MED9

mediator complex subunit 9, the group of Mediator complex

Basic information

Region (hg38): 17:17476993-17493221

Links

ENSG00000141026 ∙ NCBI:55090 ∙ OMIM:609878 ∙ HGNC:25487 ∙ Uniprot:Q9NWA0 ∙ 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 MED9 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MED9 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			10	2		12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	2	0

Variants in MED9

This is a list of pathogenic ClinVar variants found in the MED9 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-17477045-G-T		not specified	Uncertain significance (Feb 28, 2023)
17-17477052-C-G		not specified	Uncertain significance (Apr 18, 2023)
17-17477096-A-G		not specified	Uncertain significance (Mar 20, 2023)
17-17477106-A-C		not specified	Likely benign (Jun 30, 2022)
17-17477160-C-T		not specified	Uncertain significance (Oct 26, 2022)
17-17477189-C-T		not specified	Uncertain significance (Jan 04, 2022)
17-17477214-G-A		not specified	Likely benign (Jan 03, 2024)
17-17477241-C-T		not specified	Uncertain significance (Aug 19, 2023)
17-17477255-A-G		not specified	Uncertain significance (Oct 05, 2023)
17-17491296-C-T		not specified	Uncertain significance (Aug 15, 2023)
17-17491326-A-G		not specified	Uncertain significance (Apr 12, 2023)
17-17491362-C-T		not specified	Uncertain significance (Oct 22, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MED9	protein_coding	protein_coding	ENST00000268711	2	16241

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.408	0.558	120870	0	2	120872	0.00000827

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.794	65	85.7	0.759	0.00000458	952
Missense in Polyphen		25	31.313	0.7984		369
Synonymous	0.0488	38	38.4	0.990	0.00000211	289
Loss of Function	1.69	1	5.12	0.195	2.21e-7	53

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000545	0.0000482
European (Non-Finnish)	0.00000976	0.00000931
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
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: Vitamin D Receptor Pathway;Developmental Biology;Transcriptional regulation of white adipocyte differentiation (Consensus)

Recessive Scores

• pRec: 0.118

Intolerance Scores

• loftool: 0.249
• rvis_EVS: 0.19
• rvis_percentile_EVS: 66.57

Haploinsufficiency Scores

• pHI: 0.217
• hipred: Y
• hipred_score: 0.775
• ghis: 0.485

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.638

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Med9

Gene ontology

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