MED12L
protein-codingmediator complex subunit 12L, the group of Mediator complex
Gene summary
The protein encoded by this gene is part of the Mediator complex, which is involved in transcriptional coactivation of nearly all RNA polymerase II-dependent genes. The Mediator complex links gene-specific transcriptional activators with the basal transcription machinery. [provided by RefSeq, May 2010]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~351.8 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AD
Disease ID:MONDO:0030030
Submitter: Ambry Genetics
Inheritance Pattern: AD
Disease ID:MONDO:0700092
Submitter: PanelApp Australia
Inheritance Pattern: AD
Disease ID:MONDO:0030030
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AD
Disease ID:MONDO:0030030
Submitter: Ambry Genetics
Inheritance Pattern: AD
Disease ID:MONDO:0030030
Submitter: ClinGen
The *MED12L* gene is located on chromosome 3 at 3q25.1 and encodes for the 2145-amino acid mediator complex subunit 12-like (MED12L) protein, one of the subunits in the CDK8 kinase module of the Mediator complex.. The Mediator complex is a large multiprotein complex consisting of four different modules (Head, Middle, Tail and CDK8 kinase) and 26 subunits. The Mediator complex plays a key regulator of gene expression involved in cell growth, homeostasis, development and differentiation. *MED12L* was first reported in relation to autosomal dominant Nizon-Isidor syndrome in 2019 (Nizon et al 2019, PMID: 31155615). Evidence supporting this gene-disease relationship includes case-level and experimental data. Six heterozygous variants (1 missense, 1 nonsense, 2 frameshift, and 2 splice-site variants) in *MED12L* that have been reported in at least 9 unrelated patients with clinical features suggestive of autosomal dominant Nizon-Isidor syndrome in 3 publications (Nizon et al 2019, PMID: 31155615; Park et al 2022, PMID: 36212160; Ferraz et al 2022, PMID: 35920825) are included in this curation. This gene-disease relationship is also supported by biochemical function, gene expression studies, and protein interaction data (Maalouf et al 2024, PMID: 38943827; Daniels et al 2013; Vogl et al 2013, PMID:23575864). In summary, there is definitive evidence supporting the relationship between *MED12L* and autosomal dominant Nizon-Isidor syndrome. This has been repeatedly demonstrated in both the research and clinical diagnostic settings and has been upheld over time. This classification was approved by the ClinGen Syndromic Disorders GCEP on the meeting date November 19th, 2024 (SOP Version 11).
Inheritance Pattern: AD
Disease ID:MONDO:0030030
Submitter: Illumina
Inheritance Pattern: AD
Disease ID:MONDO:0030030
Submitter: Illumina
MED12L was first reported in relation to autosomal dominant Nizon-Isidor syndrome in 2019 (31155615: Nizon et al. 2019). Evidence supporting this gene-disease relationship includes case-level data and experimental data. Variants in this gene have been reported in at least four probands in one publication (31155615: Nizon et al. 2019). The four variants were all predicted loss of function and included a frameshift, a stop gained and two splice variants and at least two occurred de novo. This gene-disease relationship is supported by expression data and protein interaction data; MED12L is a component of the kinase module of the Mediator complex, other subunits of the kinase module have also been implicated in intellectual disability, including MED12, MED13L, MED13 and CDK19 (28778422: Jeronimo et al. 2017). In summary, there is moderate evidence to support this gene-disease relationship. While more evidence is needed to establish this relationship definitively, no convincing contradictory evidence has emerged.
Clinical Genomic Database (CGD)
Manifestation: Craniofacial; Gastrointestinal; Musculoskeletal; Neurologic; Ophthalmologic
Intervention: General
Rationale: Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to MED12L variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001393769.1. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 4 | 43 | 1 | 48 | ||
| missense | 1 | 2 | 457 | 41 | 2 | 503 |
| nonsense | 4 | 13 | 2 | 19 | ||
| start loss | 0 | |||||
| frameshift | 5 | 6 | 3 | 14 | ||
| splice donor/acceptor (+/-2bp) | 1 | 6 | 7 | 14 | ||
| Total | 11 | 27 | 473 | 84 | 3 | 598 |
Highest pathogenic variant AF is 0.000047091016
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001380698.1 | 44 | MANE Select | |
| Ensembl | ENSP00000508695.1 | 44 | MANE Select | |
| RefSeq | NP_443728.3 | 43 | Standard | |
| Ensembl | ENSP00000273432.4 | 37 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Thyroid hormone signaling pathway - Homo sapiens (human)
Biological Process
- regulation of transcription by RNA polymerase II
- positive regulation of nucleic acid-templated transcription
Molecular Function
- transcription coactivator activity
- beta-catenin binding
Cellular Component
- nucleus
- mediator complex
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000474524
- Coding exons
- 43
- Length
- 351377
- Individuals with no LoFs
- 125725
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 23
- Defined
- 125748
- p
- 0.0000915
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 3.13 | 869 | 1.17e+3 | 0.742 | 0.0000645 | 14032 |
| Missense (PolyPhen) | 251 | 449.12 | 0.55888 | 5520 | ||
| Synonymous | -0.464 | 465 | 452 | 1.03 | 0.0000268 | 4124 |
| Loss of Function | 9.13 | 15 | 125 | 0.120 | 0.00000683 | 1383 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00012 | 0.00012 | rare |
| Latino/Admixed American | 0.000029 | 0.000029 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00011 | 0.00011 | rare |
| Finnish | 0.000046 | 0.000046 | rare |
| European (Non-Finnish) | 0.00012 | 0.00012 | rare |
| South Asian | 0.000099 | 0.000098 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: May be a 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 (By similarity). {ECO:0000250}.;
Recessive Scores
- pRec
- 0.102
Intolerance Scores
- LoFtool
- 0.345
- RVIS EVS
- -2.54
- RVIS percentile EVS
- 0.88
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.763
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |