MED31

mediator complex subunit 31, the group of Mediator complex

Basic information

Region (hg38): 17:6643311-6651634

Links

ENSG00000108590

∙ NCBI:51003 ∙ ∙ HGNC:24260 ∙ Uniprot:Q9Y3C7 ∙ 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 MED31 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MED31 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			5 clinvar			5
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	5	0	0

Variants in MED31

This is a list of pathogenic ClinVar variants found in the MED31 region.

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

Position	Phenotype	Significance	ClinVar
17-6644523-G-A	not specified	Uncertain significance (Jan 22, 2024)	3125077
17-6644582-G-A	not specified	Uncertain significance (Nov 17, 2022)	2326247
17-6644642-T-C	not specified	Uncertain significance (Feb 23, 2023)	2460975
17-6650072-G-A	not specified	Uncertain significance (Dec 06, 2021)	2265031
17-6651509-A-T	not specified	Uncertain significance (Aug 14, 2023)	2587947
17-6651510-T-G	not specified	Uncertain significance (Jun 07, 2024)	3294074

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MED31	protein_coding	protein_coding	ENST00000225728	4	8320

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000688	0.764	125649	0	99	125748	0.000394

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.32	40	71.4	0.560	0.00000396	859
Missense in Polyphen		10	26.572	0.37634		304
Synonymous	-0.738	30	25.3	1.19	0.00000125	221
Loss of Function	0.993	6	9.26	0.648	5.43e-7	103

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000525	0.000521
Ashkenazi Jewish	0.00112	0.000993
East Asian	0.000569	0.000544
Finnish	0.000236	0.000231
European (Non-Finnish)	0.000396	0.000378
Middle Eastern	0.000569	0.000544
South Asian	0.000529	0.000457
Other	0.000669	0.000652

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;Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription;Transcriptional regulation of white adipocyte differentiation (Consensus)

Recessive Scores

pRec: 0.118

Intolerance Scores

loftool: 0.606
rvis_EVS: 0.01
rvis_percentile_EVS: 54.63

Haploinsufficiency Scores

pHI: 0.145
hipred: Y
hipred_score: 0.737
ghis: 0.618

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: S
essential_gene_gene_trap: E
gene_indispensability_pred: E
gene_indispensability_score: 0.801

Mouse Genome Informatics

Gene name: Med31
Phenotype: skeleton phenotype; 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); limbs/digits/tail 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; cellular phenotype; homeostasis/metabolism phenotype; craniofacial phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype;

Gene ontology

Biological process: regulation of transcription by RNA polymerase II;transcription initiation from RNA polymerase II promoter;protein ubiquitination;negative regulation of fibroblast proliferation;limb development;positive regulation of nucleic acid-templated transcription
Cellular component: ubiquitin ligase complex;nucleoplasm;mediator complex;core mediator complex
Molecular function: transcription coactivator activity;protein binding;ubiquitin protein ligase activity