MYLK
protein-codingmyosin light chain kinase, the group of Myosin light chain kinase family|Fibronectin type III domain containing|I-set domain containing
Gene summary
This gene, a muscle member of the immunoglobulin gene superfamily, encodes myosin light chain kinase which is a calcium/calmodulin dependent enzyme. This kinase phosphorylates myosin regulatory light chains to facilitate myosin interaction with actin filaments to produce contractile activity. This gene encodes both smooth muscle and nonmuscle isoforms. In addition, using a separate promoter in an intron in the 3' region, it encodes telokin, a small protein identical in sequence to the C-terminus of myosin light chain kinase, that is independently expressed in smooth muscle and functions to stabilize unphosphorylated myosin filaments. A pseudogene is located on the p arm of chromosome 3. Four transcript variants that produce four isoforms of the calcium/calmodulin dependent enzyme have been identified as well as two transcripts that produce two isoforms of telokin. Additional variants have been identified but lack full length transcripts. [provided by RefSeq, Jul 2008]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~274.3 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AD
Disease ID:MONDO:0013418
Submitter: Ambry Genetics
Inheritance Pattern: Unknown
Disease ID:MONDO:0019625
Submitter: ClinGen
Inheritance Pattern: AR
Disease ID:MONDO:0007960
Submitter: Ambry Genetics
Inheritance Pattern: AD
Disease ID:MONDO:0013418
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AD
Disease ID:MONDO:0003900
Submitter: Genomics England PanelApp
Inheritance Pattern: AD
Disease ID:MONDO:0019625
Submitter: Orphanet
Inheritance Pattern: AD
Disease ID:MONDO:0007960
Submitter: Orphanet
Inheritance Pattern: AR
Disease ID:MONDO:0100354
Submitter: G2P
Clinical Genomic Database (CGD)
Manifestation: Cardiovascular; Gastrointestinal; Renal
Intervention: Cardiovascular; Gastrointestinal; Renal
Rationale: In Aortic aneurysm, familial thoracic, preventive measures and medical management may be helpful to help decrease morbidity; Individuals with Megacystis-microcolon-intestinal hypoperistalsis syndrome may have intestinal anomalies and hydronephrosis, and awareness may allow prompt surgical and medical management; Multivisceral, liver-small bowel, and bowel transplant has been described in Megacystis-microcolon-intestinal hypoperistalsis syndrome
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to MYLK variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_053025.4. 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 | 22 | 675 | 13 | 710 | ||
| missense | 6 | 1364 | 118 | 8 | 1496 | |
| nonsense | 17 | 10 | 27 | 54 | ||
| start loss | 1 | 1 | ||||
| frameshift | 28 | 15 | 28 | 71 | ||
| splice donor/acceptor (+/-2bp) | 1 | 20 | 17 | 38 | ||
| Total | 46 | 51 | 1459 | 793 | 21 | 2370 |
Highest pathogenic variant AF is 0.00001971583
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_444253.3 | 31 | MANE Select | |
| Ensembl | ENSP00000353452.3 | 31 | MANE Select | |
| RefSeq | NP_001308238.1 | 28 | Standard | |
| RefSeq | NP_001424964.1 | 3 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| mylka | Danio rerio | Structure: thrombocyte Quality: shape abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- 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)
Biological Process
- protein phosphorylation
- muscle contraction
- smooth muscle contraction
- tonic smooth muscle contraction
- positive regulation of cell migration
Molecular Function
- actin binding
- protein kinase activity
- myosin light chain kinase activity
- protein binding
- calmodulin binding
Cellular Component
- stress fiber
- cytoplasm
- cytosol
- plasma membrane
- actin cytoskeleton
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000360304
- Coding exons
- 31
- Length
- 274283
- Individuals with no LoFs
- 125667
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 81
- Defined
- 125748
- p
- 0.000322
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.13 | 967 | 1.07e+3 | 0.903 | 0.0000667 | 12484 |
| Missense (PolyPhen) | 108 | 136.61 | 0.79055 | 1672 | ||
| Synonymous | -0.258 | 450 | 443 | 1.02 | 0.0000308 | 3780 |
| Loss of Function | 5.23 | 35 | 87.9 | 0.398 | 0.00000450 | 1056 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00031 | 0.00025 | rare |
| Latino/Admixed American | 0.00020 | 0.00020 | rare |
| Ashkenazi Jewish | 0.00010 | 0.000099 | rare |
| East Asian | 0.00027 | 0.00027 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00043 | 0.00042 | rare |
| South Asian | 0.00049 | 0.00049 | rare |
| Other | 0.00016 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Calcium/calmodulin-dependent myosin light chain kinase implicated in smooth muscle contraction via phosphorylation of myosin light chains (MLC). Also regulates actin-myosin interaction through a non-kinase activity. Phosphorylates PTK2B/PYK2 and myosin light-chains. Involved in the inflammatory response (e.g. apoptosis, vascular permeability, leukocyte diapedesis), cell motility and morphology, airway hyperreactivity and other activities relevant to asthma. Required for tonic airway smooth muscle contraction that is necessary for physiological and asthmatic airway resistance. Necessary for gastrointestinal motility. Implicated in the regulation of endothelial as well as vascular permeability, probably via the regulation of cytoskeletal rearrangements. In the nervous system it has been shown to control the growth initiation of astrocytic processes in culture and to participate in transmitter release at synapses formed between cultured sympathetic ganglion cells. Critical participant in signaling sequences that result in fibroblast apoptosis. Plays a role in the regulation of epithelial cell survival. Required for epithelial wound healing, especially during actomyosin ring contraction during purse-string wound closure. Mediates RhoA- dependent membrane blebbing. Triggers TRPC5 channel activity in a calcium-dependent signaling, by inducing its subcellular localization at the plasma membrane. Promotes cell migration (including tumor cells) and tumor metastasis. PTK2B/PYK2 activation by phosphorylation mediates ITGB2 activation and is thus essential to trigger neutrophil transmigration during acute lung injury (ALI). May regulate optic nerve head astrocyte migration. Probably involved in mitotic cytoskeletal regulation. Regulates tight junction probably by modulating ZO-1 exchange in the perijunctional actomyosin ring. Mediates burn-induced microvascular barrier injury; triggers endothelial contraction in the development of microvascular hyperpermeability by phosphorylating MLC. Essential for intestinal barrier dysfunction. Mediates Giardia spp.-mediated reduced epithelial barrier function during giardiasis intestinal infection via reorganization of cytoskeletal F-actin and tight junctional ZO-1. Necessary for hypotonicity-induced Ca(2+) entry and subsequent activation of volume-sensitive organic osmolyte/anion channels (VSOAC) in cervical cancer cells. Responsible for high proliferative ability of breast cancer cells through anti-apoptosis. {ECO:0000269|PubMed:11113114, ECO:0000269|PubMed:11976941, ECO:0000269|PubMed:15020676, ECO:0000269|PubMed:15825080, ECO:0000269|PubMed:16284075, ECO:0000269|PubMed:16723733, ECO:0000269|PubMed:18587400, ECO:0000269|PubMed:18710790, ECO:0000269|PubMed:19826488, ECO:0000269|PubMed:20139351, ECO:0000269|PubMed:20181817, ECO:0000269|PubMed:20375339, ECO:0000269|PubMed:20453870}.;
- Disease
- DISEASE: Aortic aneurysm, familial thoracic 7 (AAT7) [MIM:613780]: A disease characterized by permanent dilation of the thoracic aorta usually due to degenerative changes in the aortic wall. It is primarily associated with a characteristic histologic appearance known as 'medial necrosis' or 'Erdheim cystic medial necrosis' in which there is degeneration and fragmentation of elastic fibers, loss of smooth muscle cells, and an accumulation of basophilic ground substance. {ECO:0000269|PubMed:21055718}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Intolerance Scores
- LoFtool
- 0.734
- RVIS EVS
- -0.32
- RVIS percentile EVS
- 30.93
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.935
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | High | High | High |
| Primary Immunodeficiency | High | High | High |
| Cancer | High | High | High |