G-A			Likely benign (Dec 30, 2021)
6-43040959-AATCAGGACAGCT-GC			Pathogenic (Nov 30, 2019)
6-43040965-G-A			Likely benign (Dec 21, 2020)
6-43040971-T-TTGCAGGCATTGCTGCAGCTGTGCCAGCC		3M syndrome 1	Likely pathogenic (-)
6-43040974-C-T		3M syndrome 1 • CUL7-related disorder	Conflicting classifications of pathogenicity (Jan 24, 2024)
6-43041015-C-A		Inborn genetic diseases	Uncertain significance (Oct 17, 2023)
6-43041026-C-T		not specified • 3M syndrome 1 • CUL7-related disorder	Benign/Likely benign (Jan 24, 2024)
6-43041036-G-A		3M syndrome 1	Likely pathogenic (Oct 10, 2014)
6-43041056-C-T			Uncertain significance (Dec 20, 2021)
6-43041086-G-A			Likely benign (Sep 10, 2023)
6-43041089-G-A			Likely benign (Aug 14, 2023)
6-43041138-A-G			Benign (Nov 12, 2018)
6-43042768-G-T		CUL7-related disorder	Likely benign (Apr 30, 2019)
6-43042795-G-A			Likely benign (Mar 13, 2022)
6-43042799-T-C			Uncertain significance (Jan 17, 2022)
6-43042801-C-T		3-M syndrome	Likely pathogenic (Dec 06, 2022)
6-43042837-C-T			Uncertain significance (Feb 06, 2017)
6-43042842-G-A		3M syndrome 1	Uncertain significance (Sep 24, 2021)
6-43042866-A-G			Uncertain significance (May 12, 2022)
6-43042867-A-G			Likely benign (Mar 27, 2022)
6-43042868-G-A			Likely benign (Feb 18, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KLC4	protein_coding	protein_coding	ENST00000259708	16	34323

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00119	0.999	125674	0	74	125748	0.000294

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.893	340	390	0.873	0.0000239	4100
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000177	0.000177
Ashkenazi Jewish	0.00	0.00
East Asian	0.000381	0.000381
Finnish	0.000185	0.000185
European (Non-Finnish)	0.000397	0.000396
Middle Eastern	0.000381	0.000381
South Asian	0.000294	0.000294
Other	0.000653	0.000652

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 (By similarity). {ECO:0000250}.
• 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: 0.104

Intolerance Scores

• loftool: 0.477
• rvis_EVS: -0.26
• rvis_percentile_EVS: 34.93

Haploinsufficiency Scores

• pHI: 0.286
• hipred: N
• hipred_score: 0.385
• ghis: 0.529

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.940

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Klc4

Gene ontology

• Cellular component: cytoplasm;kinesin complex;microtubule
• Molecular function: microtubule motor activity;protein binding