MED19

mediator complex subunit 19, the group of Mediator complex

Basic information

Region (hg38): 11:57703710-57712221

Links

ENSG00000156603 ∙ NCBI:219541 ∙ OMIM:612385 ∙ HGNC:29600 ∙ Uniprot:A0JLT2 ∙ 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 MED19 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MED19 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			17			17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	0	0

Variants in MED19

This is a list of pathogenic ClinVar variants found in the MED19 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-57704722-G-T		not specified	Uncertain significance (Dec 14, 2021)
11-57704742-C-T		not specified	Uncertain significance (Dec 04, 2024)
11-57704768-C-A		not specified	Uncertain significance (Feb 06, 2023)
11-57704811-G-A		not specified	Uncertain significance (Mar 08, 2024)
11-57704975-G-A		not specified	Uncertain significance (Jul 20, 2021)
11-57705044-G-A		not specified	Uncertain significance (Nov 27, 2024)
11-57705062-A-C		not specified	Uncertain significance (Mar 01, 2023)
11-57705064-C-T		not specified	Uncertain significance (Nov 26, 2024)
11-57705079-T-C		not specified	Uncertain significance (Sep 15, 2021)
11-57711998-C-T		not specified	Uncertain significance (Dec 07, 2024)
11-57712009-C-A		not specified	Uncertain significance (Nov 25, 2024)
11-57712022-G-A		not specified	Uncertain significance (Dec 02, 2024)
11-57712026-G-A		not specified	Uncertain significance (Jun 30, 2022)
11-57712064-C-A		not specified	Uncertain significance (Oct 25, 2023)
11-57712088-G-C		not specified	Uncertain significance (Jun 06, 2023)
11-57712125-T-C		not specified	Uncertain significance (Oct 27, 2022)
11-57712151-G-T		not specified	Uncertain significance (Aug 05, 2024)
11-57712181-G-A		Intellectual disability	Likely benign (Jan 01, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MED19	protein_coding	protein_coding	ENST00000337672	4	8508

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.782	0.212	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.771	82	104	0.787	0.00000557	1250
Missense in Polyphen		33	46.467	0.71018		522
Synonymous	0.379	36	39.0	0.923	0.00000201	400
Loss of Function	2.08	0	5.04	0.00	2.11e-7	74

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	0.00	0.00
European (Non-Finnish)	0.00	0.00
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: Developmental Biology;Transcriptional regulation of white adipocyte differentiation (Consensus)

Recessive Scores

• pRec: 0.0998

Intolerance Scores

• loftool: 0.116
• rvis_EVS: -0.01
• rvis_percentile_EVS: 52.85

Haploinsufficiency Scores

• pHI: 0.234
• hipred: Y
• hipred_score: 0.731
• ghis: 0.615

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.740

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Med19

Zebrafish Information Network

• Gene name: med19b
• Affected structure: head
• Phenotype tag: abnormal
• Phenotype quality: decreased size

Gene ontology

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