MED1
mediator complex subunit 1, the group of Mediator complex
Basic information
Region (hg38): 17:39404285-39451272
Previous symbols: [ "TRIP2", "PPARGBP", "PPARBP" ]
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 MED1 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 | |||||
| missense | 50 | 51 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 50 | 2 | 1 |
Variants in MED1
This is a list of pathogenic ClinVar variants found in the MED1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 17-39407506-T-C | not specified | Uncertain significance (Feb 13, 2024) | ||
| 17-39407513-C-A | not specified | Uncertain significance (Nov 07, 2023) | ||
| 17-39407524-A-G | not specified | Uncertain significance (Jun 02, 2024) | ||
| 17-39407675-G-A | not specified | Uncertain significance (May 18, 2023) | ||
| 17-39407701-A-C | not specified | Uncertain significance (May 08, 2024) | ||
| 17-39407716-T-C | not specified | Uncertain significance (Jul 09, 2021) | ||
| 17-39407731-T-A | not specified | Uncertain significance (Sep 29, 2023) | ||
| 17-39407740-G-A | not specified | Uncertain significance (Aug 14, 2024) | ||
| 17-39407761-C-T | not specified | Uncertain significance (Mar 19, 2024) | ||
| 17-39408065-T-C | not specified | Uncertain significance (Sep 10, 2024) | ||
| 17-39408088-G-T | not specified | Uncertain significance (Jul 14, 2024) | ||
| 17-39408091-T-G | not specified | Uncertain significance (May 16, 2023) | ||
| 17-39408209-G-A | not specified | Uncertain significance (Nov 26, 2024) | ||
| 17-39408421-G-A | not specified | Uncertain significance (Jan 26, 2023) | ||
| 17-39408431-T-C | not specified | Uncertain significance (Jan 02, 2024) | ||
| 17-39408523-T-C | not specified | Uncertain significance (Dec 04, 2023) | ||
| 17-39408532-C-G | not specified | Uncertain significance (Feb 23, 2023) | ||
| 17-39408541-G-A | Intellectual disability | Likely benign (Jan 01, 2019) | ||
| 17-39408596-T-C | not specified | Uncertain significance (Feb 05, 2024) | ||
| 17-39408640-G-A | not specified | Uncertain significance (Jan 30, 2024) | ||
| 17-39408651-G-C | not specified | Uncertain significance (Sep 01, 2024) | ||
| 17-39408655-G-T | not specified | Uncertain significance (Sep 14, 2022) | ||
| 17-39408757-G-A | not specified | Uncertain significance (Nov 21, 2024) | ||
| 17-39408775-G-T | not specified | Uncertain significance (Dec 27, 2023) | ||
| 17-39408795-C-A | not specified | Uncertain significance (Dec 13, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| MED1 | protein_coding | protein_coding | ENST00000300651 | 17 | 47002 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.00 | 9.40e-8 | 125741 | 0 | 7 | 125748 | 0.0000278 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.14 | 661 | 835 | 0.792 | 0.0000420 | 10435 |
| Missense in Polyphen | 160 | 247.26 | 0.6471 | 3164 | ||
| Synonymous | 1.83 | 271 | 312 | 0.868 | 0.0000167 | 3159 |
| Loss of Function | 6.53 | 2 | 53.6 | 0.0373 | 0.00000287 | 724 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000295 | 0.0000295 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000443 | 0.0000439 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000327 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Component of the Mediator complex, a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors (PubMed:10406464, PubMed:11867769, PubMed:12037571, PubMed:12218053, PubMed:12556447, PubMed:14636573, PubMed:15340084, PubMed:15471764, PubMed:15989967, PubMed:16574658, PubMed:9653119). Acts as a coactivator for GATA1-mediated transcriptional activation during erythroid differentiation of K562 erythroleukemia cells (PubMed:24245781). {ECO:0000269|PubMed:10406464, ECO:0000269|PubMed:11867769, ECO:0000269|PubMed:12037571, ECO:0000269|PubMed:12218053, ECO:0000269|PubMed:12556447, ECO:0000269|PubMed:14636573, ECO:0000269|PubMed:15340084, ECO:0000269|PubMed:15471764, ECO:0000269|PubMed:15989967, ECO:0000269|PubMed:16574658, ECO:0000269|PubMed:24245781, ECO:0000269|PubMed:9653119}.;
- Pathway
- Thyroid hormone signaling pathway - Homo sapiens (human);Energy Metabolism;H19 action Rb-E2F1 signaling and CDK-β-catenin activity;role of ppar-gamma coactivators in obesity and thermogenesis;Developmental Biology;Signal Transduction;Gene expression (Transcription);mechanism of gene regulation by peroxisome proliferators via ppara;multi-step regulation of transcription by pitx2;Generic Transcription Pathway;Regulation of lipid metabolism by Peroxisome proliferator-activated receptor alpha (PPARalpha);Metabolism of lipids;Hedgehog;Nuclear Receptor transcription pathway;RNA Polymerase II Transcription;Metabolism;Transcriptional regulation of white adipocyte differentiation;Coregulation of Androgen receptor activity;Signaling by Nuclear Receptors;RXR and RAR heterodimerization with other nuclear receptor;Estrogen-dependent gene expression;ESR-mediated signaling;Validated nuclear estrogen receptor alpha network
(Consensus)
Recessive Scores
- pRec
- 0.304
Intolerance Scores
- loftool
- 0.0189
- rvis_EVS
- -1.55
- rvis_percentile_EVS
- 3.28
Haploinsufficiency Scores
- pHI
- 0.879
- hipred
- Y
- hipred_score
- 0.783
- ghis
- 0.632
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.963
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Med1
- 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); limbs/digits/tail phenotype; pigmentation 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); hematopoietic system phenotype; respiratory system phenotype; liver/biliary system phenotype; embryo phenotype; cellular phenotype; homeostasis/metabolism phenotype; muscle phenotype; endocrine/exocrine gland phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype;
Gene ontology
- Biological process
- negative regulation of transcription by RNA polymerase II;cell morphogenesis;angiogenesis;liver development;embryonic placenta development;lens development in camera-type eye;thyroid hormone mediated signaling pathway;ventricular trabecula myocardium morphogenesis;retinal pigment epithelium development;regulation of transcription by RNA polymerase I;transcription initiation from RNA polymerase II promoter;thyroid hormone generation;androgen biosynthetic process;brain development;lactation;positive regulation of gene expression;negative regulation of keratinocyte proliferation;protein ubiquitination;regulation of lipid metabolic process;keratinocyte differentiation;monocyte differentiation;intracellular steroid hormone receptor signaling pathway;androgen receptor signaling pathway;animal organ regeneration;positive regulation of intracellular estrogen receptor signaling pathway;obsolete positive regulation of protein import into nucleus, translocation;positive regulation of mammary gland epithelial cell proliferation;embryonic heart tube development;embryonic hindlimb morphogenesis;embryonic hemopoiesis;peroxisome proliferator activated receptor signaling pathway;cellular response to hepatocyte growth factor stimulus;megakaryocyte development;mRNA transcription by RNA polymerase II;negative regulation of apoptotic process;fat cell differentiation;positive regulation of keratinocyte differentiation;positive regulation of erythrocyte differentiation;negative regulation of neuron differentiation;positive regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II;erythrocyte development;enucleate erythrocyte development;regulation of cell cycle;positive regulation of interferon-gamma-mediated signaling pathway;mammary gland branching involved in thelarche;mammary gland branching involved in pregnancy;epithelial cell proliferation involved in mammary gland duct elongation;positive regulation of G0 to G1 transition;ERK1 and ERK2 cascade;regulation of vitamin D receptor signaling pathway;cellular response to epidermal growth factor stimulus;cellular response to steroid hormone stimulus;cellular response to thyroid hormone stimulus;positive regulation of signaling receptor activity;positive regulation of hepatocyte proliferation;regulation of RNA biosynthetic process
- Cellular component
- ubiquitin ligase complex;chromatin;nucleus;nucleoplasm;nucleolus;membrane;mediator complex;protein-DNA complex
- Molecular function
- RNA polymerase II proximal promoter sequence-specific DNA binding;RNA polymerase II core promoter sequence-specific DNA binding;core promoter binding;chromatin binding;transcription coregulator activity;transcription coactivator activity;transcription corepressor activity;protein binding;transcription factor binding;nuclear receptor binding;estrogen receptor binding;nuclear receptor transcription coactivator activity;thyroid hormone receptor coactivator activity;chromatin DNA binding;nuclear hormone receptor binding;mediator complex binding;signaling receptor activity;vitamin D receptor binding;retinoic acid receptor binding;peroxisome proliferator activated receptor binding;thyroid hormone receptor binding;LBD domain binding;ubiquitin protein ligase activity