MED20

mediator complex subunit 20, the group of Mediator complex

Basic information

Region (hg38): 6:41905354-41921139

Previous symbols: [ "TRFP" ]

Links

ENSG00000124641NCBI:9477OMIM:612915HGNC:16840Uniprot:Q9H944AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the MED20 gene.

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
9
clinvar
1
clinvar
10
missense
20
clinvar
20
nonsense
1
clinvar
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)3003108
6-41907091-G-A Uncertain significance (Aug 05, 2024)3608199
6-41907141-C-G Uncertain significance (Aug 02, 2023)1415514
6-41907152-C-A not specified Uncertain significance (Aug 04, 2024)3394632
6-41907158-C-T not specified Uncertain significance (Jun 17, 2024)3294047
6-41907165-C-T Likely benign (Dec 20, 2022)2975722
6-41907192-G-A Likely benign (Nov 22, 2022)2063409
6-41907209-G-A not specified Uncertain significance (Nov 08, 2022)2324483
6-41907230-G-C not specified Uncertain significance (Nov 14, 2023)3125006
6-41907237-G-A Likely benign (Feb 16, 2023)2911713
6-41907239-G-A not specified Uncertain significance (Nov 10, 2022)2373983
6-41907277-C-T not specified Uncertain significance (Jun 02, 2023)2510600
6-41909285-C-T not specified Uncertain significance (Jan 16, 2024)3125005
6-41909351-C-G Uncertain significance (Jan 01, 2015)183050
6-41909439-G-A Uncertain significance (Jun 19, 2017)432783
6-41909461-G-A Benign (Jan 04, 2024)2861377
6-41909463-C-T not specified Uncertain significance (Mar 01, 2024)3125004
6-41909464-G-A Likely benign (Jul 31, 2022)2191460
6-41909470-G-A Likely benign (Feb 11, 2023)2168540
6-41909474-A-T Uncertain significance (May 17, 2023)2798835
6-41909504-A-C Uncertain significance (Jan 28, 2022)1958182
6-41909515-G-A not specified Likely benign (Jun 21, 2023)2605016
6-41916806-C-A Uncertain significance (Nov 07, 2023)1396185
6-41916806-C-T Uncertain significance (Jan 11, 2024)2854121
6-41916807-G-A Likely benign (Feb 09, 2022)2075390

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
MED20protein_codingprotein_codingENST00000265350 415786
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.3040.6791257330151257480.0000596
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.23911300.6980.000007431401
Missense in Polyphen2336.9910.62177417
Synonymous0.6234752.80.8910.00000328415
Loss of Function2.0128.220.2433.47e-7100

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0003010.000300
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.00006180.0000615
Middle Eastern0.000.00
South Asian0.00003270.0000327
Other0.000.00

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumLowMedium
Primary ImmunodeficiencyMediumLowMedium
CancerMediumMediumMedium

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