MEF2A

myocyte enhancer factor 2A, the group of Myocyte enhancer factor 2 proteins|MADS box family

Basic information

Region (hg38): 15:99565416-99716488

Links

ENSG00000068305 ∙ NCBI:4205 ∙ OMIM:600660 ∙ HGNC:6993 ∙ Uniprot:Q02078 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the MEF2A gene.

• Inborn genetic diseases (15 variants)
• not provided (8 variants)
• not specified (2 variants)
• Coronary artery disease, autosomal dominant, 1 (1 variants)
• Coronary artery disease/myocardial infarction (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MEF2A 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				2	3	5
missense			14	2	1	17
nonsense						0
start loss						0
frameshift						0
inframe indel					2	2
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	4	6

Variants in MEF2A

This is a list of pathogenic ClinVar variants found in the MEF2A region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
15-99633128-G-A			Likely benign (Dec 14, 2018)
15-99645626-CTG-C			Uncertain significance (-)
15-99671621-G-A			Benign (Dec 11, 2018)
15-99674405-C-T		not specified	Uncertain significance (Jun 21, 2021)
15-99674409-A-G		Coronary artery disease, autosomal dominant, 1	Uncertain significance (Mar 29, 2024)
15-99674429-A-C		not specified	Uncertain significance (Jun 24, 2022)
15-99675391-G-A		MEF2A-related disorder	Benign (May 14, 2019)
15-99675411-G-A		not specified	Uncertain significance (Jul 14, 2022)
15-99675435-A-G		not specified	Uncertain significance (Dec 13, 2022)
15-99675450-G-A		not specified	Uncertain significance (Apr 18, 2023)
15-99690292-G-A		not specified	Uncertain significance (Mar 21, 2023)
15-99690352-A-G		Coronary artery disease/myocardial infarction • not specified	Benign/Likely benign (Jul 01, 2022)
15-99690400-C-T		Coronary artery disease/myocardial infarction	Pathogenic (Feb 01, 2006)
15-99690412-G-A		Coronary artery disease/myocardial infarction	Pathogenic (Dec 15, 2004)
15-99706731-T-C		MEF2A-related disorder	Benign (Oct 17, 2019)
15-99706737-G-A		MEF2A-related disorder	Benign (Oct 28, 2019)
15-99706762-C-G		not specified	Uncertain significance (May 17, 2023)
15-99706776-C-T			Benign (Dec 31, 2019)
15-99706793-C-T		not specified	Uncertain significance (Oct 25, 2022)
15-99710682-C-T		not specified	Uncertain significance (Dec 03, 2021)
15-99710698-G-A			Likely benign (Aug 09, 2018)
15-99710725-G-C		not specified	Uncertain significance (Jan 10, 2022)
15-99710736-G-C		not specified	Uncertain significance (Jul 25, 2023)
15-99710751-G-A		not specified	Uncertain significance (Jan 19, 2024)
15-99712390-T-C		MEF2A-related disorder • not specified	Likely benign (Jan 23, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MEF2A	protein_coding	protein_coding	ENST00000354410	9	239302

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.987	0.0129	122180	0	1	122181	0.00000409

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.54	205	277	0.739	0.0000146	3233
Missense in Polyphen		112	150.77	0.74285		1720
Synonymous	0.623	97	105	0.923	0.00000605	989
Loss of Function	3.95	2	22.0	0.0911	0.00000115	257

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)	0.00000910	0.00000910
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcriptional activator which binds specifically to the MEF2 element, 5'-YTA[AT](4)TAR-3', found in numerous muscle- specific genes. Also involved in the activation of numerous 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. In cerebellar granule neurons, phosphorylated and sumoylated MEF2A represses transcription of NUR77 promoting synaptic differentiation. Associates with chromatin to the ZNF16 promoter. {ECO:0000269|PubMed:11904443, ECO:0000269|PubMed:12691662, ECO:0000269|PubMed:15834131, ECO:0000269|PubMed:16371476, ECO:0000269|PubMed:16484498, ECO:0000269|PubMed:16563226, ECO:0000269|PubMed:21468593, ECO:0000269|PubMed:9858528}.
• Disease: DISEASE: Coronary artery disease, autosomal dominant, 1 (ADCAD1) [MIM:608320]: A common heart disease characterized by reduced or absent blood flow in one or more of the arteries that encircle and supply the heart. Its most important complication is acute myocardial infarction. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Apelin signaling pathway - Homo sapiens (human);Fluid shear stress and atherosclerosis - Homo sapiens (human);cGMP-PKG signaling pathway - Homo sapiens (human);EGF-Core;Energy Metabolism;SRF and miRs in Smooth Muscle Differentiation and Proliferation;miRs in Muscle Cell Differentiation;Cell Differentiation - Index expanded;Cell Differentiation - Index;Adipogenesis;Brain-Derived Neurotrophic Factor (BDNF) signaling pathway;Cardiac Hypertrophic Response;TGF-beta Signaling Pathway;EGF-EGFR Signaling Pathway;Developmental Biology;Toll Like Receptor 7/8 (TLR7/8) Cascade;Interleukin-17 signaling;Signal Transduction;Signaling by Interleukins;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;signal dependent regulation of myogenesis by corepressor mitr;mapkinase signaling pathway;Cytokine Signaling in Immune system;Toll Like Receptor 9 (TLR9) Cascade;MyD88 cascade initiated on plasma membrane;Toll Like Receptor 10 (TLR10) Cascade;Toll Like Receptor 3 (TLR3) Cascade;Toll Like Receptor 5 (TLR5) Cascade;Toll-Like Receptors Cascades;Innate Immune System;Immune System;Nuclear Events (kinase and transcription factor activation);CDO in myogenesis;Myogenesis;Signaling by NTRK1 (TRKA);control of skeletal myogenesis by hdac and calcium/calmodulin-dependent kinase (camk);Signaling by NTRKs;ERK/MAPK targets;MAPK targets/ Nuclear events mediated by MAP kinases;MAP kinase activation;TRAF6 mediated induction of NFkB and MAP kinases upon TLR7/8 or 9 activation;MyD88 dependent cascade initiated on endosome;TRIF(TICAM1)-mediated TLR4 signaling ;MyD88-independent TLR4 cascade ;Toll Like Receptor 4 (TLR4) Cascade;Signaling by Receptor Tyrosine Kinases;MyD88:Mal cascade initiated on plasma membrane;Toll Like Receptor TLR1:TLR2 Cascade;Toll Like Receptor TLR6:TLR2 Cascade;Toll Like Receptor 2 (TLR2) Cascade;Signaling mediated by p38-alpha and p38-beta (Consensus)

Recessive Scores

• pRec: 0.237

Intolerance Scores

• loftool: 0.591
• rvis_EVS: -0.31
• rvis_percentile_EVS: 31.93

Haploinsufficiency Scores

• pHI: 0.753
• hipred: Y
• hipred_score: 0.783
• ghis: 0.521

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: Mef2a
• Phenotype: 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); 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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); growth/size/body region phenotype; cellular phenotype

Zebrafish Information Network

• Gene name: mef2aa
• Affected structure: cardiac muscle cell
• Phenotype tag: abnormal
• Phenotype quality: disorganized

Gene ontology

• Biological process: mitochondrial genome maintenance;negative regulation of transcription by RNA polymerase II;MAPK cascade;transcription, DNA-templated;apoptotic process;heart development;muscle organ development;positive regulation of cardiac muscle hypertrophy;positive regulation of transcription by RNA polymerase II;positive regulation of glucose import;mitochondrion distribution;dendrite morphogenesis;positive regulation of muscle cell differentiation;ventricular cardiac myofibril assembly;cardiac conduction;ERK5 cascade;cellular response to calcium ion
• Cellular component: nuclear chromatin;nucleus;nucleoplasm;transcription factor complex;cytosol
• 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;RNA polymerase II transcription factor binding;DNA-binding transcription activator activity, RNA polymerase II-specific;chromatin binding;DNA-binding transcription factor activity;transcription coactivator activity;protein binding;protein kinase binding;activating transcription factor binding;histone acetyltransferase binding;histone deacetylase binding;sequence-specific DNA binding;SMAD binding;protein heterodimerization activity