MED20
Basic information
Region (hg38): 6:41905354-41921139
Previous symbols: [ "TRFP" ]
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 MED20 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 | 10 | |||||
missense | 20 | 20 | ||||
nonsense | 1 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 0 | |||||
Total | 0 | 0 | 21 | 9 | 1 |
Variants in MED20
This is a list of pathogenic ClinVar variants found in the MED20 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
6-41907076-C-T | Uncertain significance (Jul 07, 2023) | |||
6-41907091-G-A | Uncertain significance (Aug 05, 2024) | |||
6-41907141-C-G | Uncertain significance (Aug 02, 2023) | |||
6-41907152-C-A | not specified | Uncertain significance (Aug 04, 2024) | ||
6-41907158-C-T | not specified | Uncertain significance (Jun 17, 2024) | ||
6-41907165-C-T | Likely benign (Dec 20, 2022) | |||
6-41907192-G-A | Likely benign (Nov 22, 2022) | |||
6-41907209-G-A | not specified | Uncertain significance (Nov 08, 2022) | ||
6-41907230-G-C | not specified | Uncertain significance (Nov 14, 2023) | ||
6-41907237-G-A | Likely benign (Feb 16, 2023) | |||
6-41907239-G-A | not specified | Uncertain significance (Nov 10, 2022) | ||
6-41907277-C-T | not specified | Uncertain significance (Jun 02, 2023) | ||
6-41909285-C-T | not specified | Uncertain significance (Jan 16, 2024) | ||
6-41909351-C-G | Uncertain significance (Jan 01, 2015) | |||
6-41909439-G-A | Uncertain significance (Jun 19, 2017) | |||
6-41909461-G-A | Benign (Jan 04, 2024) | |||
6-41909463-C-T | not specified | Uncertain significance (Mar 01, 2024) | ||
6-41909464-G-A | Likely benign (Jul 31, 2022) | |||
6-41909470-G-A | Likely benign (Feb 11, 2023) | |||
6-41909474-A-T | Uncertain significance (May 17, 2023) | |||
6-41909504-A-C | Uncertain significance (Jan 28, 2022) | |||
6-41909515-G-A | not specified | Likely benign (Jun 21, 2023) | ||
6-41916806-C-A | Uncertain significance (Nov 07, 2023) | |||
6-41916806-C-T | Uncertain significance (Jan 11, 2024) | |||
6-41916807-G-A | Likely benign (Feb 09, 2022) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
MED20 | protein_coding | protein_coding | ENST00000265350 | 4 | 15786 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.304 | 0.679 | 125733 | 0 | 15 | 125748 | 0.0000596 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 1.23 | 91 | 130 | 0.698 | 0.00000743 | 1401 |
Missense in Polyphen | 23 | 36.991 | 0.62177 | 417 | ||
Synonymous | 0.623 | 47 | 52.8 | 0.891 | 0.00000328 | 415 |
Loss of Function | 2.01 | 2 | 8.22 | 0.243 | 3.47e-7 | 100 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000301 | 0.000300 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.00 | 0.00 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.0000618 | 0.0000615 |
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.;
- Pathway
- Developmental Biology;Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription;Transcriptional regulation of white adipocyte differentiation
(Consensus)
Recessive Scores
- pRec
- 0.0952
Intolerance Scores
- loftool
- 0.439
- rvis_EVS
- -0.1
- rvis_percentile_EVS
- 46.49
Haploinsufficiency Scores
- pHI
- 0.117
- hipred
- Y
- hipred_score
- 0.590
- ghis
- 0.604
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.903
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Low | Medium |
Primary Immunodeficiency | Medium | Low | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Med20
- Phenotype
- immune system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); hematopoietic system 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);
Gene ontology
- Biological process
- transcription, DNA-templated;regulation of transcription by RNA polymerase II;transcription by RNA polymerase II;transcription initiation from RNA polymerase II promoter;protein ubiquitination;skeletal muscle cell differentiation;positive regulation of nucleic acid-templated transcription
- Cellular component
- ubiquitin ligase complex;nucleoplasm;mediator complex
- Molecular function
- transcription coactivator activity;DNA-directed 5'-3' RNA polymerase activity;protein binding;ubiquitin protein ligase activity