MYLK3

myosin light chain kinase 3, the group of Myosin light chain kinase family

Basic information

Region (hg38): 16:46702282-46790407

Links

ENSG00000140795 ∙ NCBI:91807 ∙ OMIM:612147 ∙ HGNC:29826 ∙ Uniprot:Q32MK0 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• dilated cardiomyopathy (Moderate), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the MYLK3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MYLK3 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			2	177	12	191
missense			428	10	4	442
nonsense			16			16
start loss			2			2
frameshift			23			23
inframe indel			3			3
splice donor/acceptor (+/-2bp)			9			9
splice region			21	14	2	37
non coding			2	53	5	60
Total	0	0	485	240	21

Variants in MYLK3

This is a list of pathogenic ClinVar variants found in the MYLK3 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-46707704-T-G			Uncertain significance (Apr 25, 2023)
16-46707708-G-A			Uncertain significance (Mar 16, 2023)
16-46707711-G-A			Uncertain significance (Jan 08, 2025)
16-46707712-A-C			Uncertain significance (Aug 20, 2022)
16-46707714-G-T		MYLK3-related disorder	Likely benign (Feb 04, 2025)
16-46707715-T-C			Uncertain significance (Aug 21, 2024)
16-46707721-AT-A			Uncertain significance (Jul 12, 2022)
16-46707722-T-C			Likely benign (Oct 22, 2024)
16-46707729-A-G			Uncertain significance (Apr 25, 2024)
16-46707738-G-A			Uncertain significance (Jul 30, 2024)
16-46707739-C-T			Uncertain significance (Sep 01, 2022)
16-46707741-G-A			Uncertain significance (Jun 24, 2024)
16-46707750-A-C			Uncertain significance (Jun 25, 2023)
16-46707750-A-G			Uncertain significance (Mar 21, 2024)
16-46707751-C-T			Uncertain significance (Oct 03, 2024)
16-46707754-A-G		not specified	Uncertain significance (Mar 27, 2024)
16-46707756-A-T			Uncertain significance (May 18, 2024)
16-46707760-G-A			Uncertain significance (Jan 19, 2025)
16-46707767-G-C			Likely benign (Jun 24, 2024)
16-46707768-AG-A			Likely benign (Sep 22, 2022)
16-46707770-G-A			Likely benign (Sep 29, 2022)
16-46707773-A-C			Likely benign (Aug 30, 2021)
16-46707774-G-A			Likely benign (Mar 20, 2023)
16-46707776-A-G			Likely benign (Jun 03, 2024)
16-46707782-T-G			Benign (Jan 05, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MYLK3	protein_coding	protein_coding	ENST00000394809	13	83429

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.88e-7	0.999	125701	0	47	125748	0.000187

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.502	447	478	0.935	0.0000268	5305
Missense in Polyphen		116	153.03	0.75803		1937
Synonymous	-0.506	215	206	1.04	0.0000134	1688
Loss of Function	2.83	16	33.7	0.474	0.00000166	394

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000507	0.000503
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000891	0.000870
Finnish	0.00	0.00
European (Non-Finnish)	0.000115	0.000114
Middle Eastern	0.000891	0.000870
South Asian	0.0000682	0.0000653
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Kinase that phosphorylates MYL2 in vitro. Promotes sarcomere formation in cardiomyocytes and increases cardiomyocyte contractility (By similarity). {ECO:0000250}.
• Pathway: Platelet activation - Homo sapiens (human);Focal adhesion - Homo sapiens (human);Oxytocin signaling pathway - Homo sapiens (human);Gastric acid secretion - Homo sapiens (human);Regulation of actin cytoskeleton - Homo sapiens (human);Calcium signaling pathway - Homo sapiens (human);Apelin signaling pathway - Homo sapiens (human);Vascular smooth muscle contraction - Homo sapiens (human);cGMP-PKG signaling pathway - Homo sapiens (human);MicroRNAs in cardiomyocyte hypertrophy;Cardiac Progenitor Differentiation;Focal Adhesion (Consensus)

Recessive Scores

• pRec: 0.142

Intolerance Scores

• loftool: 0.585
• rvis_EVS: -1.26
• rvis_percentile_EVS: 5.28

Haploinsufficiency Scores

• pHI: 0.101
• hipred: N
• hipred_score: 0.369
• ghis: 0.486

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.271

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mylk3
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); muscle phenotype; homeostasis/metabolism phenotype

Zebrafish Information Network

• Gene name: mylk3
• Affected structure: whole organism
• Phenotype tag: abnormal
• Phenotype quality: edematous

Gene ontology

• Biological process: regulation of vascular permeability involved in acute inflammatory response;protein phosphorylation;sarcomere organization;sarcomerogenesis;cardiac myofibril assembly;positive regulation of sarcomere organization;cellular response to interleukin-1
• Cellular component: cytoplasm;cytosol;actin cytoskeleton
• Molecular function: calmodulin-dependent protein kinase activity;myosin light chain kinase activity;ATP binding