MED4

mediator complex subunit 4, the group of Mediator complex

Basic information

Region (hg38): 13:48053323-48095131

Previous symbols: [ "VDRIP" ]

Links

ENSG00000136146

∙ NCBI:29079 ∙ OMIM:605718 ∙ HGNC:17903 ∙ Uniprot:Q9NPJ6 ∙ 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 MED4 gene.

not_specified (23 variants)
not_provided (1 variants)

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. These statistics are base on transcript: NM_000014166.4. 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						0
missense			23 clinvar		1 clinvar	24
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	23	0	1

Loading clinvar variants...

GnomAD

Source: gnomAD

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: 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: 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