MED16

mediator complex subunit 16, the group of Mediator complex|WD repeat domain containing

Basic information

Region (hg38): 19:867630-893218

Previous symbols: [ "THRAP5" ]

Links

ENSG00000175221 ∙ NCBI:10025 ∙ OMIM:604062 ∙ HGNC:17556 ∙ Uniprot:Q9Y2X0 ∙ 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 MED16 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MED16 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				4	3	7
missense			96	4		100
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1		1	2
non coding				4		4
Total	0	0	97	12	3

Variants in MED16

This is a list of pathogenic ClinVar variants found in the MED16 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-868109-G-A		not specified	Uncertain significance (Aug 11, 2022)
19-868114-T-A		not specified	Uncertain significance (Nov 08, 2022)
19-868127-G-A		not specified	Uncertain significance (Apr 13, 2022)
19-868129-T-C		not specified	Uncertain significance (Aug 04, 2023)
19-868154-A-G		not specified	Likely benign (Nov 03, 2022)
19-868184-C-T		not specified	Uncertain significance (Oct 16, 2023)
19-868220-C-T		not specified	Uncertain significance (May 30, 2024)
19-868237-C-T		not specified	Likely benign (May 13, 2024)
19-868238-G-A		not specified	Uncertain significance (Jul 25, 2023)
19-868421-G-A			Benign (Aug 01, 2018)
19-868444-A-G		not specified	Uncertain significance (May 06, 2024)
19-868473-G-A		not specified	Uncertain significance (Jun 29, 2022)
19-868887-G-A		not specified	Uncertain significance (Dec 03, 2021)
19-868897-C-T		not specified	Uncertain significance (Dec 13, 2021)
19-868906-G-T		not specified	Uncertain significance (Nov 07, 2022)
19-868908-A-T		not specified	Uncertain significance (Jan 23, 2023)
19-868910-C-G		not specified	Uncertain significance (Oct 26, 2021)
19-868936-G-T		not specified	Uncertain significance (Aug 08, 2022)
19-871054-C-A		not specified	Uncertain significance (Apr 18, 2023)
19-871064-G-A		not specified	Uncertain significance (Feb 23, 2023)
19-871088-G-A		not specified	Uncertain significance (Jul 12, 2022)
19-871092-G-A		not specified	Uncertain significance (Nov 03, 2023)
19-871106-C-T		not specified	Uncertain significance (Jun 30, 2022)
19-871107-G-A		not specified	Uncertain significance (Jul 20, 2021)
19-871110-G-A		not specified	Uncertain significance (Jun 02, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MED16	protein_coding	protein_coding	ENST00000325464	15	25257

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.59e-14	0.400	125531	1	186	125718	0.000744

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.67	703	589	1.19	0.0000422	5574
Missense in Polyphen		74	82.567	0.89624		753
Synonymous	-9.45	478	278	1.72	0.0000223	1803
Loss of Function	1.41	26	35.0	0.743	0.00000159	383

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00153	0.00147
Ashkenazi Jewish	0.000333	0.000298
East Asian	0.000395	0.000381
Finnish	0.000349	0.000323
European (Non-Finnish)	0.00109	0.00100
Middle Eastern	0.000395	0.000381
South Asian	0.000270	0.000261
Other	0.00153	0.00147

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:10198638, ECO:0000269|PubMed:10235266}.
• 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: 0.125

Intolerance Scores

• loftool: 0.477
• rvis_EVS: -2.73
• rvis_percentile_EVS: 0.7

Haploinsufficiency Scores

• pHI: 0.117
• hipred: Y
• hipred_score: 0.704
• ghis: 0.589

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.957

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Med16
• Phenotype: growth/size/body region 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); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); liver/biliary system phenotype; embryo 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
• Molecular function: transcription coregulator activity;transcription coactivator activity;catalytic activity;protein binding;thyroid hormone receptor coactivator activity;signaling receptor activity;vitamin D receptor binding;thyroid hormone receptor binding