MED28

mediator complex subunit 28, the group of Mediator complex

Basic information

Region (hg38): 4:17614641-17634105

Links

ENSG00000118579 ∙ NCBI:80306 ∙ OMIM:610311 ∙ HGNC:24628 ∙ Uniprot:Q9H204 ∙ 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 MED28 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MED28 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			19			19
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			13			13
Total	0	0	33	0	0

Variants in MED28

This is a list of pathogenic ClinVar variants found in the MED28 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-17614659-C-A		not specified	Uncertain significance (Dec 20, 2023)
4-17614671-G-C		not specified	Uncertain significance (Oct 21, 2021)
4-17614671-G-T		not specified	Uncertain significance (Dec 20, 2023)
4-17614673-G-A		Focal segmental glomerulosclerosis	Uncertain significance (Nov 13, 2019)
4-17614673-G-T		not specified	Uncertain significance (Dec 06, 2021)
4-17614686-G-A		not specified	Uncertain significance (Oct 27, 2023)
4-17614703-C-T		not specified	Uncertain significance (Nov 09, 2023)
4-17614704-C-T		not specified	Uncertain significance (Aug 08, 2022)
4-17614706-C-T		Hereditary breast ovarian cancer syndrome	Uncertain significance (Aug 01, 2020)
4-17614716-C-G		not specified	Uncertain significance (Mar 12, 2024)
4-17614725-C-G		not specified	Uncertain significance (Jan 09, 2024)
4-17614791-A-G		not specified	Uncertain significance (Oct 29, 2021)
4-17621601-A-G		not specified	Uncertain significance (Oct 02, 2023)
4-17621602-T-C		not specified	Uncertain significance (Mar 08, 2024)
4-17621613-C-G		not specified	Uncertain significance (Aug 02, 2023)
4-17621638-G-A		not specified	Uncertain significance (Aug 21, 2023)
4-17621689-T-G		not specified	Uncertain significance (Feb 27, 2024)
4-17623613-C-G		not specified	Uncertain significance (Feb 12, 2024)
4-17623710-A-C		not specified	Uncertain significance (Dec 14, 2022)
4-17623721-G-A		not specified	Uncertain significance (Jun 17, 2024)
4-17623758-A-G		not specified	Uncertain significance (Mar 02, 2023)
4-17632593-T-G		not specified	Uncertain significance (Dec 17, 2023)
4-17633740-C-T		not specified	Uncertain significance (Jul 20, 2022)
4-17633777-T-C		not specified	Uncertain significance (Nov 15, 2021)
4-17633788-T-C		not specified	Uncertain significance (Nov 09, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MED28	protein_coding	protein_coding	ENST00000237380	4	19475

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000111	0.614	125724	0	23	125747	0.0000915

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.279	106	98.2	1.08	0.00000491	1144
Missense in Polyphen		16	16.485	0.97055		233
Synonymous	-2.48	62	41.6	1.49	0.00000227	355
Loss of Function	0.717	7	9.37	0.747	4.65e-7	101

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000215	0.000212
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000803	0.0000791
Middle Eastern	0.00	0.00
South Asian	0.000199	0.000196
Other	0.000330	0.000326

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. May be part of a complex containing NF2/merlin that participates in cellular signaling to the actin cytoskeleton downstream of tyrosine kinase signaling pathways. {ECO:0000269|PubMed:15467741}.
• Pathway: Developmental Biology;Transcriptional regulation of white adipocyte differentiation (Consensus)

Recessive Scores

• pRec: 0.166

Intolerance Scores

• loftool: 0.377
• rvis_EVS: -0.05
• rvis_percentile_EVS: 49.76

Haploinsufficiency Scores

• pHI: 0.125
• hipred: Y
• hipred_score: 0.719
• ghis: 0.645

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.991

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Med28
• Phenotype: cellular 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); embryo phenotype; hearing/vestibular/ear phenotype

Gene ontology

• Biological process: stem cell population maintenance;negative regulation of smooth muscle cell differentiation
• Cellular component: nucleoplasm;membrane;mediator complex;cortical actin cytoskeleton
• Molecular function: actin binding;protein binding