MEF2D
myocyte enhancer factor 2D, the group of MADS box family|Myocyte enhancer factor 2 proteins
Basic information
Region (hg38): 1:156463727-156500779
Links
Phenotypes
GenCC
Source:
No genCC data.
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 MEF2D 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 | 0 | |||||
| missense | 12 | 12 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 1 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 13 | 0 | 0 |
Variants in MEF2D
This is a list of pathogenic ClinVar variants found in the MEF2D region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 1-156468051-G-C | not specified | Uncertain significance (Apr 20, 2024) | ||
| 1-156468076-C-T | not specified | Uncertain significance (Sep 27, 2021) | ||
| 1-156468087-C-T | not specified | Uncertain significance (Sep 03, 2024) | ||
| 1-156468088-G-A | not specified | Uncertain significance (Oct 26, 2022) | ||
| 1-156468124-C-T | not specified | Uncertain significance (Mar 29, 2022) | ||
| 1-156468150-G-A | not specified | Uncertain significance (Oct 01, 2024) | ||
| 1-156468192-G-A | not specified | Uncertain significance (Jul 05, 2024) | ||
| 1-156468294-C-G | not specified | Uncertain significance (Dec 09, 2024) | ||
| 1-156468790-TGA-T | See cases | Uncertain significance (Jun 26, 2020) | ||
| 1-156475126-G-A | not specified | Uncertain significance (Feb 23, 2023) | ||
| 1-156477073-C-A | not specified | Uncertain significance (Sep 27, 2021) | ||
| 1-156477091-G-C | not specified | Uncertain significance (Sep 20, 2024) | ||
| 1-156477106-G-A | not specified | Uncertain significance (Nov 17, 2023) | ||
| 1-156477146-T-C | not specified | Uncertain significance (Jun 22, 2023) | ||
| 1-156477176-A-C | not specified | Uncertain significance (Jan 30, 2024) | ||
| 1-156477191-C-G | not specified | Uncertain significance (Jun 01, 2023) | ||
| 1-156479346-C-T | not specified | Uncertain significance (Apr 12, 2024) | ||
| 1-156479595-C-G | MEF2D-related disorder | Uncertain significance (Jan 10, 2023) | ||
| 1-156479644-C-G | not specified | Uncertain significance (May 04, 2023) | ||
| 1-156479649-G-T | not specified | Uncertain significance (Nov 09, 2024) | ||
| 1-156482624-C-T | Uncertain significance (Jul 01, 2019) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| MEF2D | protein_coding | protein_coding | ENST00000348159 | 11 | 37102 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.997 | 0.00295 | 125047 | 0 | 10 | 125057 | 0.0000400 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.25 | 211 | 325 | 0.649 | 0.0000200 | 3344 |
| Missense in Polyphen | 74 | 136.1 | 0.54373 | 1358 | ||
| Synonymous | -0.314 | 145 | 140 | 1.03 | 0.00000936 | 1100 |
| Loss of Function | 4.36 | 2 | 25.9 | 0.0771 | 0.00000133 | 256 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000621 | 0.0000615 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.000394 | 0.000372 |
| European (Non-Finnish) | 0.00000919 | 0.00000885 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Transcriptional activator which binds specifically to the MEF2 element, 5'-YTA[AT](4)TAR-3', found in numerous muscle- specific, growth factor- and stress-induced genes. Mediates cellular functions not only in skeletal and cardiac muscle development, but also in neuronal differentiation and survival. Plays diverse roles in the control of cell growth, survival and apoptosis via p38 MAPK signaling in muscle-specific and/or growth factor-related transcription. Plays a critical role in the regulation of neuronal apoptosis (By similarity). {ECO:0000250, ECO:0000269|PubMed:10849446, ECO:0000269|PubMed:11904443, ECO:0000269|PubMed:12691662, ECO:0000269|PubMed:15743823, ECO:0000269|PubMed:15834131}.;
- Pathway
- Apelin signaling pathway - Homo sapiens (human);cGMP-PKG signaling pathway - Homo sapiens (human);Energy Metabolism;SRF and miRs in Smooth Muscle Differentiation and Proliferation;miRs in Muscle Cell Differentiation;Cell Differentiation - Index expanded;Cell Differentiation - Index;B Cell Receptor Signaling Pathway;Adipogenesis;p38 MAPK Signaling Pathway;EMT transition in Colorectal Cancer;EGF-EGFR Signaling Pathway;Developmental Biology;role of erk5 in neuronal survival pathway;regulation of pgc-1a;p38 mapk signaling pathway;angiotensin ii mediated activation of jnk pathway via pyk2 dependent signaling;role of mef2d in t-cell apoptosis;signal dependent regulation of myogenesis by corepressor mitr;mapkinase signaling pathway;CDO in myogenesis;Myogenesis;control of skeletal myogenesis by hdac and calcium/calmodulin-dependent kinase (camk);Signaling events mediated by HDAC Class III;Role of Calcineurin-dependent NFAT signaling in lymphocytes
(Consensus)
Recessive Scores
- pRec
- 0.193
Intolerance Scores
- loftool
- 0.0385
- rvis_EVS
- -0.62
- rvis_percentile_EVS
- 17.16
Haploinsufficiency Scores
- pHI
- 0.866
- hipred
- Y
- hipred_score
- 0.783
- ghis
- 0.589
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.978
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Mef2d
- Phenotype
- 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); 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); skeleton 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); vision/eye phenotype; growth/size/body region phenotype; cellular phenotype; muscle phenotype;
Gene ontology
- Biological process
- osteoblast differentiation;endochondral ossification;chondrocyte differentiation;apoptotic process;nervous system development;adult heart development;muscle organ development;skeletal muscle cell differentiation;positive regulation of transcription by RNA polymerase II;positive regulation of vascular smooth muscle cell proliferation
- Cellular component
- nuclear chromatin;nucleus;nucleoplasm;cytoplasm;intracellular membrane-bounded organelle
- 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 factor activity;protein binding;activating transcription factor binding;protein homodimerization activity;histone deacetylase binding;protein heterodimerization activity