MYLK

protein-coding

myosin 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

NM_053025.4

Inheritance

AD, AR

ClinVar variants

P:97U:1459B:814

Top phenotype

Aortic aneurysm, familial thoracic 7; Megacystis-microcolon-intestinal hypoperistalsis syndrome 1

gnomAD constraint

pLI —, LoF o/e 0.4

Max pathogenic AF

—

Genomic locus

chr3:123,610,049-123,884,332

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~274.3 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

aortic aneurysm, familial thoracic 7MODERATE

Inheritance Pattern: AD

Disease ID:MONDO:0013418

Submitter: Ambry Genetics

familial thoracic aortic aneurysm and aortic dissectionSTRONG

Inheritance Pattern: Unknown

Disease ID:MONDO:0019625

Submitter: ClinGen

megacystis-microcolon-intestinal hypoperistalsis syndromeLIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0007960

Submitter: Ambry Genetics

aortic aneurysm, familial thoracic 7STRONG

Inheritance Pattern: AD

Disease ID:MONDO:0013418

Submitter: Labcorp Genetics (formerly Invitae)

connective tissue disorderMODERATE

Inheritance Pattern: AD

Disease ID:MONDO:0003900

Submitter: Genomics England PanelApp

familial thoracic aortic aneurysm and aortic dissectionSUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0019625

Submitter: Orphanet

megacystis-microcolon-intestinal hypoperistalsis syndromeSUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0007960

Submitter: Orphanet

megacystis-microcolon-intestinal hypoperistalsis syndrome 1STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0100354

Submitter: G2P

Clinical Genomic Database (CGD)

Aortic aneurysm, familial thoracic 7; Megacystis-microcolon-intestinal hypoperistalsis syndrome 1AD/AR

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

Refs: 21055718; 20301299; 28602422Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to MYLK variants in ClinVar

22 Conditions Cataloged
Aortic aneurysm, familial thoracic 7Total: 2047
Familial thoracic aortic aneurysm and aortic dissectionTotal: 1371
not providedTotal: 692
not specifiedTotal: 354
Megacystis-microcolon-intestinal hypoperistalsis syndrome 1Total: 154
MYLK-related disorderTotal: 131
Connective tissue disorderTotal: 37
Cardiovascular phenotypeTotal: 5

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.

EffectPLPVUSLBBSum
synonymous
22
clinvar
675
clinvar
13
clinvar
710
missense
6
clinvar
1364
clinvar
118
clinvar
8
clinvar
1496
nonsense
17
clinvar
10
clinvar
27
clinvar
54
start loss
1
clinvar
1
frameshift
28
clinvar
15
clinvar
28
clinvar
71
splice donor/acceptor (+/-2bp)
1
clinvar
20
clinvar
17
clinvar
38
Total46511459793212370

Highest pathogenic variant AF is 0.00001971583

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 93 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_053025.4RefSeqNP_444253.331MANE Select
ENST00000360304.8EnsemblENSP00000353452.331MANE Select
NM_001321309.2RefSeqNP_001308238.128Standard
NM_001438035.1RefSeqNP_001424964.13Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / ModelOrganismObserved Phenotype
mylkaDanio 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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense1.139671.07e+30.9030.000066712484
Missense (PolyPhen)108136.610.790551672
Synonymous-0.2584504431.020.00003083780
Loss of Function5.233587.90.3980.000004501056

Population LoF Frequency

PopulationCAFp-valueStatus
African0.000310.00025rare
Latino/Admixed American0.000200.00020rare
Ashkenazi Jewish0.000100.000099rare
East Asian0.000270.00027rare
Finnish00.0absent
European (Non-Finnish)0.000430.00042rare
South Asian0.000490.00049rare
Other0.000160.00016rare

dbNSFP Gene Annotations

Source: dbNSFP

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

AllRecessiveDominant
MendelianHighHighHigh
Primary ImmunodeficiencyHighHighHigh
CancerHighHighHigh
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