MYL3
protein-codingmyosin light chain 3, the group of Myosin light chains, class 1
Gene summary
MYL3 encodes myosin light chain 3, an alkali light chain also referred to in the literature as both the ventricular isoform and the slow skeletal muscle isoform. Mutations in MYL3 have been identified as a cause of mid-left ventricular chamber type hypertrophic cardiomyopathy. [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 ~47.1 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AD
Disease ID:MONDO:0005045
Submitter: ClinGen
MYL3: Hypertrophic Cardiomyopathy. The MYL3 gene has been associated with autosomal dominant hypertrophic cardiomyopathy (HCM) in at least 20 probands in 13 publications. More than 8 unique variants (mostly missense, 1 splice acceptor variant) have been reported in humans, and variants in this gene segregated with disease in 24 additional family members. MYL3 was first associated with HCM in humans in 1996 (Poetter et al, PMID 8673105). The MYL3 gene was significantly enriched for missense variants in Walsh et al. 2016 (PMID 27532257), with an Odds Ratio of 5.00 (3.43-7.27) for HCM. This gene-disease association is supported by expression studies (Fujimoto et al, 1993, PMD 8417110), a mouse model (Vemuri et al, 1991, PMID 9927691), and evidence of interaction with MYH7 (Petzhold et al, 2011, PMID 21262909) as well as ACTC1 (Haase et al, 2006, PMID 16675844). In summary, MYL3 is definitively associated with autosomal dominant HCM. This has been repeatedly demonstrated in both the research and clinical diagnostic settings, and has been upheld over time. This classification was approved by the ClinGen Hypertrophic Cardiomyopathy Gene Curation Expert Panel on December 22, 2017 using version 5 of the SOP and was recurated on March 15, 2021. As a result of this reevaluation, the classification did not change but one publication was added for additional experimental evidence (PMID:12186978).
Inheritance Pattern: AD
Disease ID:MONDO:0005021
Submitter: ClinGen
MYL3 was originally evaluated for DCM by the ClinGen DCM GCEP on September 11, 2020. Evidence of the association of this gene with DCM was re-evaluated using SOP v10 on May 29, 2025. As a result, the classification did not change. A summary of the information contributing to the classification of this gene at the time of re-evaluation is summarized herein. MYL3 was first reported in relation to autosomal dominant dilated cardiomyopathy (DCM) in 2015 (Zhao et al., 2015, PMID 26458567). MYL3 has also been curated by the Hypertrophic Cardiomyopathy (HCM) Gene Curation Expert Panel for hypertrophic cardiomyopathy (Definitive, October 4, 2016) and the Arrhythmogenic Right Ventricular Cardiomyopathy (ARVC) Gene Curation Expert Panel for ARVC (Limited, September 13, 2019). Human genetic evidence supporting this gene-disease relationship includes case-level data. At least one variant (missense) has been reported in humans with DCM (Zhao et al., 2015, PMID 26458567). Next-generation sequencing and followed by variant confirmation with traditional capillary Sanger sequencing analysis was completed in 21 individuals with DCM and revealed possible causative variants in ~57% of patients, including a novel variant in MYL3 (c.377A>G, p.D126G). Experimental evidence includes expression data, but is nonspecific to dilated cardiomyopathy. In brief, Deb et al 2022 PMID: 35714796 utilized RNA-sequencing, differentially expressed gene (DEG) computational analysis and protein-protein interaction computational analysis to identify the top 15 DEGs in pig hearts affected with PCV2 compared to 5 healthy controls which identified MYL3 as one of these highly DEG genes. These findings were consistent on qRT-PCR. In summary, the evidence presented for this gene-disease relationship does not provide convincing human genetic evidence in support of or refuting the role of MYL3 and autosomal dominant DCM. The relationship of MYL3 with DCM is unclear and therefore classified as disputed. This classification was approved by the ClinGen Dilated Cardiomyopathy Working Group on May 29th, 2025 (SOP Version 10).
Inheritance Pattern: AD
Disease ID:MONDO:0012111
Submitter: G2P
Inheritance Pattern: AD
Disease ID:MONDO:0012111
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AD
Disease ID:MONDO:0016587
Submitter: ClinGen
There is limited evidence that MYL3 is associated with ARVC. Screening of ARVC patient cohorts for MYL3 mutations has been performed in two studies (29709087, 22421524). In first study (29709087) 137 ARVC patients were investigated for putative pathogenic variants. A missense variant causing the aminoacid substitution Arg154His was identified in one patient. This previously report variant is classified as likely pathogenic according to current ACMG criteria and has been demonstrate in vitro to disturb the binding of this protein to myosin. However, this variant has not been linked to ARVC phenotype and no segregation data were available. In the second study (22421524) 14 ARVC patients were investigated but no MYL3 variants were reported. There is no clear evidence that the identified MYL3 contribute to the ARVC phenotype and there is no known disease mechanism that would link MYL3 with ARVC.
Inheritance Pattern: AD
Disease ID:MONDO:0016333
Submitter: G2P
Inheritance Pattern: SD
Disease ID:MONDO:0012111
Submitter: Ambry Genetics
Inheritance Pattern: AD
Disease ID:MONDO:0016587
Submitter: G2P
Clinical Genomic Database (CGD)
Manifestation: Cardiovascular
Intervention: Cardiovascular
Rationale: Early recognition may allow preventive measures and early medical management, which may ameliorate severe sequelae
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to MYL3 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_000258.3. 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 | 4 | 87 | 4 | 95 | ||
| missense | 13 | 245 | 7 | 265 | ||
| nonsense | 2 | 2 | ||||
| start loss | 1 | 5 | 6 | |||
| frameshift | 2 | 17 | 19 | |||
| splice donor/acceptor (+/-2bp) | 1 | 13 | 14 | |||
| Total | 0 | 17 | 286 | 94 | 4 | 401 |
Highest pathogenic variant AF is 0.000022303975
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_000249.1 | 6 | MANE Select | |
| Ensembl | ENSP00000292327.4 | 6 | MANE Select | |
| RefSeq | NP_001393866.1 | 6 | Standard | |
| RefSeq | NP_001393867.1 | 6 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Cardiac muscle contraction - Homo sapiens (human)
- Dilated cardiomyopathy (DCM) - Homo sapiens (human)
- Hypertrophic cardiomyopathy (HCM) - Homo sapiens (human)
- Adrenergic signaling in cardiomyocytes - Homo sapiens (human)
- Apelin signaling pathway - Homo sapiens (human)
Biological Process
- regulation of the force of heart contraction
- regulation of striated muscle contraction
- skeletal muscle tissue development
- muscle filament sliding
- positive regulation of ATPase activity
Molecular Function
- motor activity
- actin monomer binding
- calcium ion binding
- structural constituent of muscle
- myosin II heavy chain binding
Cellular Component
- cytosol
- muscle myosin complex
- sarcomere
- A band
- I band
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000395869
- Coding exons
- 6
- Length
- 24298
- Individuals with no LoFs
- 125741
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 7
- Defined
- 125748
- p
- 0.0000278
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.756 | 92 | 115 | 0.801 | 0.00000699 | 1300 |
| Missense (PolyPhen) | 24 | 38.5 | 0.62337 | 460 | ||
| Synonymous | -0.959 | 51 | 43.0 | 1.19 | 0.00000269 | 364 |
| Loss of Function | 1.78 | 3 | 8.64 | 0.347 | 3.77e-7 | 115 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00012 | 0.00012 | rare |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000035 | 0.000035 | rare |
| South Asian | 0.000033 | 0.000033 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Regulatory light chain of myosin. Does not bind calcium.;
- Disease
- DISEASE: Cardiomyopathy, familial hypertrophic 8 (CMH8) [MIM:608751]: A hereditary heart disorder characterized by ventricular hypertrophy, which is usually asymmetric and often involves the interventricular septum. The symptoms include dyspnea, syncope, collapse, palpitations, and chest pain. They can be readily provoked by exercise. The disorder has inter- and intrafamilial variability ranging from benign to malignant forms with high risk of cardiac failure and sudden cardiac death. Rarely, patients present a variant of familial hypertrophic cardiomyopathy, characterized by mid-left ventricular chamber thickening. {ECO:0000269|PubMed:12021217, ECO:0000269|PubMed:12707239, ECO:0000269|PubMed:23594557, ECO:0000269|PubMed:8673105}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Recessive Scores
- pRec
- 0.227
Intolerance Scores
- LoFtool
- 0.218
- RVIS EVS
- -0.38
- RVIS percentile EVS
- 27.42
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.830
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |