MED11

mediator complex subunit 11, the group of Mediator complex

Basic information

Region (hg38): 17:4731428-4733608

Links

ENSG00000161920

∙ NCBI:400569 ∙ OMIM:612383 ∙ HGNC:32687 ∙ Uniprot:Q9P086 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

neurodegeneration with developmental delay, early respiratory failure, myoclonic seizures, and brain abnormalities (Strong), mode of inheritance: AR
neurodegeneration with developmental delay, early respiratory failure, myoclonic seizures, and brain abnormalities (Limited), mode of inheritance: AR
neurodegeneration with developmental delay, early respiratory failure, myoclonic seizures, and brain abnormalities (Moderate), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Neurodegeneration with developmental delay, early respiratory failure, myoclonic seizures, and brain abnormalities	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Audiologic/Otolaryngologic; Cardiovascular; Craniofacial; Genitourinary; Neurologic	36001086

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the MED11 gene.

not_specified (14 variants)
Neurodegeneration_with_developmental_delay,_early_respiratory_failure,_myoclonic_seizures,_and_brain_abnormalities (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MED11 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001001683.4. 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			15 clinvar			15
nonsense	1 clinvar					1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	1	0	15	0	0

Highest pathogenic variant AF is 0.000014250292

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MED11	protein_coding	protein_coding	ENST00000293777	3	2183

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.36e-8	0.0509	125700	0	47	125747	0.000187

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.646	54	69.1	0.781	0.00000337	740
Missense in Polyphen		17	16.911	1.0053		201
Synonymous	-0.812	34	28.5	1.19	0.00000137	244
Loss of Function	-1.17	9	5.92	1.52	3.35e-7	62

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000431	0.000431
Ashkenazi Jewish	0.00	0.00
East Asian	0.00141	0.00141
Finnish	0.00	0.00
European (Non-Finnish)	0.000114	0.000114
Middle Eastern	0.00141	0.00141
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;Transcriptional regulation of white adipocyte differentiation (Consensus)

Recessive Scores

pRec: 0.126

Intolerance Scores

loftool: 0.605
rvis_EVS: 0.01
rvis_percentile_EVS: 54.63

Haploinsufficiency Scores

pHI: 0.139
hipred: Y
hipred_score: 0.662
ghis: 0.575

Essentials

essential_gene_CRISPR: E
essential_gene_CRISPR2: E
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.781

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

Gene name: Med11
Phenotype: hearing/vestibular/ear phenotype; limbs/digits/tail 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); embryo phenotype; homeostasis/metabolism phenotype;

Gene ontology

Biological process: regulation of transcription by RNA polymerase II;protein ubiquitination
Cellular component: ubiquitin ligase complex;mediator complex
Molecular function: transcription coregulator activity;protein binding;ubiquitin protein ligase activity