LMOD3

gene
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Summary

LMOD3 (leiomodin 3, HGNC:6649) is a protein-coding gene on chromosome 3p14.1, encoding Leiomodin-3 (Q0VAK6). Essential for the organization of sarcomeric actin thin filaments in skeletal muscle.

The protein encoded by this gene is a member of the leiomodin family of proteins. This protein contains three actin-binding domains, a tropomyosin domain, a leucine-rich repeat domain, and a Wiskott-Aldrich syndrome protein homology 2 domain (WH2). Localization of this protein to the pointed ends of thin filaments has been observed, and there is evidence that this protein acts as a catalyst of actin nucleation, and is important to the organization of sarcomeric thin filaments in skeletal muscles. Mutations in this gene have been associated as one cause of Nemaline myopathy, as other genes have also been linked to this disorder. Nemaline myopathy is a disorder characterized by nonprogressive generalized muscle weakness and protein inclusions (nemaline bodies) in skeletal myofibers. Patients with mutations in this gene often present with a severe congenital form of the disorder.

Source: NCBI Gene 56203 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): nemaline myopathy 10 (Definitive, ClinGen) — +2 more curated relationships
  • Clinical variants (ClinVar): 458 total — 39 pathogenic, 5 likely-pathogenic
  • Phenotypes (HPO): 79
  • MANE Select transcript: NM_198271

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:6649
Approved symbolLMOD3
Nameleiomodin 3
Location3p14.1
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000163380
Ensembl biotypeprotein_coding
OMIM616112
Entrez56203

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 4 protein_coding

ENST00000420581, ENST00000475434, ENST00000489031, ENST00000949407

RefSeq mRNA: 2 — MANE Select: NM_198271 NM_001304418, NM_198271

CCDS: CCDS46862

Canonical transcript exons

ENST00000420581 — 3 exons

ExonStartEnd
ENSE000017427026910606569109121
ENSE000017659226911869969120060
ENSE000018463946912209369122595

Expression profiles

Bgee: expression breadth ubiquitous, 170 present calls, max score 98.93.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 2.5826 / max 447.9657, expressed in 113 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter IDTPM avgSamples expressed
429631.132773
429620.909176
429610.403974
429590.085327
429600.051522

Top tissues by expression

247 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
biceps brachiiUBERON:000150798.93gold quality
vastus lateralisUBERON:000137998.85gold quality
quadriceps femorisUBERON:000137798.77gold quality
skeletal muscle tissueUBERON:000113498.71gold quality
skeletal muscle tissue of rectus abdominisUBERON:000451198.57gold quality
skeletal muscle tissue of biceps brachiiUBERON:000450298.55gold quality
hindlimb stylopod muscleUBERON:000425298.44gold quality
deltoidUBERON:000147698.11gold quality
gastrocnemiusUBERON:000138897.96gold quality
left ventricle myocardiumUBERON:000656697.63gold quality
tibialis anteriorUBERON:000138597.40gold quality
muscle of legUBERON:000138396.50gold quality
body of tongueUBERON:001187695.13gold quality
heart left ventricleUBERON:000208494.41gold quality
cardiac ventricleUBERON:000208294.32gold quality
heart right ventricleUBERON:000208094.09gold quality
apex of heartUBERON:000209893.84gold quality
muscle tissueUBERON:000238593.21gold quality
myocardiumUBERON:000234992.92gold quality
oocyteCL:000002390.69gold quality
right atrium auricular regionUBERON:000663190.21gold quality
cardiac atriumUBERON:000208189.95gold quality
heartUBERON:000094889.51gold quality
secondary oocyteCL:000065589.25gold quality
cardiac muscle of right atriumUBERON:000337987.06gold quality
tongueUBERON:000172385.60gold quality
buccal mucosa cellCL:000233683.41gold quality
parotid glandUBERON:000183178.98gold quality
superior surface of tongueUBERON:000737172.57gold quality
pharyngeal mucosaUBERON:000035567.05gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 2.

ExperimentMarker?Max mean expression
E-GEOD-75367yes32.65
E-ANND-3yes5.86

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

24 targeting LMOD3, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-4533100.0069.482758
HSA-MIR-570-3P99.9672.414910
HSA-MIR-141-3P99.9472.792421
HSA-MIR-200A-3P99.9472.682420
HSA-MIR-6835-3P99.9370.492904
HSA-MIR-4659A-3P99.8072.624248
HSA-MIR-4659B-3P99.8072.624248
HSA-MIR-442299.7272.072908
HSA-MIR-33A-3P99.7070.273362
HSA-MIR-4677-5P99.7070.091940
HSA-MIR-3136-3P99.5766.59781
HSA-MIR-7155-3P99.5766.48794
HSA-MIR-302B-5P99.5069.491857
HSA-MIR-302D-5P99.5069.341863
HSA-MIR-57899.4668.361787
HSA-MIR-318299.4068.152454
HSA-MIR-4777-5P99.3367.531148
HSA-MIR-4727-5P99.2367.551154
HSA-MIR-6738-3P99.0367.141326
HSA-MIR-5001-3P98.9167.281394
HSA-MIR-5197-3P98.7167.051905
HSA-MIR-22-5P97.6768.921355
HSA-MIR-668-3P96.1865.80673
HSA-MIR-425-3P93.0663.6568

Literature-anchored findings (GeneRIF, showing 5)

  • LMOD3 is essential for the organization of sarcomeric thin filaments in skeletal muscle. (PMID:25250574)
  • LMOD3 mutation is associated with congenital myopathy. (PMID:28815944)
  • The LMOD3 gene encodes leiomodin 3, a member of the tropomodulin family of proteins, which is expressed in skeletal muscle from the early stages of differentiation and plays a role in actin thin-filament nucleation. (PMID:29331079)
  • LMOD3 is expressed in the brain and colocalized with major structures involved in the regulation of vigilance states. LMOD proteins are structural proteins and seem to be developmentally regulated. (PMID:29923248)
  • We characterized the clinical features and the genetic status of 4 unrelated adolescent or adult patients with nemaline myopathy due to the missense variant c.1648C>T, p.(Leu550Phe) in the LMOD3 gene, either on both alleles or in trans with another missense variant (c.1004A>G, p.Gln335Arg). (PMID:30291184)

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
mus_musculusLmod3ENSMUSG00000044086
rattus_norvegicusLmod3ENSRNOG00000032443
drosophila_melanogastertmodFBGN0082582
caenorhabditis_elegansunc-94WBGENE00006823

Paralogs (6): TMOD2 (ENSG00000128872), TMOD1 (ENSG00000136842), TMOD3 (ENSG00000138594), TMOD4 (ENSG00000163157), LMOD1 (ENSG00000163431), LMOD2 (ENSG00000170807)

Protein

Protein identifiers

Leiomodin-3Q0VAK6 (reviewed: Q0VAK6)

Alternative names: Leiomodin, fetal form

All UniProt accessions (1): Q0VAK6

UniProt curated annotations — full annotation on UniProt →

Function. Essential for the organization of sarcomeric actin thin filaments in skeletal muscle. Increases the rate of actin polymerization.

Subunit / interactions. May interact with tropomyosin alpha (TPM1/2) N-terminus. Interacts with KLHL40; leading to stabilization.

Subcellular location. Cytoplasm. Myofibril. Sarcomere. M line. A band. Cytoskeleton.

Tissue specificity. Expressed in cardiac and at higher levels in skeletal muscles (at protein level).

Post-translational modifications. Ubiquitinated, leading to its degradation. Interaction with KLHL40 negatively regulates ubiquitination and degradation.

Disease relevance. Nemaline myopathy 10 (NEM10) [MIM:616165] An autosomal recessive severe form of nemaline myopathy. Nemaline myopathies are muscular disorders characterized by muscle weakness of varying severity and onset, and abnormal thread-like or rod-shaped structures in muscle fibers on histologic examination. NEM10 is characterized by early-onset generalized muscle weakness and hypotonia with respiratory insufficiency and feeding difficulties. Additional features include arthrogryposis or congenital contractures, ophthalmoplegia, a history of prematurity, reduced fetal movements, and polyhydramnios. Most patients die of respiratory failure in early infancy. The disease is caused by variants affecting the gene represented in this entry.

Similarity. Belongs to the tropomodulin family.

Isoforms (2)

UniProt IDNamesCanonical?
Q0VAK6-11yes
Q0VAK6-22

RefSeq proteins (2): NP_001291347, NP_938012* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR004934TMODFamily
IPR032675LRR_dom_sfHomologous_superfamily

Pfam: PF03250

UniProt features (27 total): compositionally biased region 6, sequence variant 5, region of interest 5, splice variant 4, sequence conflict 3, coiled-coil region 2, chain 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q0VAK6-F167.790.29

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 305 (showing top): GOBP_NEGATIVE_REGULATION_OF_PROTEIN_CONTAINING_COMPLEX_ASSEMBLY, GOBP_REGULATION_OF_PROTEIN_POLYMERIZATION, GOBP_REGULATION_OF_SKELETAL_MUSCLE_TISSUE_DEVELOPMENT, GOBP_MUSCLE_TISSUE_DEVELOPMENT, GOBP_POSITIVE_REGULATION_OF_MUSCLE_CELL_DIFFERENTIATION, LFA1_Q6, GOBP_NEGATIVE_REGULATION_OF_PROTEIN_POLYMERIZATION, GOBP_STRIATED_MUSCLE_CELL_DIFFERENTIATION, GOBP_REGULATION_OF_STRIATED_MUSCLE_CELL_DIFFERENTIATION, GOBP_NEGATIVE_REGULATION_OF_ACTIN_FILAMENT_DEPOLYMERIZATION, GOBP_REGULATION_OF_CELLULAR_COMPONENT_BIOGENESIS, CAGCTG_AP4_Q5, COUP_01, GOBP_NEGATIVE_REGULATION_OF_CELLULAR_COMPONENT_ORGANIZATION, GOBP_REGULATION_OF_ACTIN_FILAMENT_BASED_PROCESS

GO Biological Process (10): muscle contraction (GO:0006936), striated muscle contraction (GO:0006941), actin filament organization (GO:0007015), myofibril assembly (GO:0030239), skeletal muscle thin filament assembly (GO:0030240), actin nucleation (GO:0045010), skeletal muscle fiber development (GO:0048741), positive regulation of skeletal muscle fiber development (GO:0048743), pointed-end actin filament capping (GO:0051694), striated muscle cell development (GO:0055002)

GO Molecular Function (3): actin monomer binding (GO:0003785), tropomyosin binding (GO:0005523), protein binding (GO:0005515)

GO Cellular Component (6): cytoplasm (GO:0005737), cytoskeleton (GO:0005856), striated muscle thin filament (GO:0005865), myofibril (GO:0030016), M band (GO:0031430), A band (GO:0031672)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure3
supramolecular fiber organization2
actin filament organization2
sarcomere2
muscle system process1
muscle contraction1
actin cytoskeleton organization1
cellular component assembly involved in morphogenesis1
actomyosin structure organization1
striated muscle cell development1
membraneless organelle assembly1
skeletal myofibril assembly1
skeletal muscle tissue development1
myotube cell development1
positive regulation of cell development1
positive regulation of skeletal muscle tissue development1
skeletal muscle fiber development1
regulation of skeletal muscle fiber development1
positive regulation of striated muscle cell differentiation1
actin filament capping1
striated muscle cell differentiation1
muscle cell development1
actin binding1
cytoskeletal protein binding1
binding1
intracellular anatomical structure1
intracellular membraneless organelle1
actin cytoskeleton1
myofilament1
contractile muscle fiber1
A band1

Protein interactions and networks

STRING

826 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
LMOD3KLHL40Q2TBA0813
LMOD3KBTBD13C9JR72799
LMOD3KLHL41O60662775
LMOD3NEBP20929703
LMOD3TNNT1P13805664
LMOD3TPM2P06468649
LMOD3MYPNQ86TC9628
LMOD3TPM1P09493624
LMOD3CFL2Q9Y281616
LMOD3TPM3P06753605
LMOD3ACTA1P02568587
LMOD3MYO18BQ8IUG5585
LMOD3COBLO75128578
LMOD3JMYQ8N9B5498
LMOD3PFN4Q8NHR9488

IntAct

5 interactions, top by confidence:

ABTypeScore
LMO2LMOD3psi-mi:“MI:0915”(physical association)0.560
LMOD3PLS1psi-mi:“MI:0915”(physical association)0.400

BioGRID (7): LMOD3 (Two-hybrid), PLS1 (Affinity Capture-MS), LMOD3 (Cross-Linking-MS (XL-MS)), LMOD3 (Cross-Linking-MS (XL-MS)), LMOD3 (Cross-Linking-MS (XL-MS)), KLHL40 (Affinity Capture-Western), LMOD3 (Two-hybrid)

ESM2 similar proteins: A0M8S4, A0M8T5, A1A5Q0, B9EJA2, E1BTG2, E7F7X0, E9QA62, F7AEX0, O35867, O88665, Q00PJ1, Q02225, Q07DV1, Q07DW4, Q07DX4, Q07DY4, Q07E15, Q07E28, Q07E41, Q09YG9, Q09YI1, Q09YJ3, Q09YK4, Q09YM8, Q0VAK6, Q108T9, Q2IBA2, Q2IBD4, Q2IBE6, Q2IBF7, Q2IBF8, Q2QL82, Q2QLA2, Q2QLB3, Q2QLF8, Q2QLG9, Q2V2M9, Q3UHZ5, Q3UQU0, Q4V8E4

Diamond homologs: A0A0G2K0D3, A0JNC0, A1A5Q0, E1BTG2, E7F7X0, E9QA62, O01479, P28289, P29536, P49813, P70566, P70567, Q0VAK6, Q0VC48, Q3UHZ5, Q6P5Q4, Q8BVA4, Q9JHJ0, Q9JKK7, Q9JLH8, Q9NYL9, Q9NZQ9, Q9NZR1

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

458 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic39
Likely pathogenic5
Uncertain significance232
Likely benign134
Benign23

Top pathogenic / likely-pathogenic (30)

Variant IDHGVSClassification
1323241NM_198271.5(LMOD3):c.1342C>T (p.Gln448Ter)Pathogenic
1323243NM_198271.5(LMOD3):c.1020_1023del (p.Thr341fs)Pathogenic
1354391NM_198271.5(LMOD3):c.1192del (p.Arg398fs)Pathogenic
1395938NM_198271.5(LMOD3):c.1472dup (p.Arg492fs)Pathogenic
1417273NM_198271.5(LMOD3):c.971del (p.Gly324fs)Pathogenic
1451345NM_198271.5(LMOD3):c.704C>G (p.Ser235Ter)Pathogenic
1451618NM_198271.5(LMOD3):c.1219C>T (p.Gln407Ter)Pathogenic
1457468NM_198271.5(LMOD3):c.80_95del (p.Asn26_Leu27insTer)Pathogenic
162215NM_198271.5(LMOD3):c.138dup (p.Ser47fs)Pathogenic
162217NM_198271.5(LMOD3):c.1201C>T (p.Arg401Ter)Pathogenic
162219NM_198271.5(LMOD3):c.1069G>T (p.Glu357Ter)Pathogenic
2149678NM_198271.5(LMOD3):c.1330C>T (p.Gln444Ter)Pathogenic
2169511NM_198271.5(LMOD3):c.882dup (p.Asp295fs)Pathogenic
2176069NM_198271.5(LMOD3):c.278_288del (p.Thr93fs)Pathogenic
2501771NM_198271.5(LMOD3):c.944_945del (p.Leu315fs)Pathogenic
2571781NM_198271.5(LMOD3):c.360dup (p.Glu121fs)Pathogenic
2712484NM_198271.5(LMOD3):c.131_132del (p.Pro44fs)Pathogenic
2898508NM_198271.5(LMOD3):c.780del (p.Asn261fs)Pathogenic
3012412NM_198271.5(LMOD3):c.637dup (p.Ile213fs)Pathogenic
3643646NM_198271.5(LMOD3):c.1434C>G (p.Tyr478Ter)Pathogenic
3656192NM_198271.5(LMOD3):c.1543_1544del (p.Ile515fs)Pathogenic
3691947NM_198271.5(LMOD3):c.1012G>T (p.Glu338Ter)Pathogenic
3720520NM_198271.5(LMOD3):c.1372C>T (p.Gln458Ter)Pathogenic
374498NM_198271.5(LMOD3):c.1648C>T (p.Leu550Phe)Pathogenic
374499NM_198271.5(LMOD3):c.1004A>G (p.Gln335Arg)Pathogenic
3906263NM_198271.5(LMOD3):c.112del (p.Glu38fs)Pathogenic
4070599NM_198271.5(LMOD3):c.391A>T (p.Lys131Ter)Pathogenic
4070600NM_198271.5(LMOD3):c.106C>T (p.Gln36Ter)Pathogenic
4726249NM_198271.5(LMOD3):c.658A>T (p.Lys220Ter)Pathogenic
4731299NM_198271.5(LMOD3):c.319G>T (p.Glu107Ter)Pathogenic

SpliceAI

360 predictions. Top by Δscore:

VariantEffectΔscore
3:69120058:TTCC:Tacceptor_loss0.9900
3:69120059:TCC:Tacceptor_loss0.9900
3:69120061:CTAC:Cacceptor_loss0.9900
3:69120062:T:Aacceptor_loss0.9900
3:69122087:GGTTA:Gdonor_loss0.9900
3:69122088:GTTAC:Gdonor_loss0.9900
3:69122089:TTA:Tdonor_loss0.9900
3:69122090:TA:Tdonor_loss0.9900
3:69122091:A:AGdonor_loss0.9900
3:69122195:T:Adonor_gain0.9900
3:69122268:T:TAdonor_gain0.9900
3:69118691:CTACT:Cdonor_loss0.9800
3:69118692:TACTT:Tdonor_loss0.9800
3:69118693:ACTTA:Adonor_loss0.9800
3:69118694:CT:Cdonor_loss0.9800
3:69118695:TTACA:Tdonor_loss0.9800
3:69118696:TACAG:Tdonor_loss0.9800
3:69118697:A:ACdonor_gain0.9800
3:69118697:ACAG:Adonor_loss0.9800
3:69118698:C:CCdonor_gain0.9800
3:69118698:CAG:Cdonor_gain0.9800
3:69120061:C:CCacceptor_gain0.9800
3:69118690:TCTAC:Tdonor_loss0.9700
3:69121523:TCAAA:Tdonor_gain0.9700
3:69109121:CCTGC:Cacceptor_loss0.9600
3:69109122:C:CAacceptor_loss0.9600
3:69109123:T:Cacceptor_loss0.9600
3:69118698:CA:Cdonor_gain0.9600
3:69118698:CAGG:Cdonor_gain0.9600
3:69120059:TC:Tacceptor_gain0.9600

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000213784 (3:69107067 C>G), RS1000277100 (3:69112697 C>T), RS1000424422 (3:69121784 G>A,C), RS1000492842 (3:69123277 T>G), RS1000651914 (3:69111278 G>A), RS1000662429 (3:69116896 T>C), RS1000820899 (3:69117831 TG>T,TGG), RS1001263961 (3:69115582 C>G), RS1001428054 (3:69120502 T>A,C), RS1001549141 (3:69112095 T>A), RS1001650806 (3:69109774 T>C), RS1001695460 (3:69115841 T>C), RS1002233831 (3:69112395 A>C), RS1002665233 (3:69115065 A>G), RS1002669038 (3:69114653 G>A,C)

Disease associations

OMIM: gene MIM:616112 | disease phenotypes: MIM:616165, MIM:616654

GenCC curated gene-disease

DiseaseClassificationInheritance
nemaline myopathy 10DefinitiveAutosomal recessive
severe congenital nemaline myopathySupportiveAutosomal recessive
typical nemaline myopathySupportiveAutosomal dominant

ClinGen Gene-Disease Validity (1)

Expert-panel classifications — Definitive > Strong > Moderate > Limited > Disputed > Refuted.

DiseaseClassificationInheritance
nemaline myopathy 10DefinitiveAR

Mondo (4): nemaline myopathy 10 (MONDO:0014513), Joubert syndrome 24 (MONDO:0014724), severe congenital nemaline myopathy (MONDO:0015735), typical nemaline myopathy (MONDO:0015737)

Orphanet (1): Isolated Joubert syndrome (Orphanet:475)

HPO phenotypes

79 total (30 of 79 shown, HPO-id order):

HPOTerm
HP:0000007Autosomal recessive inheritance
HP:0000047Hypospadias
HP:0000054Micropenis
HP:0000218High palate
HP:0000239Large fontanelles
HP:0000275Narrow face
HP:0000347Micrognathia
HP:0000369Low-set ears
HP:0000470Short neck
HP:0000508Ptosis
HP:0000602Ophthalmoplegia
HP:0000765Abnormal thorax morphology
HP:0000767Pectus excavatum
HP:0000774Narrow chest
HP:0000775Abnormality of the diaphragm
HP:0000883Thin ribs
HP:0001181Adducted thumb
HP:0001265Hyporeflexia
HP:0001270Motor delay
HP:0001283Bulbar palsy
HP:0001288Gait disturbance
HP:0001290Generalized hypotonia
HP:0001319Neonatal hypotonia
HP:0001324Muscle weakness
HP:0001337Tremor
HP:0001349Facial diplegia
HP:0001371Flexion contracture
HP:0001522Death in infancy
HP:0001558Decreased fetal movement
HP:0001561Polyhydramnios

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

13 total (human), top 13 by PubMed support.

ChemicalActions (top 5)PubMed papers
Doxorubicindecreases expression2
isobutyl alcoholdecreases expression, increases abundance, affects cotreatment1
CGP 52608affects binding, increases reaction1
erucylphospho-N,N,N-trimethylpropylammoniumincreases expression1
incobotulinumtoxinAdecreases expression1
Temozolomidedecreases expression1
Sunitinibdecreases expression1
Benzo(a)pyreneaffects methylation, increases methylation1
Cisplatinincreases expression1
Gasolineaffects cotreatment, decreases expression, increases abundance1
Polycyclic Aromatic Hydrocarbonsdecreases expression, increases abundance, affects cotreatment1
Valproic Aciddecreases methylation1
Particulate Matteraffects cotreatment, decreases expression, increases abundance1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.