MED15
Basic information
Region (hg38): 22:20495913-20587632
Previous symbols: [ "TNRC7", "PCQAP" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (77 variants)
- not_provided (7 variants)
- Aganglionic_megacolon (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the MED15 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001003891.3. 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 | 3 | |||||
| missense | 74 | 78 | ||||
| nonsense | 1 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 75 | 7 | 0 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| MED15 | protein_coding | protein_coding | ENST00000263205 | 18 | 91720 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.00 | 0.000255 | 125736 | 0 | 12 | 125748 | 0.0000477 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.53 | 319 | 474 | 0.673 | 0.0000284 | 5141 |
| Missense in Polyphen | 46 | 95.771 | 0.48031 | 1064 | ||
| Synonymous | -0.678 | 214 | 202 | 1.06 | 0.0000136 | 1532 |
| Loss of Function | 5.96 | 7 | 54.5 | 0.128 | 0.00000281 | 480 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000184 | 0.000181 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000218 | 0.000217 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000354 | 0.0000352 |
| Middle Eastern | 0.000218 | 0.000217 |
| South Asian | 0.00 | 0.00 |
| 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. Required for cholesterol-dependent gene regulation. Positively regulates the Nodal signaling pathway. {ECO:0000269|PubMed:12167862, ECO:0000269|PubMed:16630888, ECO:0000269|PubMed:16799563}.;
- Pathway
- Sterol Regulatory Element-Binding Proteins (SREBP) signalling;SREBF and miR33 in cholesterol and lipid homeostasis;Developmental Biology;Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription;Transcriptional regulation of white adipocyte differentiation;Regulation of nuclear SMAD2/3 signaling
(Consensus)
Recessive Scores
- pRec
- 0.166
Intolerance Scores
- loftool
- 0.0513
- rvis_EVS
- -1.46
- rvis_percentile_EVS
- 3.78
Haploinsufficiency Scores
- pHI
- 0.730
- hipred
- Y
- hipred_score
- 0.756
- ghis
- 0.625
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- E
- 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
- Med15
- Phenotype
Zebrafish Information Network
- Gene name
- med15
- Affected structure
- mesendoderm development
- Phenotype tag
- abnormal
- Phenotype quality
- disrupted
Gene ontology
- Biological process
- regulation of transcription by RNA polymerase II;transcription initiation from RNA polymerase II promoter;stem cell population maintenance
- Cellular component
- nucleus;nucleoplasm;cytoplasm;membrane;mediator complex
- Molecular function
- transcription coregulator activity;protein binding