MED29

mediator complex subunit 29, the group of Mediator complex

Basic information

Region (hg38): 19:39391303-39400641

Previous symbols: [ "IXL" ]

Links

ENSG00000063322 ∙ NCBI:55588 ∙ OMIM:612914 ∙ HGNC:23074 ∙ Uniprot:Q9NX70 ∙ 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 MED29 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MED29 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		1
missense			9	2		11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	10	3	0

Variants in MED29

This is a list of pathogenic ClinVar variants found in the MED29 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-39391369-A-C		not specified	Likely benign (Dec 26, 2023)
19-39391375-G-A		not specified	Likely benign (Mar 07, 2023)
19-39391379-A-T		not specified	Uncertain significance (Dec 20, 2023)
19-39391384-C-T		not specified	Uncertain significance (May 28, 2024)
19-39391385-G-T		not specified	Uncertain significance (Nov 09, 2024)
19-39391409-T-C		not specified	Likely benign (Sep 03, 2024)
19-39391415-C-G		not specified	Uncertain significance (Feb 02, 2024)
19-39391475-C-T		not specified	Uncertain significance (Oct 12, 2024)
19-39391600-T-C		not specified	Uncertain significance (Jun 26, 2024)
19-39391617-G-T			Likely benign (Apr 01, 2022)
19-39392479-G-A		not specified	Uncertain significance (Feb 27, 2024)
19-39393569-C-G		not specified	Uncertain significance (Apr 11, 2023)
19-39393576-A-G		not specified	Uncertain significance (Nov 22, 2022)
19-39393579-G-A		not specified	Uncertain significance (Aug 20, 2023)
19-39397488-G-T		not specified	Uncertain significance (Aug 11, 2024)
19-39397506-C-T		not specified	Uncertain significance (Dec 08, 2023)
19-39397581-C-T		not specified	Uncertain significance (Mar 06, 2023)
19-39397638-G-A		not specified	Uncertain significance (Apr 26, 2024)
19-39397682-C-T		not specified	Uncertain significance (Oct 08, 2024)
19-39397694-C-G		not specified	Uncertain significance (Jul 13, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MED29	protein_coding	protein_coding	ENST00000315588	4	9335

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00102	0.833	125725	0	23	125748	0.0000915

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.325	138	128	1.08	0.00000641	1416
Missense in Polyphen		22	32.005	0.68738		364
Synonymous	-0.520	61	56.0	1.09	0.00000308	450
Loss of Function	1.19	6	10.1	0.595	4.31e-7	108

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000491	0.000482
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000978	0.0000967
Middle Eastern	0.0000544	0.0000544
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. {ECO:0000269|PubMed:15555573}.
• Pathway: Developmental Biology;Transcriptional regulation of white adipocyte differentiation (Consensus)

Recessive Scores

• pRec: 0.108

Intolerance Scores

• loftool: 0.415
• rvis_EVS: -0.36
• rvis_percentile_EVS: 28.63

Haploinsufficiency Scores

• pHI: 0.137
• hipred: Y
• hipred_score: 0.637
• ghis: 0.623

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.725

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Med29

Zebrafish Information Network

• Gene name: med29
• Affected structure: muscle
• Phenotype tag: abnormal
• Phenotype quality: disorganized

Gene ontology

• Cellular component: nucleoplasm;mediator complex
• Molecular function: protein binding