MED20

mediator complex subunit 20, the group of Mediator complex

Basic information

Region (hg38): 6:41905354-41921139

Previous symbols: [ "TRFP" ]

Links

ENSG00000124641 ∙ NCBI:9477 ∙ OMIM:612915 ∙ HGNC:16840 ∙ Uniprot:Q9H944 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

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	1	10
missense			20			20
nonsense			1			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: gnomAD

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: 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

	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