MYL3

protein-coding

myosin 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

NM_000258.3

Inheritance

AD, SD, AR

ClinVar variants

P:17U:286B:98

Top phenotype

Cardiomyopathy, familial hypertrophic, 8

gnomAD constraint

pLI —, LoF o/e 0.35

Max pathogenic AF

—

Genomic locus

chr3:46,835,110-46,882,178

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~47.1 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

hypertrophic cardiomyopathyDEFINITIVE

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).

dilated cardiomyopathyNO_KNOWN

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).

hypertrophic cardiomyopathy 8DEFINITIVE

Inheritance Pattern: AD

Disease ID:MONDO:0012111

Submitter: G2P

hypertrophic cardiomyopathy 8STRONG

Inheritance Pattern: AD

Disease ID:MONDO:0012111

Submitter: Labcorp Genetics (formerly Invitae)

arrhythmogenic right ventricular cardiomyopathyLIMITED

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.

familial dilated cardiomyopathyNO_KNOWN

Inheritance Pattern: AD

Disease ID:MONDO:0016333

Submitter: G2P

hypertrophic cardiomyopathy 8STRONG

Inheritance Pattern: SD

Disease ID:MONDO:0012111

Submitter: Ambry Genetics

arrhythmogenic right ventricular cardiomyopathyLIMITED

Inheritance Pattern: AD

Disease ID:MONDO:0016587

Submitter: G2P

Clinical Genomic Database (CGD)

Cardiomyopathy, familial hypertrophic, 8AD/AR

Manifestation: Cardiovascular

Intervention: Cardiovascular

Rationale: Early recognition may allow preventive measures and early medical management, which may ameliorate severe sequelae

Refs: 6211078; 8673105; 12021217; 16267253; 21239446; 21896538Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to MYL3 variants in ClinVar

16 Conditions Cataloged
Hypertrophic cardiomyopathyTotal: 383
CardiomyopathyTotal: 171
Cardiovascular phenotypeTotal: 154
not providedTotal: 126
not specifiedTotal: 70
Hypertrophic cardiomyopathy 8Total: 48
MYL3-related disorderTotal: 40
Primary familial hypertrophic cardiomyopathyTotal: 6

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.

EffectPLPVUSLBBSum
synonymous
4
clinvar
87
clinvar
4
clinvar
95
missense
13
clinvar
245
clinvar
7
clinvar
265
nonsense
2
clinvar
2
start loss
1
clinvar
5
clinvar
6
frameshift
2
clinvar
17
clinvar
19
splice donor/acceptor (+/-2bp)
1
clinvar
13
clinvar
14
Total017286944401

Highest pathogenic variant AF is 0.000022303975

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 130 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_000258.3RefSeqNP_000249.16MANE Select
ENST00000292327.6EnsemblENSP00000292327.46MANE Select
NM_001406937.1RefSeqNP_001393866.16Standard
NM_001406938.1RefSeqNP_001393867.16Standard

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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense0.756921150.8010.000006991300
Missense (PolyPhen)2438.50.62337460
Synonymous-0.9595143.01.190.00000269364
Loss of Function1.7838.640.3473.77e-7115

Population LoF Frequency

PopulationCAFp-valueStatus
African0.000120.00012rare
Latino/Admixed American00.0absent
Ashkenazi Jewish00.0absent
East Asian00.0absent
Finnish00.0absent
European (Non-Finnish)0.0000350.000035rare
South Asian0.0000330.000033rare
Other00.0absent

dbNSFP Gene Annotations

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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