MED12L

protein-coding

mediator 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

NM_001393769.1

Inheritance

AD

ClinVar variants

P:38U:473B:87

Top phenotype

Nizon-Isidor syndrome

gnomAD constraint

pLI —, LoF o/e 0.12

Max pathogenic AF

—

Genomic locus

chr3:151,085,286-151,437,072

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~351.8 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

Nizon-Isidor syndromeMODERATE

Inheritance Pattern: AD

Disease ID:MONDO:0030030

Submitter: Ambry Genetics

neurodevelopmental disorderSTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0700092

Submitter: PanelApp Australia

Nizon-Isidor syndromeSTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0030030

Submitter: Labcorp Genetics (formerly Invitae)

Nizon-Isidor syndromeMODERATE

Inheritance Pattern: AD

Disease ID:MONDO:0030030

Submitter: Ambry Genetics

Nizon-Isidor syndromeDEFINITIVE

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).

Nizon-Isidor syndromeMODERATE

Inheritance Pattern: AD

Disease ID:MONDO:0030030

Submitter: Illumina

Nizon-Isidor syndromeMODERATE

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)

Nizon-Isidor syndromeAD

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

Refs: 31155615Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to MED12L variants in ClinVar

18 Conditions Cataloged
not providedTotal: 346
not specifiedTotal: 284
Inborn genetic diseasesTotal: 239
Nizon-Isidor syndromeTotal: 90
MED12L-related disorderTotal: 52
Platelet-type bleeding disorder 8Total: 9
P2RY12-related disorderTotal: 8
Intellectual disabilityTotal: 4

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.

EffectPLPVUSLBBSum
synonymous
4
clinvar
43
clinvar
1
clinvar
48
missense
1
clinvar
2
clinvar
457
clinvar
41
clinvar
2
clinvar
503
nonsense
4
clinvar
13
clinvar
2
clinvar
19
start loss
0
frameshift
5
clinvar
6
clinvar
3
clinvar
14
splice donor/acceptor (+/-2bp)
1
clinvar
6
clinvar
7
clinvar
14
Total1127473843598

Highest pathogenic variant AF is 0.000047091016

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 41 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_001393769.1RefSeqNP_001380698.144MANE Select
ENST00000687756.1EnsemblENSP00000508695.144MANE Select
NM_053002.6RefSeqNP_443728.343Standard
ENST00000273432.8EnsemblENSP00000273432.437Standard

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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense3.138691.17e+30.7420.000064514032
Missense (PolyPhen)251449.120.558885520
Synonymous-0.4644654521.030.00002684124
Loss of Function9.13151250.1200.000006831383

Population LoF Frequency

PopulationCAFp-valueStatus
African0.000120.00012rare
Latino/Admixed American0.0000290.000029rare
Ashkenazi Jewish00.0absent
East Asian0.000110.00011rare
Finnish0.0000460.000046rare
European (Non-Finnish)0.000120.00012rare
South Asian0.0000990.000098rare
Other00.0absent

dbNSFP Gene Annotations

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
For research and educational, non-commercial use only. Not for clinical or diagnostic use. GeneBe does not provide medical advice. Data use for AI modeling is prohibited: if used, the cost is $0.001 per byte of downloaded uncompressed data.