MED15

mediator complex subunit 15, the group of Mediator complex

Basic information

Region (hg38): 22:20495913-20587632

Previous symbols: [ "TNRC7", "PCQAP" ]

Links

ENSG00000099917 ∙ NCBI:51586 ∙ OMIM:607372 ∙ HGNC:14248 ∙ Uniprot:Q96RN5 ∙ 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 MED15 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MED15 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				2		2
missense			44	3		47
nonsense			1		1	2
start loss						0
frameshift						0
inframe indel				2	1	3
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding					2	2
Total	0	0	45	7	4

Variants in MED15

This is a list of pathogenic ClinVar variants found in the MED15 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-20507691-G-C		not specified	Uncertain significance (Mar 19, 2024)
22-20537211-C-CCCTA			Benign (Apr 12, 2018)
22-20551451-C-G		not specified	Uncertain significance (Dec 15, 2023)
22-20553168-G-A		not specified	Uncertain significance (Aug 15, 2024)
22-20554945-A-G		not specified	Uncertain significance (Apr 23, 2024)
22-20554959-C-G		not specified	Uncertain significance (Aug 12, 2021)
22-20554986-G-A		not specified	Uncertain significance (Jan 24, 2025)
22-20554998-A-T		not specified	Uncertain significance (Jul 06, 2021)
22-20555013-C-G		not specified	Uncertain significance (Jun 04, 2024)
22-20555028-G-A		not specified	Uncertain significance (May 31, 2023)
22-20555029-G-A		not specified	Uncertain significance (May 27, 2022)
22-20555042-C-G		not specified	Uncertain significance (Sep 01, 2021)
22-20555052-A-G		not specified	Uncertain significance (Dec 08, 2023)
22-20555054-G-A		not specified	Uncertain significance (Jan 16, 2024)
22-20555084-G-A			Likely benign (Feb 01, 2023)
22-20564522-C-T		not specified	Likely benign (May 17, 2023)
22-20564529-ACAG-A		Hepatocellular carcinoma	Pathogenic (Jun 15, 2021)
22-20564581-G-A		not specified	Uncertain significance (Sep 20, 2024)
22-20564609-TGCAGCAGCAGCAGCAGCTCCAGCAGCA-T			Benign (Mar 01, 2023)
22-20564628-CCAG-C		Hepatocellular carcinoma	Pathogenic (Jun 15, 2021)
22-20564628-C-CCAG			Likely benign (Dec 01, 2022)
22-20566526-ACAG-A		Hepatocellular carcinoma	Pathogenic (Jun 15, 2021)
22-20566526-ACAGCAGCAG-A			Likely benign (Feb 01, 2023)
22-20566526-A-ACAG		Hepatocellular carcinoma	Pathogenic (Jun 15, 2021)
22-20566526-A-ACAGCAGCAG		Hepatocellular carcinoma	Pathogenic (Jun 15, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MED15	protein_coding	protein_coding	ENST00000263205	18	91720

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.000255	125736	0	12	125748	0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.53	319	474	0.673	0.0000284	5141
Missense in Polyphen		46	95.771	0.48031		1064
Synonymous	-0.678	214	202	1.06	0.0000136	1532
Loss of Function	5.96	7	54.5	0.128	0.00000281	480

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000184	0.000181
Ashkenazi Jewish	0.00	0.00
East Asian	0.000218	0.000217
Finnish	0.00	0.00
European (Non-Finnish)	0.0000354	0.0000352
Middle Eastern	0.000218	0.000217
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. Required for cholesterol-dependent gene regulation. Positively regulates the Nodal signaling pathway. {ECO:0000269|PubMed:12167862, ECO:0000269|PubMed:16630888, ECO:0000269|PubMed:16799563}.
• Pathway: Sterol Regulatory Element-Binding Proteins (SREBP) signalling;SREBF and miR33 in cholesterol and lipid homeostasis;Developmental Biology;Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription;Transcriptional regulation of white adipocyte differentiation;Regulation of nuclear SMAD2/3 signaling (Consensus)

Recessive Scores

• pRec: 0.166

Intolerance Scores

• loftool: 0.0513
• rvis_EVS: -1.46
• rvis_percentile_EVS: 3.78

Haploinsufficiency Scores

• pHI: 0.730
• hipred: Y
• hipred_score: 0.756
• ghis: 0.625

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 1.00

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Med15

Zebrafish Information Network

• Gene name: med15
• Affected structure: mesendoderm development
• Phenotype tag: abnormal
• Phenotype quality: disrupted

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;transcription initiation from RNA polymerase II promoter;stem cell population maintenance
• Cellular component: nucleus;nucleoplasm;cytoplasm;membrane;mediator complex
• Molecular function: transcription coregulator activity;protein binding