MED23

gene
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Also known as CRSP130DRIP130Sur2

Summary

MED23 (mediator complex subunit 23, HGNC:2372) is a protein-coding gene on chromosome 6q23.2, encoding Mediator of RNA polymerase II transcription subunit 23 (Q9ULK4). Required for transcriptional activation subsequent to the assembly of the pre-initiation complex. It is a selective cancer dependency (DepMap: 20.4% of cell lines).

The activation of gene transcription is a multistep process that is triggered by factors that recognize transcriptional enhancer sites in DNA. These factors work with co-activators to direct transcriptional initiation by the RNA polymerase II apparatus. The protein encoded by this gene is a subunit of the CRSP (cofactor required for SP1 activation) complex, which, along with TFIID, is required for efficient activation by SP1. This protein is also a component of other multisubunit complexes e.g. thyroid hormone receptor-(TR-) associated proteins which interact with TR and facilitate TR function on DNA templates in conjunction with initiation factors and cofactors. This protein also acts as a metastasis suppressor. Several alternatively spliced transcript variants encoding different isoforms have been described for this gene.

Source: NCBI Gene 9439 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): intellectual disability, autosomal recessive 18 (Strong, GenCC) — +2 more curated relationships
  • GWAS associations: 2
  • Clinical variants (ClinVar): 347 total — 16 pathogenic, 15 likely-pathogenic
  • Phenotypes (HPO): 26
  • Druggable target: yes — 1 molecules with ChEMBL bioactivity
  • Cancer driver (intOGen): loss-of-function (tumor-suppressor-like) across 1 cancer types
  • Cancer dependency (DepMap): dependent in 20.4% of screened cell lines
  • MANE Select transcript: NM_004830

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:2372
Approved symbolMED23
Namemediator complex subunit 23
Location6q23.2
Locus typegene with protein product
StatusApproved
AliasesCRSP130, DRIP130, Sur2
Ensembl geneENSG00000112282
Ensembl biotypeprotein_coding
OMIM605042
Entrez9439

Gene structure

Transcript identifiers

Ensembl transcripts: 10 — 7 protein_coding, 3 protein_coding_CDS_not_defined

ENST00000354577, ENST00000368053, ENST00000368058, ENST00000368060, ENST00000368068, ENST00000479213, ENST00000484885, ENST00000489888, ENST00000539158, ENST00000883258

RefSeq mRNA: 12 — MANE Select: NM_004830 NM_001270521, NM_001270522, NM_001376517, NM_001376518, NM_001376519, NM_001376520, NM_001376521, NM_001376522, NM_001376523, NM_001376524, NM_004830, NM_015979

CCDS: CCDS5146, CCDS5147, CCDS59039

Canonical transcript exons

ENST00000368068 — 29 exons

ExonStartEnd
ENSE00000763903131598556131598761
ENSE00000763904131598287131598467
ENSE00000763906131596518131596688
ENSE00000763923131593006131593171
ENSE00001239178131595947131596163
ENSE00001239211131592388131592460
ENSE00001360585131586732131587846
ENSE00002433787131623351131623462
ENSE00002435309131615907131616002
ENSE00002440561131624865131624989
ENSE00002443375131604178131604320
ENSE00002445073131619827131619896
ENSE00002450530131621881131621979
ENSE00002454886131602218131602381
ENSE00002462934131618407131618519
ENSE00002484276131605240131605485
ENSE00002486990131600038131600162
ENSE00002496051131606479131606624
ENSE00002519291131627396131627483
ENSE00002521411131620628131620729
ENSE00002524881131607928131608071
ENSE00002536568131610046131610246
ENSE00003553030131589465131589596
ENSE00003584394131627641131627672
ENSE00003588291131591313131591527
ENSE00003601507131594099131594335
ENSE00003605356131590322131590442
ENSE00003655610131603030131603204
ENSE00003843964131628011131628242

Expression profiles

Bgee: expression breadth ubiquitous, 283 present calls, max score 91.73.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 16.9427 / max 188.4298, expressed in 1809 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
7555814.66551799
755572.27721171

Top tissues by expression

288 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
right hemisphere of cerebellumUBERON:001489091.73gold quality
calcaneal tendonUBERON:000370191.48gold quality
cerebellar hemisphereUBERON:000224591.44gold quality
cerebellar cortexUBERON:000212991.38gold quality
adrenal tissueUBERON:001830391.33gold quality
choroid plexus epitheliumUBERON:000391190.81gold quality
cerebellumUBERON:000203790.67gold quality
endometriumUBERON:000129590.46gold quality
body of pancreasUBERON:000115090.09gold quality
mucosa of paranasal sinusUBERON:000503089.98gold quality
mucosa of sigmoid colonUBERON:000499389.91gold quality
secondary oocyteCL:000065589.60gold quality
pylorusUBERON:000116689.48gold quality
colonic epitheliumUBERON:000039789.31gold quality
bone marrow cellCL:000209289.22gold quality
rectumUBERON:000105289.14gold quality
germinal epithelium of ovaryUBERON:000130489.10gold quality
jejunal mucosaUBERON:000039989.09gold quality
urethraUBERON:000005789.04gold quality
right uterine tubeUBERON:000130289.00gold quality
colonic mucosaUBERON:000031788.93gold quality
palpebral conjunctivaUBERON:000181288.71gold quality
ovaryUBERON:000099288.67gold quality
left ovaryUBERON:000211988.64gold quality
body of uterusUBERON:000985388.59gold quality
thyroid glandUBERON:000204688.56gold quality
right lobe of thyroid glandUBERON:000111988.54gold quality
left lobe of thyroid glandUBERON:000112088.53gold quality
mucosa of stomachUBERON:000119988.51gold quality
uterusUBERON:000099588.44gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

ExperimentMarker?Max mean expression
E-ANND-3no4.52

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

2 targets.

TargetRegulation
KISS1Activation
TXNIPUnknown

Upstream regulators (CollecTRI, top): ELF3, STAT1

miRNA regulators (miRDB)

34 targeting MED23, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-574-5P100.0066.01989
HSA-MIR-551B-5P99.9671.283493
HSA-MIR-806399.9169.763146
HSA-MIR-129099.5969.902079
HSA-MIR-516A-3P99.4667.961378
HSA-MIR-516B-3P99.4667.961378
HSA-MIR-7162-5P99.4668.081368
HSA-MIR-127699.3668.181642
HSA-MIR-520F-5P99.3470.401632
HSA-MIR-431199.3170.473041
HSA-MIR-361-3P99.1966.451381
HSA-MIR-628-3P99.0468.37814
HSA-MIR-6737-3P98.9568.561577
HSA-MIR-7157-3P98.9568.701582
HSA-MIR-219A-1-3P98.9167.87639
HSA-MIR-6889-3P98.8467.351198
HSA-MIR-5008-3P98.7367.501433
HSA-MIR-60698.7267.34960
HSA-MIR-58398.7167.441791
HSA-MIR-6529-3P98.6866.761020
HSA-MIR-124698.5466.21959
HSA-MIR-3187-5P98.3665.741776
HSA-MIR-541-5P98.2467.771181
HSA-MIR-6881-3P98.0468.241777
HSA-MIR-3664-3P97.8567.621452
HSA-MIR-1285-3P97.7267.021932
HSA-MIR-5189-5P97.7266.961814
HSA-MIR-61897.6267.46861
HSA-MIR-61297.2665.951597
HSA-MIR-686097.2166.311656

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 20.4% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 17)

  • Sur2(CRSP3) is required for activation by Adenovirus E1A CR3 activation domain and is required for MAPK-mediated activation of Elk-1. (PMID:11934987)
  • DRIP130 regulates HER2 expression by binding to ESX (PMID:12242338)
  • loss of DRIP-130 expression, as a result of the gross loss of human chromosome 6q16.3-q23, provokes increased tumor metastasis (PMID:16964286)
  • missense mutation (p. R617Q) in MED23 that cosegregates with nonsyndromic autosomal recessive intellectual disability; mutation impaired response of JUN and FOS to mitogens by altering interaction between enhancer-bound transcription factors and Mediator (PMID:21868677)
  • Data show that Med23 RNAi specifically inhibits the proliferation and tumorigenicity of lung cancer cells with hyperactive Ras activity. (PMID:22988093)
  • Mediator MED23 regulates basal transcription in vivo via an interaction with P-TEFb. (PMID:23340209)
  • Upregulation of mediator MED23 in non-small-cell lung cancer promotes the growth, migration, and metastasis of cancer cells. (PMID:25273169)
  • MED23 plays an important role in hepatocarcinogenesis, and it may be a novel target for HCC therapy. (PMID:25684393)
  • MED23-associated intellectual disability has been found in two brothers from a non-consanguineous family. (PMID:25845469)
  • intra-tumor heterogeneity data suggest that there could be an under- or over-estimation of the occurrence of MED23 frameshift mutations in microsatellite instability-high colorectal cancers (PMID:26152846)
  • This is the first patient with documented refractory epilepsy caused by a novel homozygous pathogenic variant in MED23 expanding the phenotypic spectrum. Identification of the underlying genetic defect in MED23 sheds light on the possible mechanism of complete response to the ketogenic diet in this child. (PMID:27311965)
  • a 7-gene signature was identified which correctly predicted the primary prefibrotic myelofibrosis group with a sensitivity of 100% and a specificity of 89%. The 7 genes included MPO, CEACAM8, CRISP3, MS4A3, CEACAM6, HEMGN, and MMP8 (PMID:27579896)
  • Higher l-arginine was associated with higher risk of Ischemic heart disease (odds ratio and of myocardial infarction, based on 2 SNPs from MED23. (PMID:27914500)
  • MED23 adopts an arch-shaped conformation, with an N-terminal domain (Nter) protruding from a large core region. (PMID:30140054)
  • LINC00921 reduces lung cancer radiosensitivity by destabilizing NUDT21 and driving aberrant MED23 alternative polyadenylation. (PMID:37999979)
  • MED23 pathogenic variant: genomic-phenotypic analysis. (PMID:39144687)
  • MED23 depletion induces premature senescence in NSCLC cells by interacting with BCLAF1 and then suppressing NUPR1 expression. (PMID:39366174)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriomed23ENSDARG00000029157
mus_musculusMed23ENSMUSG00000019984
rattus_norvegicusMed23ENSRNOG00000013422
drosophila_melanogasterMED23FBGN0034795
caenorhabditis_eleganssur-2WBGENE00006349

Protein

Protein identifiers

Mediator of RNA polymerase II transcription subunit 23Q9ULK4 (reviewed: Q9ULK4)

Alternative names: Activator-recruited cofactor 130 kDa component, Cofactor required for Sp1 transcriptional activation subunit 3, Mediator complex subunit 23, Protein sur-2 homolog, Transcriptional coactivator CRSP130, Vitamin D3 receptor-interacting protein complex 130 kDa component

All UniProt accessions (2): Q9ULK4, Q5JWT2

UniProt curated annotations — full annotation on UniProt →

Function. Required for transcriptional activation subsequent to the assembly of the pre-initiation complex. 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 pre-initiation complex with RNA polymerase II and the general transcription factors. Required for transcriptional activation by adenovirus E1A protein. Required for ELK1-dependent transcriptional activation in response to activated Ras signaling.

Subunit / interactions. Interacts with ELK1. Component of the Mediator complex, which is composed of MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The MED12, MED13, CCNC and CDK8 subunits form a distinct module termed the CDK8 module. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. Interacts with CEBPB (when not methylated), CTNNB1, and GLI3. Interacts with the adenovirus E1A protein.

Subcellular location. Nucleus.

Disease relevance. Intellectual developmental disorder, autosomal recessive 18, with or without epilepsy (MRT18) [MIM:614249] A disorder characterized by significantly below average general intellectual functioning associated with impairments in adaptive behavior and manifested during the developmental period. The disease is caused by variants affecting the gene represented in this entry.

Similarity. Belongs to the Mediator complex subunit 23 family.

Isoforms (6)

UniProt IDNamesCanonical?
Q9ULK4-11yes
Q9ULK4-22
Q9ULK4-33
Q9ULK4-44
Q9ULK4-55
Q9ULK4-66

RefSeq proteins (12): NP_001257450, NP_001257451, NP_001363446, NP_001363447, NP_001363448, NP_001363449, NP_001363450, NP_001363451, NP_001363452, NP_001363453, NP_004821, NP_057063 (=MANE)

Domains & families (InterPro)

IDNameType
IPR021629Mediator_Med23Family

Pfam: PF11573

UniProt features (137 total): helix 87, strand 18, turn 13, sequence conflict 8, splice variant 7, chain 1, region of interest 1, sequence variant 1, compositionally biased region 1

Structure

Experimental structures (PDB)

13 structures.

PDBMethodResolution (Å)
6H02X-RAY DIFFRACTION2.8
9F6YELECTRON MICROSCOPY2.98
9F76ELECTRON MICROSCOPY3.1
7EMFELECTRON MICROSCOPY3.5
8TRHELECTRON MICROSCOPY3.7
7ENAELECTRON MICROSCOPY4.07
7ENCELECTRON MICROSCOPY4.13
8GXSELECTRON MICROSCOPY4.16
7ENJELECTRON MICROSCOPY4.4
8T9DELECTRON MICROSCOPY4.66
7LBMELECTRON MICROSCOPY4.8
8GXQELECTRON MICROSCOPY5.04
8TQWELECTRON MICROSCOPY8.2

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9ULK4-F187.300.57

Antibody-complex structures (SAbDab): 16H02

Function

Pathways and Gene Ontology

Reactome pathways

20 pathways

IDPathway
R-HSA-1989781PPARA activates gene expression
R-HSA-212436Generic Transcription Pathway
R-HSA-381340Transcriptional regulation of white adipocyte differentiation
R-HSA-9833110RSV-host interactions
R-HSA-9841922MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis
R-HSA-1266738Developmental Biology
R-HSA-1430728Metabolism
R-HSA-1643685Disease
R-HSA-212165Epigenetic regulation of gene expression
R-HSA-400206Regulation of lipid metabolism by PPARalpha
R-HSA-556833Metabolism of lipids
R-HSA-5663205Infectious disease
R-HSA-73857RNA Polymerase II Transcription
R-HSA-74160Gene expression (Transcription)
R-HSA-9818564Epigenetic regulation of gene expression by MLL3 and MLL4 complexes
R-HSA-9820952Respiratory Syncytial Virus Infection Pathway
R-HSA-9824446Viral Infection Pathways
R-HSA-9843745Adipogenesis
R-HSA-9851695Epigenetic regulation of adipogenesis genes by MLL3 and MLL4 complexes
R-HSA-9917777Epigenetic regulation by WDR5-containing histone modifying complexes

MSigDB gene sets: 271 (showing top): REACTOME_TRANSCRIPTIONAL_REGULATION_OF_WHITE_ADIPOCYTE_DIFFERENTIATION, GOBP_POSITIVE_REGULATION_OF_DNA_TEMPLATED_TRANSCRIPTION_INITIATION, GOBP_POSITIVE_REGULATION_OF_LYMPHOCYTE_MIGRATION, GOBP_POSITIVE_REGULATION_OF_CELLULAR_EXTRAVASATION, GOBP_REGULATION_OF_LEUKOCYTE_MIGRATION, GOBP_REGULATION_OF_MONONUCLEAR_CELL_MIGRATION, GOBP_CELLULAR_EXTRAVASATION, GOBP_LEUKOCYTE_MIGRATION, GOBP_POSITIVE_REGULATION_OF_LEUKOCYTE_MIGRATION, GOBP_REGULATION_OF_DNA_TEMPLATED_TRANSCRIPTION_INITIATION, GOBP_REGULATION_OF_CELLULAR_EXTRAVASATION, GOBP_DNA_TEMPLATED_TRANSCRIPTION_INITIATION, GOBP_TRANSCRIPTION_INITIATION_AT_RNA_POLYMERASE_II_PROMOTER, GOBP_T_CELL_MIGRATION, GOBP_PROTEIN_DNA_COMPLEX_ORGANIZATION

GO Biological Process (8): regulation of DNA-templated transcription (GO:0006355), regulation of transcription by RNA polymerase II (GO:0006357), transcription initiation at RNA polymerase II promoter (GO:0006367), positive regulation of gene expression (GO:0010628), positive regulation of transcription elongation by RNA polymerase II (GO:0032968), RNA polymerase II preinitiation complex assembly (GO:0051123), positive regulation of transcription initiation by RNA polymerase II (GO:0060261), positive regulation of T cell extravasation (GO:2000409)

GO Molecular Function (2): transcription coactivator activity (GO:0003713), protein binding (GO:0005515)

GO Cellular Component (5): nucleus (GO:0005634), nucleoplasm (GO:0005654), transcription regulator complex (GO:0005667), mediator complex (GO:0016592), core mediator complex (GO:0070847)

Reactome top-level categories

Rollup of top-15 pathways:

CategoryPathways
Gene expression (Transcription)2
Regulation of lipid metabolism by PPARalpha1
RNA Polymerase II Transcription1
Adipogenesis1
Respiratory Syncytial Virus Infection Pathway1
Epigenetic regulation of adipogenesis genes by MLL3 and MLL4 complexes1
Metabolism of lipids1
Metabolism1
Disease1
Epigenetic regulation by WDR5-containing histone modifying complexes1
Viral Infection Pathways1
Infectious disease1
Developmental Biology1
Epigenetic regulation of gene expression by MLL3 and MLL4 complexes1
Epigenetic regulation of gene expression1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
regulation of gene expression2
transcription by RNA polymerase II2
positive regulation of transcription by RNA polymerase II2
transcription initiation at RNA polymerase II promoter2
DNA-templated transcription1
regulation of RNA biosynthetic process1
regulation of DNA-templated transcription1
DNA-templated transcription initiation1
gene expression1
positive regulation of macromolecule biosynthetic process1
transcription elongation by RNA polymerase II1
positive regulation of DNA-templated transcription, elongation1
regulation of transcription elongation by RNA polymerase II1
transcription preinitiation complex assembly1
regulation of transcription initiation by RNA polymerase II1
positive regulation of DNA-templated transcription initiation1
positive regulation of cellular extravasation1
T cell extravasation1
positive regulation of T cell migration1
regulation of T cell extravasation1
transcription coregulator activity1
positive regulation of DNA-templated transcription1
binding1
intracellular membrane-bounded organelle1
nuclear lumen1
cellular anatomical structure1
protein-containing complex1
core mediator complex1
nuclear protein-containing complex1
RNA polymerase II transcription regulator complex1

Protein interactions and networks

STRING

1594 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
MED23MED15Q96RN5969
MED23MED14O60244964
MED23MED16Q9Y2X0961
MED23MED12Q93074945
MED23MED4Q9NPJ6941
MED23MED13Q9UHV7888
MED23ELK1P19419870
MED23MED22Q15528851
MED23MED1Q15648850
MED23MED6O75586832
MED23IRF7Q92985822
MED23MED17Q9NVC6817
MED23MED26O95402808
MED23CDK8P49336805
MED23MED21Q13503787

IntAct

140 interactions, top by confidence:

ABTypeScore
MED10MED19psi-mi:“MI:0914”(association)0.910
MED10MED19psi-mi:“MI:0915”(physical association)0.910
CDK8MED14psi-mi:“MI:0914”(association)0.900
MED4MED19psi-mi:“MI:0914”(association)0.900
MED29MED19psi-mi:“MI:0914”(association)0.890
MED21MED19psi-mi:“MI:0914”(association)0.880
CDK8MED19psi-mi:“MI:2364”(proximity)0.850
CDK8MED19psi-mi:“MI:0914”(association)0.850
MED20MED19psi-mi:“MI:0914”(association)0.840
MED31MED19psi-mi:“MI:0914”(association)0.840
MED7MED19psi-mi:“MI:0914”(association)0.840
MED11MED19psi-mi:“MI:0914”(association)0.840
MED18MED19psi-mi:“MI:0914”(association)0.840

BioGRID (421): MED23 (Reconstituted Complex), MED23 (Phenotypic Suppression), MED23 (Affinity Capture-MS), MED23 (Affinity Capture-MS), MED23 (Affinity Capture-MS), MED23 (Affinity Capture-MS), MED23 (Affinity Capture-MS), MED23 (Affinity Capture-MS), MED23 (Affinity Capture-MS), MED23 (Affinity Capture-MS), MED23 (Affinity Capture-MS), MED23 (Affinity Capture-Western), MED10 (Co-fractionation), MED14 (Co-fractionation), MED22 (Co-fractionation)

ESM2 similar proteins: A1Z8X3, A1ZAK1, G5ED39, H2QII6, O01510, O08662, O94668, P42173, P42286, P49792, Q00416, Q03280, Q0IEK6, Q10573, Q10669, Q13535, Q18508, Q18892, Q196Z9, Q29L39, Q2U639, Q5EAK6, Q5EB59, Q5RIW8, Q5ZKU4, Q61CW2, Q61WP7, Q6CP76, Q6CT34, Q6V3W0, Q70PP2, Q751J3, Q756G2, Q75DV4, Q80YQ2, Q8IRS9, Q8IRT0, Q9DE14, Q9GNN7, Q9H0H0

Diamond homologs: Q16HH9, Q5EB59, Q5RIW8, Q6P423, Q80YQ2, Q9ULK4, Q9W1X7

SIGNOR signaling

1 interactions.

AEffectBMechanism
MED23“form complex”“Core mediator complex”binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 92 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

PathwayPartnersFoldFDR
Respiratory Syncytial Virus Infection Pathway2774.9×1e-43
RSV-host interactions2759.5×9e-41
Adipogenesis2759.5×9e-41
Regulation of lipid metabolism by PPARalpha2753.6×2e-39
Transcriptional regulation of white adipocyte differentiation2749.4×2e-38
Epigenetic regulation of adipogenesis genes by MLL3 and MLL4 complexes1545.5×4e-20
Epigenetic regulation of gene expression by MLL3 and MLL4 complexes1541.6×2e-19
PPARA activates gene expression2735.9×3e-34

GO biological processes:

GO termPartnersFoldFDR
positive regulation of transcription initiation by RNA polymerase II2579.9×8e-40
positive regulation of transcription elongation by RNA polymerase II2277.9×7e-35
RNA polymerase II preinitiation complex assembly2476.8×7e-38
somatic stem cell population maintenance1029.2×3e-10
transcription initiation at RNA polymerase II promoter626.4×1e-05
protein ubiquitination125.8×1e-04

Disease & clinical

Cancer significance

From intOGen — cancer-driver classification: loss-of-function (tumor-suppressor-like) across 1 cancer types — BRCA.

Clinical variants and AI predictions

ClinVar

347 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic16
Likely pathogenic15
Uncertain significance187
Likely benign71
Benign5

Top pathogenic / likely-pathogenic (30)

Variant IDHGVSClassification
1032717NM_004830.4(MED23):c.2832dup (p.Val945fs)Pathogenic
1075875NM_000045.4(ARG1):c.819del (p.Asp274fs)Pathogenic
1076486NM_000045.4(ARG1):c.93del (p.Arg32fs)Pathogenic
1327487NM_004830.4(MED23):c.506A>G (p.Tyr169Cys)Pathogenic
1327489NM_004830.4(MED23):c.382G>A (p.Gly128Arg)Pathogenic
1327491NM_004830.4(MED23):c.1919A>G (p.Gln640Arg)Pathogenic
143192NM_004830.4(MED23):c.3638A>G (p.His1213Arg)Pathogenic
2276892NM_004830.4(MED23):c.815dup (p.Tyr272Ter)Pathogenic
2980910NM_000045.4(ARG1):c.493dup (p.Val165fs)Pathogenic
423225NM_004830.4(MED23):c.597+1G>TPathogenic
437437NM_004830.4(MED23):c.670C>G (p.Arg224Gly)Pathogenic
4813535NM_004830.4(MED23):c.3983G>C (p.Arg1328Pro)Pathogenic
557931NM_000045.4(ARG1):c.129del (p.Glu44fs)Pathogenic
657467NM_000045.4(ARG1):c.425del (p.Gly142fs)Pathogenic
852613NM_000045.4(ARG1):c.464dup (p.Ile156fs)Pathogenic
871322NM_000045.4(ARG1):c.666-2A>GPathogenic
1012785NM_004830.4(MED23):c.1387A>T (p.Arg463Ter)Likely pathogenic
1029420NM_004830.4(MED23):c.1181C>T (p.Pro394Leu)Likely pathogenic
1215415NM_004830.4(MED23):c.2750G>A (p.Trp917Ter)Likely pathogenic
1327674NM_004830.4(MED23):c.3508_3511del (p.Val1171fs)Likely pathogenic
1726533NM_000045.4(ARG1):c.637G>T (p.Glu213Ter)Likely pathogenic
1726742NM_000045.4(ARG1):c.432_448del (p.Val145fs)Likely pathogenic
191215NM_004830.4(MED23):c.479T>C (p.Leu160Pro)Likely pathogenic
235773NM_004830.4(MED23):c.1932-1G>ALikely pathogenic
30442NM_004830.4(MED23):c.1832G>A (p.Arg611Gln)Likely pathogenic
3382460NM_004830.4(MED23):c.3145del (p.Tyr1048_Leu1049insTer)Likely pathogenic
432703NM_004830.4(MED23):c.599T>G (p.Leu200Ter)Likely pathogenic
4685525NM_000045.4(ARG1):c.545T>G (p.Val182Gly)Likely pathogenic
559910NM_004830.4(MED23):c.2368_2371del (p.Leu790fs)Likely pathogenic
978881NM_004830.4(MED23):c.953del (p.Glu318fs)Likely pathogenic

SpliceAI

6028 predictions. Top by Δscore:

VariantEffectΔscore
6:131579252:G:GTdonor_gain1.0000
6:131581217:A:Gacceptor_gain1.0000
6:131581218:G:GGacceptor_gain1.0000
6:131581375:A:Tdonor_gain1.0000
6:131582716:G:GGdonor_gain1.0000
6:131583353:A:Gacceptor_gain1.0000
6:131583740:A:AGacceptor_gain1.0000
6:131583741:G:GGacceptor_gain1.0000
6:131587843:CTAC:Cacceptor_gain1.0000
6:131589461:TTA:Tdonor_loss1.0000
6:131589462:TA:Tdonor_loss1.0000
6:131589463:A:ACdonor_gain1.0000
6:131589463:AC:Adonor_loss1.0000
6:131589464:C:CTdonor_gain1.0000
6:131589464:CT:Cdonor_gain1.0000
6:131589464:CTT:Cdonor_gain1.0000
6:131589464:CTTG:Cdonor_gain1.0000
6:131589592:CCAAT:Cacceptor_gain1.0000
6:131589593:CAAT:Cacceptor_gain1.0000
6:131589593:CAATC:Cacceptor_gain1.0000
6:131589594:AATCT:Aacceptor_loss1.0000
6:131589597:C:CCacceptor_gain1.0000
6:131592386:A:ACdonor_gain1.0000
6:131592387:C:CCdonor_gain1.0000
6:131592461:C:CCacceptor_gain1.0000
6:131592468:C:CTacceptor_gain1.0000
6:131592469:G:Tacceptor_gain1.0000
6:131594158:T:Adonor_gain1.0000
6:131594198:TTAGA:Tdonor_gain1.0000
6:131594199:TAGAC:Tdonor_gain1.0000

AlphaMissense

9063 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
6:131587793:G:CF1331L1.000
6:131587793:G:TF1331L1.000
6:131587795:A:GF1331L1.000
6:131587800:A:GL1329P1.000
6:131589484:C:TG1307D1.000
6:131589496:T:CY1303C1.000
6:131589497:A:GY1303H1.000
6:131589498:C:AK1302N1.000
6:131589498:C:GK1302N1.000
6:131589500:T:CK1302E1.000
6:131589517:T:AD1296V1.000
6:131590377:A:GL1251P1.000
6:131591353:A:GW1216R1.000
6:131591353:A:TW1216R1.000
6:131592392:A:GL1156P1.000
6:131593113:A:CF1097L1.000
6:131593113:A:TF1097L1.000
6:131593115:A:GF1097L1.000
6:131593122:G:CF1094L1.000
6:131593122:G:TF1094L1.000
6:131593124:A:GF1094L1.000
6:131593125:T:AR1093S1.000
6:131593125:T:GR1093S1.000
6:131593126:C:GR1093T1.000
6:131593130:A:GW1092R1.000
6:131593130:A:TW1092R1.000
6:131594254:A:GL1026P1.000
6:131594305:A:GL1009P1.000
6:131594317:A:GL1005P1.000
6:131595951:A:CF997L1.000

dbSNP variants (sampled 300 via entrez): RS1000094228 (6:131593135 CA>C), RS1000157171 (6:131574975 A>G), RS1000166403 (6:131610000 G>A), RS1000195393 (6:131598065 G>A), RS1000231540 (6:131621697 A>G), RS1000331080 (6:131614131 G>T), RS1000421608 (6:131591258 A>G,T), RS1000451954 (6:131584017 G>T), RS1000488475 (6:131607185 G>A,C), RS1000525126 (6:131589401 T>C), RS1000526551 (6:131593280 C>T), RS1000561522 (6:131587416 C>T), RS1000582041 (6:131621360 C>G), RS1000585240 (6:131591043 C>T), RS1000747067 (6:131628291 C>G,T)

Disease associations

OMIM: gene MIM:605042 | disease phenotypes: MIM:207800, MIM:614249, MIM:617667

GenCC curated gene-disease

DiseaseClassificationInheritance
intellectual disability, autosomal recessive 18StrongAutosomal recessive
syndromic intellectual disabilityModerateAutosomal recessive
autosomal recessive non-syndromic intellectual disabilitySupportiveAutosomal recessive

ClinGen Gene-Disease Validity (1)

Expert-panel classifications — Definitive > Strong > Moderate > Limited > Disputed > Refuted.

DiseaseClassificationInheritance
syndromic intellectual disabilityModerateAR

Mondo (7): arginase deficiency (MONDO:0008814), intellectual disability, autosomal recessive 18 (MONDO:0013651), neurodevelopmental disorder (MONDO:0700092), Fraser syndrome 3 (MONDO:0054739), intellectual disability (MONDO:0001071), syndromic intellectual disability (MONDO:0000508), autosomal recessive non-syndromic intellectual disability (MONDO:0019502)

Orphanet (3): Argininemia (Orphanet:90), Autosomal recessive non-syndromic intellectual disability (Orphanet:88616), NON RARE IN EUROPE: Unexplained intellectual disability (Orphanet:319658)

HPO phenotypes

26 total (26 of 26 shown, HPO-id order):

HPOTerm
HP:0000007Autosomal recessive inheritance
HP:0000252Microcephaly
HP:0000737Irritability
HP:0000750Delayed speech and language development
HP:0001249Intellectual disability
HP:0001257Spasticity
HP:0001263Global developmental delay
HP:0001266Choreoathetosis
HP:0001288Gait disturbance
HP:0001332Dystonia
HP:0001344Absent speech
HP:0001629Ventricular septal defect
HP:0001631Atrial septal defect
HP:0002187Profound intellectual disability
HP:0002353EEG abnormality
HP:0002360Sleep disturbance
HP:0002474Expressive language delay
HP:0003577Congenital onset
HP:0003593Infantile onset
HP:0007030Nonprogressive encephalopathy
HP:0008936Axial hypotonia
HP:0011463Childhood onset
HP:0011968Feeding difficulties
HP:0012110Hypoplasia of the pons
HP:0033725Thin corpus callosum
HP:0100021Cerebral palsy

GWAS associations

2 associations (top):

StudyTraitp-value
GCST002623_1L-arginine levels4.000000e-19
GCST006867_54Type 2 diabetes2.000000e-08

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0006524L-arginine measurement

MeSH disease descriptors (3)

DescriptorNameTree numbers
D020162HyperargininemiaC10.228.140.163.100.937.500; C16.320.565.100.940.500; C16.320.565.189.937.500; C18.452.132.100.937.437; C18.452.648.100.940.437; C18.452.648.189.937.437
D008607Intellectual DisabilityC10.597.606.360; C23.888.592.604.646; F01.700.687; F03.625.539
D065886Neurodevelopmental DisordersF03.625

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (2): CHEMBL2111426 (PROTEIN-PROTEIN INTERACTION), CHEMBL4146 (SINGLE PROTEIN)

Molecules with ChEMBL bioactivity

1 molecules (phase ≥1), by development phase (incl. off-target/promiscuous compounds). Patent mentions across the top 20 by phase: 13,102 (via chembl_molecule»patent_compound — counts attach to the compound, not the gene–compound relationship, so off-target/promiscuous molecules can dominate).

MoleculeNamePhasePatents
CHEMBL189963PALBOCICLIB413,102

PharmGKB: 1 entry (VIP=true, CPIC=false)

PharmGKB variants

1 variants.

VariantGenesLevelScore#Clin annotsDrugs
rs2781659ARG1, MED2333.001selective beta-2-adrenoreceptor agonists

Binding affinities (BindingDB)

1 measured of 1 human assays (1 total across all organisms); most potent 1 below. Values come from heterogeneous assays and are not directly comparable.

LigandMeasureValue
CHEMBL2170196KD1800 nM

ChEMBL bioactivities

10 potent at pChembl≥5 of 10 total, top 10 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChemblTypeValueUnitMolecule
6.23Kd590nMCHEMBL1077445
6.21Kd620nMCHEMBL1077474
6.00Kd1000nMCHEMBL1077454
5.75Kd1800nMWRENCHNOLOL
5.52Kd2998nMPALBOCICLIB
5.33Kd4690nMCHEMBL5653589
5.33ED504728nMCHEMBL5653589
5.31Kd4854nMCHEMBL3752910
5.31ED504894nMCHEMBL3752910
5.23Kd5900nMCHEMBL1077475

PubChem BioAssay actives

7 with measured affinity, of 19 total; 7 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

CompoundAssayTypeValueUnit
5-[[(3S,5R)-3-(2-hydroxyethyl)-3-(2-methylpropyl)-2-[[4-(trifluoromethyl)phenyl]methyl]-1,2-oxazolidin-5-yl]methylcarbamothioylamino]-2-(3-hydroxy-6-oxoxanthen-9-yl)benzoic acid469608: Inhibition of ESX-Med23 interaction in human BT474 cells assessed as down regulation of ErbB2 expression by Western blottingkd0.5900uM
5-[[(3S,5R)-3-(2-hydroxyethyl)-3-(2-methylpropyl)-2-[(4-phenylphenyl)methyl]-1,2-oxazolidin-5-yl]methylcarbamothioylamino]-2-(3-hydroxy-6-oxoxanthen-9-yl)benzoic acid469608: Inhibition of ESX-Med23 interaction in human BT474 cells assessed as down regulation of ErbB2 expression by Western blottingkd0.6200uM
5-[[(3S,5R)-3-(2-hydroxyethyl)-3-(2-methylpropyl)-2-(naphthalen-2-ylmethyl)-1,2-oxazolidin-5-yl]methylcarbamothioylamino]-2-(3-hydroxy-6-oxoxanthen-9-yl)benzoic acid469608: Inhibition of ESX-Med23 interaction in human BT474 cells assessed as down regulation of ErbB2 expression by Western blottingkd1.0000uM
4-[1-(adamantane-1-carbonyl)piperidin-4-yl]-N-(5-aminopentyl)-N-[2-hydroxy-3-[1-(4-methylphenyl)sulfonylindol-4-yl]oxypropyl]piperidine-1-carboxamide700859: Binding affinity to Sur2kd1.8000uM
4-methyl-3-[(2-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide2148741: Binding affinity to human MED23 incubated for 45 mins by Kinobead based pull down assaykd4.6896uM
4-methyl-3-[(1-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide2148741: Binding affinity to human MED23 incubated for 45 mins by Kinobead based pull down assaykd4.8541uM
5-[[(3S,5R)-2-benzyl-3-(2-hydroxyethyl)-3-(2-methylpropyl)-1,2-oxazolidin-5-yl]methylcarbamothioylamino]-2-(3-hydroxy-6-oxoxanthen-9-yl)benzoic acid469608: Inhibition of ESX-Med23 interaction in human BT474 cells assessed as down regulation of ErbB2 expression by Western blottingkd5.9000uM

CTD chemical–gene interactions

31 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
Formaldehydedecreases expression, increases expression2
Valproic Acidaffects expression, decreases expression2
aristolochic acid Idecreases expression1
methylmercuric chloridedecreases expression1
triphenyl phosphateaffects expression1
alpha-pineneaffects cotreatment, increases expression, increases abundance1
arseniteaffects binding, decreases reaction1
methacrylaldehydeaffects cotreatment, increases expression, increases abundance1
di-n-butylphosphoric acidaffects expression1
jinfukangdecreases expression1
Resveratrolaffects cotreatment, increases expression1
Sunitinibincreases expression1
Zoledronic Acidaffects cotreatment, increases expression1
Fluvastatinaffects cotreatment, increases expression1
Acroleinaffects cotreatment, increases expression, increases abundance1
Air Pollutantsaffects cotreatment, increases abundance, increases expression1
Cisplatinincreases expression1
Diethylhexyl Phthalatedecreases expression1
Doxorubicindecreases expression1
Estradiolaffects expression1
Ethyl Methanesulfonateincreases expression1
Ivermectindecreases expression1
Methyl Methanesulfonateincreases expression1
Ozoneaffects cotreatment, increases expression, increases abundance1
Plant Extractsincreases expression, affects cotreatment1
Testosteronedecreases expression1
Thiramincreases expression1
Urethaneincreases expression1
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxideincreases expression1
Aflatoxin B1decreases methylation1

ChEMBL screening assays

9 unique, capped per target: 9 binding

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL1099983BindingInhibition of ESX-Med23 interaction in human BT474 cells assessed as down regulation of ErbB2 expression up to 50 uM by Western blottingInhibition of ErbB2(Her2) expression with small molecule transcription factor mimics. — Bioorg Med Chem Lett

Cellosaurus cell lines

1 cell lines: 1 transformed cell line

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_D9K4Ubigene HEK293 MED23 KOTransformed cell lineFemale

Clinical trials (associated diseases)

288 trials via MONDO — disease-level, not drug-specific.

TrialPhaseStatusTitle
NCT04586348PHASE4UNKNOWNPrenatal Iodine Supplementation and Early Childhood Neurodevelopment
NCT04873115PHASE4UNKNOWNDouble-blind, Placebo-controlled, Randomized Clinical Trial Comparing the Efficacy and Safety of Sialanar Plus orAl rehabiLitation Against Placebo Plus Oral Rehabilitation for chIldren and Adolescents With seVere Sialorrhoea and Neurodisabilties,
NCT05657860PHASE4COMPLETEDGuanfacine Extended Release for the Reduction of Aggression and Self-injurious Behavior Associated With Prader-Willi Syndrome
NCT05744479PHASE4RECRUITINGMetformin for Antipsychotic-induced Weight Gain in Adults With Intellectual Disability
NCT06107829PHASE4WITHDRAWNValbenazine Treatment of Tardive Dyskinesia in Adults With Intellectual/Developmental Disabilities
NCT06997198PHASE4NOT_YET_RECRUITINGDeutetrabenazine Treatment for Tardive Dyskinesia in Intellectual/Developmental Disabilities
NCT03921541PHASE3COMPLETEDEfficacy and Safety of Pegzilarginase in Patients With Arginase 1 Deficiency
NCT05676853PHASE3TERMINATEDA Study of Safety of Weekly Subcutaneous Pegzilarginase in Subjects With Arginase 1 Deficiency
NCT02559102PHASE3COMPLETEDDexmedetomidine Sedation Versus General Anaesthesia for Inguinal Hernia Surgery in Infants
NCT02757079PHASE3COMPLETEDStudy of the Efficacy and Safety of NPC-15 for Sleep Disorders of Children With Neurodevelopmental Disorders
NCT06915480PHASE3RECRUITINGReducing Missed Appointments
NCT07377032PHASE3RECRUITINGTAP-GRIN: Interventional Study on Patients With GRIN-related Neurodevelopmental Disorders
NCT02270736PHASE3COMPLETEDClinical Study to Investigate the Efficacy and Safety of NT 201 Compared to Placebo in the Treatment of Chronic Troublesome Drooling Associated With Neurological Disorders and/or Intellectual Disability
NCT03378531PHASE2COMPLETEDA Study of AEB1102 (Pegzilarginase) in Patients With Arginase I Deficiency
NCT02909959PHASE2COMPLETEDSulforaphane for the Treatment of Young Men With Autism Spectrum Disorder
NCT06081348PHASE2RECRUITINGSertraline vs. Placebo in the Treatment of Anxiety in Children and AdoLescents With NeurodevelopMental Disorders
NCT06352372PHASE2COMPLETEDSafety and Efficacy of tPBM for Epileptiform Activity in Autism
NCT02304302PHASE2COMPLETEDDown Syndrome Memantine Follow-up Study
NCT03862950PHASE2COMPLETEDA Trial of Metformin in Individuals With Fragile X Syndrome (Met)
NCT04529226PHASE2UNKNOWNStudy to Compare Clozapine vs Treatment as Usual in People With Intellectual Disability & Treatment-resistant Psychosis
NCT04821856PHASE2COMPLETEDEvaluation of the Effectiveness of Cannabidiol in Treating Severe Behavioural Problems in Children and Adolescents With Intellectual Disability
NCT00503191PHASE1COMPLETEDNeuroModulation Technique Treatment of Autism
NCT04475848PHASE1COMPLETEDA Study to Investigate the Safety, Tolerability, Pharmacokinetics, Pharmacodynamics and Food Effect of RO6953958 in Healthy Participants
NCT06300398PHASE1COMPLETEDIAMA-6 Oral Dose Study in Healthy Adults
NCT05273320PHASE1COMPLETEDClinical Trial of Nabilone for Aggression in Adults With Intellectual and Developmental Disabilities
NCT05301361PHASE1ENROLLING_BY_INVITATIONSensitivity of the NIH Toolbox to Stimulant Treatment in Intellectual Disabilities
NCT06016764PHASE1COMPLETEDUse of MRI and cTBS for Catatonia in Autism
NCT06586827PHASE1COMPLETEDImpact of Competency-Based Training and Technical Assistance Employment Outcomes of Individuals With ID/DD
NCT07531940PHASE1NOT_YET_RECRUITINGEscalating Doses of Memantine in Down Syndrome (MEDS-123)
NCT02488044PHASE1/PHASE2COMPLETEDA Phase 1/2 Study of AEB1102 in Patients With Arginase I Deficiency
NCT01421888Not specifiedTERMINATEDThe NIH UNI Study: Urea Cycle Disorders, Nutrition and Immunity
NCT03655223Not specifiedENROLLING_BY_INVITATIONEarly Check: Expanded Screening in Newborns
NCT04612764Not specifiedACTIVE_NOT_RECRUITINGLiver Disease in Urea Cycle Disorders
NCT04908319Not specifiedRECRUITINGHepatic Histopathology in Urea Cycle Disorders
NCT05412160Not specifiedCOMPLETEDImproving Quality of Life and Daily Life Activities With Bioarginine in Patients With COPD
NCT05687474Not specifiedCOMPLETEDBaby Detect : Genomic Newborn Screening
NCT05910151Not specifiedUNKNOWNSelective Screening of Children for Hereditary Metabolic Diseases by Tandem Mass Spectrometry in Kazakhstan
NCT01783041PHASE2/PHASE3COMPLETEDEffect of Early L-Carnitine Supplementation on Neurodevelopmental Outcomes in Very Preterm Infants
NCT05767385PHASE2/PHASE3RECRUITINGFetal Cerebrovascular Autoregulation in Congenital Heart Disease and Association With Neonatal Neurobehavior
NCT05675098EARLY_PHASE1NOT_YET_RECRUITINGCentral Nervous System Stimulants and Physical Function in Children With Cerebral Palsy