MYF5
myogenic factor 5, the group of Myogenic regulatory family|Basic helix-loop-helix proteins
Basic information
Region (hg38): 12:80716912-80719671
Links
Phenotypes
GenCC
Source:
- ophthalmoplegia, external, with rib and vertebral anomalies (Limited), mode of inheritance: AR
- ophthalmoplegia, external, with rib and vertebral anomalies (Strong), mode of inheritance: AR
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Ophthalmoplegia, external, with rib and vertebral anomalies | 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 | Musculoskeletal; Ophthalmologic | 29887215 |
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the MYF5 gene is commonly pathogenic or not.
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.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 3 | |||||
| missense | 17 | 17 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 1 | 1 | ||||
| non coding | 0 | |||||
| Total | 0 | 0 | 17 | 2 | 1 |
Variants in MYF5
This is a list of pathogenic ClinVar variants found in the MYF5 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 12-80717083-GCCAGTTCTCA-G | External ophthalmoplegia;Abnormal rib morphology;Scoliosis • Ophthalmoplegia, external, with rib and vertebral anomalies | Pathogenic (Oct 26, 2018) | ||
| 12-80717114-C-G | Ophthalmoplegia, external, with rib and vertebral anomalies | Uncertain significance (Nov 14, 2019) | ||
| 12-80717114-C-T | EBV-positive nodal T- and NK-cell lymphoma | Likely benign (-) | ||
| 12-80717117-C-T | MYF5-related disorder | Likely benign (Jun 13, 2019) | ||
| 12-80717143-A-G | not specified | Uncertain significance (Dec 14, 2021) | ||
| 12-80717146-T-C | not specified | Uncertain significance (Feb 15, 2023) | ||
| 12-80717170-T-A | not specified | Uncertain significance (Dec 20, 2021) | ||
| 12-80717201-G-A | MYF5-related disorder | Benign (Jun 12, 2018) | ||
| 12-80717206-G-A | not specified | Uncertain significance (Feb 27, 2024) | ||
| 12-80717296-A-G | not specified | Uncertain significance (May 12, 2024) | ||
| 12-80717313-C-G | not specified | Uncertain significance (Oct 20, 2023) | ||
| 12-80717316-C-T | Ophthalmoplegia, external, with rib and vertebral anomalies | Uncertain significance (Sep 19, 2024) | ||
| 12-80717346-C-T | External ophthalmoplegia;Abnormal rib morphology;Scoliosis • Ophthalmoplegia, external, with rib and vertebral anomalies | Pathogenic (Oct 26, 2018) | ||
| 12-80717384-G-C | not specified | Uncertain significance (Dec 13, 2022) | ||
| 12-80717403-C-A | not specified | Uncertain significance (Sep 06, 2022) | ||
| 12-80717410-A-G | not specified | Uncertain significance (Mar 12, 2024) | ||
| 12-80717491-A-G | not specified | Uncertain significance (Apr 18, 2023) | ||
| 12-80717524-C-G | not specified | Uncertain significance (Dec 06, 2023) | ||
| 12-80717526-G-C | not specified | Uncertain significance (Oct 12, 2021) | ||
| 12-80718355-T-C | MYF5-related disorder | Likely benign (Jun 26, 2019) | ||
| 12-80718386-G-T | not specified | Uncertain significance (Dec 14, 2023) | ||
| 12-80718416-G-C | not specified | Uncertain significance (Jan 10, 2022) | ||
| 12-80718424-G-A | not specified | Uncertain significance (Dec 01, 2022) | ||
| 12-80718430-A-G | not specified | Uncertain significance (Jul 14, 2021) | ||
| 12-80718907-C-A | MYF5-related disorder | Likely benign (May 20, 2019) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| MYF5 | protein_coding | protein_coding | ENST00000228644 | 3 | 2762 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.000229 | 0.766 | 125727 | 0 | 21 | 125748 | 0.0000835 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -0.283 | 165 | 155 | 1.06 | 0.00000941 | 1663 |
| Missense in Polyphen | 67 | 67.123 | 0.99817 | 709 | ||
| Synonymous | -0.317 | 69 | 65.7 | 1.05 | 0.00000426 | 512 |
| Loss of Function | 1.05 | 7 | 10.7 | 0.653 | 5.84e-7 | 116 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000370 | 0.000369 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000163 | 0.000163 |
| Finnish | 0.0000462 | 0.0000462 |
| European (Non-Finnish) | 0.0000440 | 0.0000439 |
| Middle Eastern | 0.000163 | 0.000163 |
| South Asian | 0.000164 | 0.000163 |
| Other | 0.000163 | 0.000163 |
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 MYOG and MYOD1, co-occupies muscle-specific gene promoter core region during myogenesis. Induces fibroblasts to differentiate into myoblasts. Probable sequence specific DNA-binding protein.;
- Pathway
- Signaling pathways regulating pluripotency of stem cells - Homo sapiens (human);miRs in Muscle Cell Differentiation;Developmental Biology;CDO in myogenesis;Myogenesis;Regulation of nuclear beta catenin signaling and target gene transcription
(Consensus)
Recessive Scores
- pRec
- 0.304
Intolerance Scores
- loftool
- 0.367
- rvis_EVS
- -0.54
- rvis_percentile_EVS
- 20.26
Haploinsufficiency Scores
- pHI
- 0.980
- hipred
- Y
- hipred_score
- 0.524
- ghis
- 0.468
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.801
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Myf5
- Phenotype
- vision/eye phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); skeleton phenotype; immune system phenotype; respiratory system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); embryo phenotype; neoplasm; 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); normal phenotype; growth/size/body region phenotype; craniofacial phenotype; muscle phenotype; cellular phenotype; homeostasis/metabolism phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan);
Zebrafish Information Network
- Gene name
- myf5
- Affected structure
- pharyngeal arch 6
- Phenotype tag
- abnormal
- Phenotype quality
- absent
Gene ontology
- Biological process
- cartilage condensation;ossification;somitogenesis;regulation of cell-matrix adhesion;regulation of transcription by RNA polymerase II;muscle organ development;skeletal muscle tissue development;extracellular matrix organization;skeletal muscle cell differentiation;muscle cell fate commitment;camera-type eye development;positive regulation of myoblast differentiation;positive regulation of transcription by RNA polymerase II;embryonic skeletal system morphogenesis;positive regulation of skeletal muscle fiber development;positive regulation of muscle cell differentiation;muscle tissue morphogenesis;positive regulation of myoblast fusion
- Cellular component
- nucleus;nucleoplasm;RNA polymerase II transcription factor complex
- Molecular function
- 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;protein binding;protein heterodimerization activity;E-box binding