MYOD1
myogenic differentiation 1, the group of Basic helix-loop-helix proteins|Myogenic regulatory family
Basic information
Region (hg38): 11:17719571-17722136
Previous symbols: [ "MYF3" ]
Links
Phenotypes
GenCC
Source:
- myopathy, congenital, with diaphragmatic defects, respiratory insufficiency, and dysmorphic facies (Limited), mode of inheritance: AR
- fetal akinesia deformation sequence 1 (Supportive), mode of inheritance: AR
- myopathy, congenital, with diaphragmatic defects, respiratory insufficiency, and dysmorphic facies (Strong), mode of inheritance: AR
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Congenital myopathy 17 | AR | General | Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing | Craniofacial; Musculoskeletal; Pulmonary; Renal | 26733463; 30403323; 31260566 |
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (52 variants)
- not_provided (14 variants)
- MYOD1-related_disorder (8 variants)
- Myopathy,_congenital,_with_diaphragmatic_defects,_respiratory_insufficiency,_and_dysmorphic_facies (7 variants)
- Autosomal_dominant_centronuclear_myopathy (1 variants)
- Arthrogryposis_multiplex_congenita (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the MYOD1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000002478.5. Only rare variants are included in the table.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 9 | |||||
| missense | 53 | 59 | ||||
| nonsense | 4 | |||||
| start loss | 0 | |||||
| frameshift | 1 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 3 | 2 | 53 | 12 | 3 |
Highest pathogenic variant AF is 0.000030817064
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| MYOD1 | protein_coding | protein_coding | ENST00000250003 | 3 | 2564 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.152 | 0.783 | 125369 | 0 | 5 | 125374 | 0.0000199 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -0.394 | 201 | 186 | 1.08 | 0.00000876 | 2032 |
| Missense in Polyphen | 70 | 72.04 | 0.97168 | 852 | ||
| Synonymous | -0.421 | 90 | 85.1 | 1.06 | 0.00000426 | 684 |
| Loss of Function | 1.51 | 2 | 5.99 | 0.334 | 2.53e-7 | 83 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000365 | 0.0000353 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000343 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Acts as a transcriptional activator that promotes transcription of muscle-specific target genes and plays a role in muscle differentiation. Together with MYF5 and MYOG, co-occupies muscle-specific gene promoter core region during myogenesis. Induces fibroblasts to differentiate into myoblasts. Interacts with and is inhibited by the twist protein. This interaction probably involves the basic domains of both proteins (By similarity). {ECO:0000250}.;
- Pathway
- miRs in Muscle Cell Differentiation;Cell Differentiation - Index expanded;Cell Differentiation - Index;ID signaling pathway;Developmental Biology;signal dependent regulation of myogenesis by corepressor mitr;CDO in myogenesis;Myogenesis;control of skeletal myogenesis by hdac and calcium/calmodulin-dependent kinase (camk);C-MYB transcription factor network;ID;Notch-mediated HES/HEY network;Signaling events mediated by HDAC Class III;Regulation of retinoblastoma protein;Regulation of nuclear SMAD2/3 signaling
(Consensus)
Recessive Scores
- pRec
- 0.820
Intolerance Scores
- loftool
- 0.264
- rvis_EVS
- -0.14
- rvis_percentile_EVS
- 43.29
Haploinsufficiency Scores
- pHI
- 0.985
- hipred
- Y
- hipred_score
- 0.584
- ghis
- 0.556
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 1.00
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Myod1
- Phenotype
- skeleton phenotype; neoplasm; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); normal phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); reproductive system phenotype; respiratory system phenotype; homeostasis/metabolism phenotype; muscle phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); growth/size/body region phenotype;
Zebrafish Information Network
- Gene name
- myod1
- Affected structure
- fast muscle cell
- Phenotype tag
- abnormal
- Phenotype quality
- decreased amount
Gene ontology
- Biological process
- regulation of alternative mRNA splicing, via spliceosome;regulation of transcription by RNA polymerase II;protein phosphorylation;muscle organ development;myoblast fate determination;skeletal muscle tissue development;myoblast fusion;cellular response to starvation;myotube cell development;myotube differentiation involved in skeletal muscle regeneration;skeletal muscle cell differentiation;muscle cell fate commitment;positive regulation of skeletal muscle tissue regeneration;regulation of RNA splicing;skeletal muscle fiber adaptation;histone H3 acetylation;histone H4 acetylation;positive regulation of myoblast differentiation;positive regulation of transcription by RNA polymerase II;skeletal muscle fiber development;positive regulation of skeletal muscle fiber development;positive regulation of muscle cell differentiation;cellular response to tumor necrosis factor;cellular response to glucocorticoid stimulus;cellular response to estradiol stimulus;cellular response to oxygen levels;positive regulation of myoblast fusion;positive regulation of snRNA transcription by RNA polymerase II;negative regulation of myoblast proliferation
- Cellular component
- nuclear chromatin;nucleus;nucleoplasm;transcription factor complex;cytosol;nuclear body;myofibril
- Molecular function
- RNA polymerase II regulatory region sequence-specific DNA binding;RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription activator activity, RNA polymerase II-specific;chromatin binding;transcription coactivator activity;protein binding;chromatin DNA binding;ubiquitin protein ligase binding;nuclear hormone receptor binding;protein heterodimerization activity;E-box binding;promoter-specific chromatin binding