MED21

mediator complex subunit 21, the group of Mediator complex

Basic information

Region (hg38): 12:27022546-27066343

Previous symbols: [ "SURB7" ]

Links

ENSG00000152944

∙ NCBI:9412 ∙ OMIM:603800 ∙ HGNC:11473 ∙ Uniprot:Q13503 ∙ 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 MED21 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MED21 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			3 clinvar			3
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	3	0	0

Variants in MED21

This is a list of pathogenic ClinVar variants found in the MED21 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Phenotype	Significance	ClinVar
12-27027424-G-A	not specified	Uncertain significance (Oct 17, 2023)	3125008
12-27027433-A-G	not specified	Uncertain significance (Oct 20, 2024)	3394633
12-27028430-G-A	not specified	Uncertain significance (Mar 11, 2024)	3125009

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MED21	protein_coding	protein_coding	ENST00000282892	4	43798

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0143	0.881	125725	0	15	125740	0.0000596

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.577	62	76.2	0.814	0.00000346	933
Missense in Polyphen		7	10.75	0.65118		143
Synonymous	0.711	23	27.8	0.828	0.00000129	284
Loss of Function	1.35	4	8.16	0.490	5.11e-7	81

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000214	0.000213
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.000139	0.000139
European (Non-Finnish)	0.0000618	0.0000615
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000164	0.000163

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. {ECO:0000269|PubMed:15249124, ECO:0000269|PubMed:9660976}.;
Pathway: Developmental Biology;Transcriptional regulation of white adipocyte differentiation (Consensus)

Recessive Scores

pRec: 0.230

Intolerance Scores

loftool: 0.464
rvis_EVS: -0.01
rvis_percentile_EVS: 52.85

Haploinsufficiency Scores

pHI: 0.168
hipred: Y
hipred_score: 0.849
ghis: 0.670

Essentials

essential_gene_CRISPR: E
essential_gene_CRISPR2: N
essential_gene_gene_trap: E
gene_indispensability_pred: E
gene_indispensability_score: 0.539

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Low	Low	Low
Primary Immunodeficiency	Low	Low	Low
Cancer	Low	Low	Low

Mouse Genome Informatics

Gene name: Med21
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: blastocyst development;regulation of transcription by RNA polymerase II;protein ubiquitination;stem cell population maintenance;RNA biosynthetic process;positive regulation of transcription by RNA polymerase II
Cellular component: ubiquitin ligase complex;mediator complex
Molecular function: transcription coregulator activity;transcription coactivator activity;DNA-directed 5'-3' RNA polymerase activity;protein binding;ubiquitin protein ligase activity