MED24

mediator complex subunit 24, the group of Mediator complex|MicroRNA protein coding host genes|Small nucleolar RNA protein coding host genes

Basic information

Region (hg38): 17:40019097-40061215

Previous symbols: [ "THRAP4", "CRSP4" ]

Links

ENSG00000008838 ∙ NCBI:9862 ∙ OMIM:607000 ∙ HGNC:22963 ∙ Uniprot:O75448 ∙ 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 MED24 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MED24 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				1	2	3
missense			48		1	49
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding					1	1
Total	0	0	48	1	4

Variants in MED24

This is a list of pathogenic ClinVar variants found in the MED24 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-40019536-G-A		not specified	Uncertain significance (Jan 23, 2024)
17-40019587-G-A		not specified	Uncertain significance (Oct 12, 2021)
17-40019613-G-A			Benign (Dec 26, 2018)
17-40019641-G-A		not specified	Uncertain significance (Dec 11, 2023)
17-40019778-T-C			Benign (Jun 10, 2018)
17-40019797-C-T		not specified	Uncertain significance (Jul 12, 2023)
17-40019819-C-T		not specified	Uncertain significance (Dec 28, 2022)
17-40019856-T-G		not specified	Uncertain significance (Jun 13, 2024)
17-40019873-T-C		not specified	Uncertain significance (Mar 15, 2024)
17-40019891-G-A		not specified	Uncertain significance (Sep 25, 2023)
17-40019895-G-A		not specified	Uncertain significance (May 23, 2023)
17-40020297-G-A		not specified	Uncertain significance (Sep 01, 2021)
17-40021963-G-A		not specified	Uncertain significance (Aug 17, 2022)
17-40021979-C-T		not specified	Uncertain significance (May 24, 2023)
17-40022004-C-T		not specified	Uncertain significance (Apr 13, 2022)
17-40022014-G-A		not specified	Uncertain significance (Feb 27, 2023)
17-40022407-C-T		not specified	Uncertain significance (Dec 02, 2022)
17-40022434-G-A		not specified	Uncertain significance (Jul 20, 2022)
17-40022663-G-A		not specified	Uncertain significance (May 16, 2023)
17-40022688-T-C		not specified	Uncertain significance (May 31, 2023)
17-40022693-G-A		not specified	Uncertain significance (Mar 07, 2024)
17-40022757-G-T		not specified	Uncertain significance (Sep 14, 2022)
17-40022789-C-T		Short stature	Likely pathogenic (Nov 18, 2001)
17-40022790-G-A		not specified	Uncertain significance (Apr 22, 2022)
17-40022808-G-C		not specified	Uncertain significance (May 04, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MED24	protein_coding	protein_coding	ENST00000394128	25	42119

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.32e-11	1.00	125637	0	111	125748	0.000441

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.63	414	594	0.697	0.0000356	6425
Missense in Polyphen		106	172.13	0.61582		1995
Synonymous	0.715	235	249	0.942	0.0000157	1964
Loss of Function	3.31	26	51.7	0.503	0.00000255	576

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000873	0.000867
Ashkenazi Jewish	0.00	0.00
East Asian	0.000764	0.000761
Finnish	0.000143	0.000139
European (Non-Finnish)	0.000505	0.000492
Middle Eastern	0.000764	0.000761
South Asian	0.000338	0.000327
Other	0.000996	0.000978

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:12218053, ECO:0000269|PubMed:16595664}.
• 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: 0.132

Intolerance Scores

• loftool: 0.902
• rvis_EVS: -1.41
• rvis_percentile_EVS: 4.13

Haploinsufficiency Scores

• pHI: 0.216
• hipred: Y
• hipred_score: 0.648
• ghis: 0.582

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.747

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Med24
• Phenotype: embryo phenotype; 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); hematopoietic system 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); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); growth/size/body region phenotype; muscle phenotype; cellular phenotype

Zebrafish Information Network

• Gene name: med24
• Affected structure: mid intestine
• Phenotype tag: abnormal
• Phenotype quality: has fewer parts of type

Gene ontology

• Biological process: 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;mediator complex
• Molecular function: transcription coregulator activity;protein binding;nuclear receptor transcription coactivator activity;signaling receptor activity;vitamin D receptor binding;thyroid hormone receptor binding