MED4
Basic information
Region (hg38): 13:48053323-48095131
Previous symbols: [ "VDRIP" ]
Links
Phenotypes
GenCC
Source:
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 MED4 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 | 7 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 6 | 0 | 1 |
Variants in MED4
This is a list of pathogenic ClinVar variants found in the MED4 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 13-48077193-A-T | Benign (Aug 07, 2018) | |||
| 13-48079892-C-G | not specified | Uncertain significance (Nov 07, 2023) | ||
| 13-48086375-A-T | not specified | Uncertain significance (Jan 19, 2024) | ||
| 13-48086383-T-C | not specified | Uncertain significance (Oct 26, 2022) | ||
| 13-48086404-T-G | not specified | Uncertain significance (Jun 14, 2022) | ||
| 13-48086430-C-T | not specified | Uncertain significance (May 17, 2023) | ||
| 13-48090361-C-G | not specified | Uncertain significance (Jun 07, 2024) | ||
| 13-48090363-C-T | not specified | Uncertain significance (Jul 06, 2021) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| MED4 | protein_coding | protein_coding | ENST00000258648 | 7 | 41809 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.00761 | 0.979 | 125715 | 0 | 31 | 125746 | 0.000123 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.02 | 104 | 138 | 0.756 | 0.00000641 | 1756 |
| Missense in Polyphen | 25 | 48.237 | 0.51827 | 632 | ||
| Synonymous | -1.10 | 61 | 51.0 | 1.20 | 0.00000250 | 485 |
| Loss of Function | 2.16 | 6 | 15.0 | 0.399 | 7.28e-7 | 185 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000307 | 0.000305 |
| Ashkenazi Jewish | 0.0000992 | 0.0000992 |
| East Asian | 0.000598 | 0.000598 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.000106 | 0.000105 |
| Middle Eastern | 0.000598 | 0.000598 |
| 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.;
- Pathway
- Thyroid hormone signaling pathway - Homo sapiens (human);Developmental Biology;Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription;Transcriptional regulation of white adipocyte differentiation
(Consensus)
Recessive Scores
- pRec
- 0.139
Intolerance Scores
- loftool
- 0.311
- rvis_EVS
- 0.37
- rvis_percentile_EVS
- 75.12
Haploinsufficiency Scores
- pHI
- 0.234
- hipred
- Y
- hipred_score
- 0.707
- ghis
- 0.481
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.984
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Med4
- Phenotype
Gene ontology
- Biological process
- regulation of transcription by RNA polymerase II;transcription by RNA polymerase II;transcription initiation from RNA polymerase II promoter;intracellular steroid hormone receptor signaling pathway;androgen receptor signaling pathway;positive regulation of transcription, DNA-templated
- Cellular component
- nucleus;nucleoplasm;membrane;mediator complex;core mediator complex
- Molecular function
- transcription coregulator activity;protein binding;nuclear receptor transcription coactivator activity;signaling receptor activity;vitamin D receptor binding;thyroid hormone receptor binding