GON4L

Summary

GON4L (gon-4 like, HGNC:25973) is a protein-coding gene on chromosome 1q22, encoding GON-4-like protein (Q3T8J9). Acts as a key transcription regulator of histones. It is a selective cancer dependency (DepMap: 11.3% of cell lines).

Predicted to enable transcription corepressor activity. Predicted to be involved in negative regulation of DNA-templated transcription. Predicted to act upstream of or within B cell differentiation. Located in nuclear body.

Source: NCBI Gene 54856 — RefSeq curated summary.

At a glance

• Gene–disease (curated): complex neurodevelopmental disorder (Strong, GenCC) — +1 more curated relationship
• GWAS associations: 22
• Clinical variants (ClinVar): 88 total — 2 pathogenic
• Phenotypes (HPO): 63
• Cancer dependency (DepMap): dependent in 11.3% of screened cell lines
• MANE Select transcript: NM_001282860

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:25973
Approved symbol	GON4L
Name	gon-4 like
Location	1q22
Locus type	gene with protein product
Status	Approved
Aliases	FLJ20203, GON-4, YARP
Ensembl gene	ENSG00000116580
Ensembl biotype	protein_coding
OMIM	610393
Entrez	54856

Gene structure

Transcript identifiers

Ensembl transcripts: 22 — 10 protein_coding, 8 protein_coding_CDS_not_defined, 4 retained_intron

ENST00000271883, ENST00000361040, ENST00000368331, ENST00000437809, ENST00000460075, ENST00000466224, ENST00000467009, ENST00000468867, ENST00000471341, ENST00000473267, ENST00000482386, ENST00000483032, ENST00000488251, ENST00000490801, ENST00000496021, ENST00000497369, ENST00000615926, ENST00000622608, ENST00000852419, ENST00000938294, ENST00000938295, ENST00000963987

RefSeq mRNA: 5 — MANE Select: NM_001282860 NM_001282856, NM_001282858, NM_001282860, NM_001282861, NM_032292

CCDS: CCDS1121, CCDS44242, CCDS60296

Canonical transcript exons

ENST00000368331 — 32 exons

Exon	Start	End
ENSE00000960945	155754375	155754488
ENSE00000960946	155753204	155753414
ENSE00001446898	155751960	155752590
ENSE00001446899	155765000	155766709
ENSE00002350299	155763312	155763564
ENSE00002354909	155751767	155751869
ENSE00002396447	155757891	155758034
ENSE00002404392	155760444	155760641
ENSE00002421847	155762190	155762374
ENSE00003465744	155826837	155827028
ENSE00003467263	155813634	155813804
ENSE00003484790	155771067	155771217
ENSE00003504740	155853276	155853806
ENSE00003517228	155773066	155773210
ENSE00003534348	155816212	155816262
ENSE00003551603	155757180	155757323
ENSE00003563503	155815805	155815900
ENSE00003591953	155776395	155776481
ENSE00003605289	155820606	155820656
ENSE00003614267	155821474	155821548
ENSE00003623668	155785334	155785374
ENSE00003628847	155814330	155814449
ENSE00003649754	155783986	155784089
ENSE00003658150	155756958	155757077
ENSE00003661503	155775002	155775173
ENSE00003661691	155777622	155777820
ENSE00003665999	155804949	155805141
ENSE00003669431	155822286	155822476
ENSE00003670106	155767425	155767541
ENSE00003679342	155795050	155795151
ENSE00003910276	155857147	155857214
ENSE00003914169	155749659	155750733

Expression profiles

Bgee: expression breadth ubiquitous, 255 present calls, max score 95.26.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 16.1852 / max 473.6693, expressed in 1783 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
14987	15.9607	1783
14988	0.2245	102

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
sural nerve	UBERON:0015488	95.26	gold quality
granulocyte	CL:0000094	93.46	gold quality
colonic epithelium	UBERON:0000397	93.26	gold quality
buccal mucosa cell	CL:0002336	93.25	silver quality
tibial nerve	UBERON:0001323	92.95	gold quality
calcaneal tendon	UBERON:0003701	92.59	gold quality
right uterine tube	UBERON:0001302	92.15	gold quality
apex of heart	UBERON:0002098	91.76	gold quality
metanephros cortex	UBERON:0010533	91.73	gold quality
adenohypophysis	UBERON:0002196	91.59	gold quality
mucosa of stomach	UBERON:0001199	91.55	gold quality
right lobe of thyroid gland	UBERON:0001119	91.53	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	91.25	gold quality
skin of leg	UBERON:0001511	91.24	gold quality
right ovary	UBERON:0002118	91.18	gold quality
left lobe of thyroid gland	UBERON:0001120	91.16	gold quality
body of uterus	UBERON:0009853	91.07	gold quality
small intestine Peyer’s patch	UBERON:0003454	91.02	gold quality
body of pancreas	UBERON:0001150	91.01	gold quality
skin of abdomen	UBERON:0001416	91.00	gold quality
spleen	UBERON:0002106	90.84	gold quality
endocervix	UBERON:0000458	90.81	gold quality
right hemisphere of cerebellum	UBERON:0014890	90.61	gold quality
upper lobe of left lung	UBERON:0008952	90.52	gold quality
left ovary	UBERON:0002119	90.50	gold quality
left uterine tube	UBERON:0001303	90.37	gold quality
cerebellar hemisphere	UBERON:0002245	90.35	gold quality
ectocervix	UBERON:0012249	90.34	gold quality
cerebellar cortex	UBERON:0002129	90.33	gold quality
pituitary gland	UBERON:0000007	90.28	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	5.36

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

11 targeting GON4L, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-511-3P	99.99	68.85	1467
HSA-MIR-6778-3P	99.96	67.29	2693
HSA-MIR-3910	99.95	71.13	2227
HSA-MIR-374A-5P	99.90	71.34	2923
HSA-MIR-374B-5P	99.90	69.98	2734
HSA-MIR-7856-5P	99.75	69.99	2901
HSA-MIR-4306	99.72	70.50	3630
HSA-MIR-889-3P	99.40	69.76	2103
HSA-MIR-4477B	99.23	70.49	1733
HSA-MIR-125A-3P	97.04	66.92	902

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 11.3% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 5)

• study describes the cloning of a novel homolog of YY1AP, referred to as YARP; it is proposed that YARP is multifunctional and plays not only a role analogous to YY1AP, but also its own specific roles in DNA-utilizing processes such as transcription (PMID:17297563)
• Sin3a, HDAC1, and YY1 are co-factors for Gon4l and that Gon4l may function as a platform for the assembly of complexes that regulate gene expression. (PMID:21454521)
• The conserved C-terminal domain shared by FLASH, YARP, and Mute recognizes the C-terminal sequence of NPAT orthologues, thus acting as a signal targeting proteins to histone locus bodies. (PMID:25339177)
• our results define GON4L as a novel driver of cancer growth (PMID:27312530)
• Structural Analysis of the SANT/Myb Domain of FLASH and YARP Proteins and Their Complex with the C-Terminal Fragment of NPAT by NMR Spectroscopy and Computer Simulations. (PMID:32722282)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Gon4l	ENSMUSG00000054199
rattus_norvegicus	Gon4l	ENSRNOG00000020297

Paralogs (1): YY1AP1 (ENSG00000163374)

Protein

Protein identifiers

GON-4-like protein — Q3T8J9 (reviewed: Q3T8J9)

Alternative names: GON-4 homolog, Yin Yang 1-associated-related protein

All UniProt accessions (2): A0A087WUE6, Q3T8J9

UniProt curated annotations — full annotation on UniProt →

Function. Acts as a key transcription regulator of histones. Activates transcription of the histone H2A, histone H2B, histone H3 and histone H4 genes in conjunction with GON4L and MIZF. Together with CRAMP1, binds to the promoters of H1 genes (H1-2, H1-3, H1-4, H1-5 and H1-10/H1x), driving their transcription. Also acts as a transcription corepressor, as part of a complex with YY1, SIN3A and HDAC1. Required for B-cell lymphopoiesis.

Subunit / interactions. Interacts with NPAT. Interacts with CRAMP1; promoting CRAMP1 recruitment to histone locus bodies (HLB). Found in a complex with YY1, SIN3A and HDAC1.

Subcellular location. Nucleus. Chromosome.

Tissue specificity. Widely expressed.

Disease relevance. Li-Takada-Miyake syndrome (LTMS) [MIM:621212] An autosomal recessive neurodevelopmental disorder characterized by prenatal-onset growth impairment, developmental delay with intellectual disability and speech delay, microcephaly, cardiac anomalies, and brain abnormalites. The disease is caused by variants affecting the gene represented in this entry.

Isoforms (3)

UniProt ID	Names	Canonical?
Q3T8J9-1	1, Isoform A	yes
Q3T8J9-2	2, Isoform B
Q3T8J9-3	3

RefSeq proteins (5): NP_001269785, NP_001269787, NP_001269789, NP_001269790, NP_115668 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001005	SANT/Myb	Domain
IPR003822	PAH	Repeat
IPR009057	Homeodomain-like_sf	Homologous_superfamily
IPR036600	PAH_sf	Homologous_superfamily
IPR049257	Gon4l/CASP8AP2_myb-like	Domain
IPR052435	YY1-Transcr_Regul	Family

Pfam: PF02671, PF21227

UniProt features (54 total): compositionally biased region 15, region of interest 12, modified residue 9, sequence conflict 6, sequence variant 5, domain 3, splice variant 3, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q3T8J9-F1	48.51	0.10

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (9): 206, 346, 775, 1268, 1426, 1896, 1902, 1977, 2107

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 100 (showing top): MONNIER_POSTRADIATION_TUMOR_ESCAPE_UP, PATIL_LIVER_CANCER, TERAMOTO_OPN_TARGETS_CLUSTER_5, SHEDDEN_LUNG_CANCER_GOOD_SURVIVAL_A4, SCHAEFFER_PROSTATE_DEVELOPMENT_6HR_DN, GGCKCATGS_UNKNOWN, chr1q22, MODULE_397, RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_DN, GOCC_NUCLEAR_BODY, VANHARANTA_UTERINE_FIBROID_WITH_7Q_DELETION_UP, SCGGAAGY_ELK1_02, GGGATGC_MIR3245P, KOYAMA_SEMA3B_TARGETS_DN, GOMF_TRANSCRIPTION_COREGULATOR_ACTIVITY

GO Biological Process (1): regulation of DNA-templated transcription (GO:0006355)

GO Molecular Function (1): transcription coregulator activity (GO:0003712)

GO Cellular Component (3): nucleus (GO:0005634), nucleoplasm (GO:0005654), nuclear body (GO:0016604)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
DNA-templated transcription	1
regulation of gene expression	1
regulation of RNA biosynthetic process	1
transcription regulator activity	1
intracellular membrane-bounded organelle	1
nuclear lumen	1
cellular anatomical structure	1
nucleoplasm	1
intracellular membraneless organelle	1

Protein interactions and networks

STRING

1876 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
GON4L	ASH1L	Q9NR48	944
GON4L	NPAT	Q14207	584
GON4L	TTC24	A2A3L6	567
GON4L	DEGS2	Q6QHC5	460
GON4L	RCAN3	Q9UKA8	458
GON4L	RNF34	Q969K3	448
GON4L	HDAC1	Q13547	446
GON4L	ZNF692	Q9BU19	438
GON4L	UQCC1	Q9NVA1	433
GON4L	GSTO2	Q9H4Y5	425
GON4L	LSM11	P83369	419
GON4L	TNPO3	Q9Y5L0	409
GON4L	SIN3A	Q96ST3	406
GON4L	OSBPL2	Q9H1P3	405
GON4L	CRAMP1	Q96RY5	404

IntAct

39 interactions, top by confidence:

A	B	Type	Score
H2AX	PPM1G	psi-mi:“MI:0914”(association)	0.730
H2AC4	PPM1G	psi-mi:“MI:0914”(association)	0.670
H2BC1	PPM1G	psi-mi:“MI:0914”(association)	0.640
NEUROG3	GXYLT2	psi-mi:“MI:0914”(association)	0.640
SS18L2	GON4L	psi-mi:“MI:0914”(association)	0.610
SS18L2	SMARCA2	psi-mi:“MI:0914”(association)	0.570
H2BC26	PPM1G	psi-mi:“MI:0914”(association)	0.530
H2AC18	PPM1G	psi-mi:“MI:0914”(association)	0.530
H2AC20	PPM1G	psi-mi:“MI:0914”(association)	0.530
CRAMP1	NPAT	psi-mi:“MI:0914”(association)	0.530
SS18L2	ARID1A	psi-mi:“MI:2364”(proximity)	0.480
SS18L2	ARID1A	psi-mi:“MI:0914”(association)	0.480
GON4L		psi-mi:“MI:0915”(physical association)	0.370
ESR1	ESYT2	psi-mi:“MI:0914”(association)	0.350
ILF3	RPS3A	psi-mi:“MI:0914”(association)	0.350
ASB3	ZSWIM8	psi-mi:“MI:0914”(association)	0.350
H2AC11	U2SURP	psi-mi:“MI:0914”(association)	0.350
H2AJ	WDR46	psi-mi:“MI:0914”(association)	0.350
H2AC11		psi-mi:“MI:0914”(association)	0.350
H2AC4	MPHOSPH10	psi-mi:“MI:0914”(association)	0.350
CRAMP1	LCN1	psi-mi:“MI:0914”(association)	0.350
AFG2B	MMP24OS	psi-mi:“MI:0914”(association)	0.350

BioGRID (63): GON4L (Affinity Capture-MS), GON4L (Affinity Capture-MS), GON4L (Synthetic Lethality), GON4L (Proximity Label-MS), GON4L (Affinity Capture-MS), GON4L (Affinity Capture-MS), GON4L (Affinity Capture-MS), GON4L (Affinity Capture-MS), GON4L (Affinity Capture-MS), GON4L (Affinity Capture-RNA), GON4L (Affinity Capture-MS), GON4L (Affinity Capture-MS), GON4L (Affinity Capture-MS), GON4L (Affinity Capture-RNA), GON4L (Affinity Capture-MS)

ESM2 similar proteins: A0A3Q2UEI8, A0JNH9, A2BIL8, A8PUI7, B1H1S4, B2GUZ2, E7FAP1, E9Q309, F1R983, O60284, P49452, P51960, P86345, Q0P5H2, Q3T0A6, Q3T8J9, Q4KLP8, Q4QY64, Q4R731, Q535K8, Q563C3, Q58EL7, Q5FBB7, Q5QJE6, Q5VT06, Q5XG21, Q65Z40, Q6KAQ7, Q6NWJ0, Q6P0N0, Q6P6I6, Q76FK4, Q7YQM1, Q7YQM2, Q80WQ8, Q8C263, Q8C551, Q8IYH5, Q8NA57, Q8R2M2

Diamond homologs: Q3T8J9, Q535K8, Q9DB00, Q9H869, Q9UKL3, Q9WUF3

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 41 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:

Pathway	Partners	Fold	FDR
Packaging Of Telomere Ends	8	56.7×	7e-11
Recognition and association of DNA glycosylase with site containing an affected purine	8	52.6×	7e-11
Cleavage of the damaged purine	8	52.6×	7e-11
Recognition and association of DNA glycosylase with site containing an affected pyrimidine	8	47.5×	8e-11
Cleavage of the damaged pyrimidine	8	47.5×	8e-11
RNA Polymerase I Promoter Opening	8	47.5×	8e-11
ChAHP complex assembly	8	47.5×	8e-11
DNA methylation	8	46.0×	1e-10

GO biological processes:

GO term	Partners	Fold	FDR
heterochromatin formation	7	47.0×	2e-08

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	2
Likely pathogenic	0
Uncertain significance	5
Likely benign	24
Benign	2

Top pathogenic / likely-pathogenic (2)

Variant ID	HGVS	Classification
3899954	NM_001282860.2(GON4L):c.62_63del (p.Gln21fs)	Pathogenic
3899955	NM_001282860.2(GON4L):c.5517+1G>A	Pathogenic

SpliceAI

5739 predictions. Top by Δscore:

Variant	Effect	Δscore
1:155750734:C:CC	acceptor_gain	1.0000
1:155750734:CT:C	acceptor_loss	1.0000
1:155756962:T:C	donor_gain	1.0000
1:155757073:TCAAA:T	acceptor_gain	1.0000
1:155757074:CAAA:C	acceptor_gain	1.0000
1:155757074:CAAAC:C	acceptor_gain	1.0000
1:155757078:C:CC	acceptor_gain	1.0000
1:155757169:AGGT:A	donor_gain	1.0000
1:155757178:ACCTC:A	donor_loss	1.0000
1:155757179:C:CT	donor_loss	1.0000
1:155757183:ATACT:A	donor_gain	1.0000
1:155757185:A:AC	donor_gain	1.0000
1:155757185:ACT:A	donor_gain	1.0000
1:155757186:C:CC	donor_gain	1.0000
1:155757186:CTC:C	donor_gain	1.0000
1:155757188:C:CA	donor_gain	1.0000
1:155757193:T:A	donor_gain	1.0000
1:155757322:AGC:A	acceptor_loss	1.0000
1:155757324:C:CC	acceptor_gain	1.0000
1:155757324:CTGAG:C	acceptor_loss	1.0000
1:155757885:GAATA:G	donor_loss	1.0000
1:155757887:ATAC:A	donor_loss	1.0000
1:155757888:TA:T	donor_loss	1.0000
1:155758030:TCAAA:T	acceptor_gain	1.0000
1:155758031:CAAA:C	acceptor_gain	1.0000
1:155758031:CAAAC:C	acceptor_gain	1.0000
1:155758032:AAA:A	acceptor_gain	1.0000
1:155758033:AA:A	acceptor_gain	1.0000
1:155758034:ACTAC:A	acceptor_loss	1.0000
1:155758035:C:CA	acceptor_loss	1.0000

AlphaMissense

14779 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:155750711:A:G	L2200P	1.000
1:155751849:A:G	L2165P	1.000
1:155751965:C:A	W2156C	1.000
1:155751965:C:G	W2156C	1.000
1:155751967:A:G	W2156R	1.000
1:155751967:A:T	W2156R	1.000
1:155785356:A:G	L589P	1.000
1:155795055:A:G	I581T	1.000
1:155816250:A:G	W343R	1.000
1:155816250:A:T	W343R	1.000
1:155820631:A:G	L330P	1.000
1:155822317:A:G	L286P	1.000
1:155750702:A:G	L2203P	0.999
1:155750720:A:G	F2197S	0.999
1:155751841:A:G	C2168R	0.999
1:155751849:A:T	L2165H	0.999
1:155751858:C:G	R2162P	0.999
1:155751861:T:A	D2161V	0.999
1:155751862:C:G	D2161H	0.999
1:155757298:A:G	L1760P	0.999
1:155757985:A:G	L1720P	0.999
1:155760475:A:G	L1693P	0.999
1:155762197:A:G	L1635P	0.999
1:155763548:A:G	L1497P	0.999
1:155765004:A:G	L1490P	0.999
1:155785344:A:G	L593P	0.999
1:155795055:A:C	I581S	0.999
1:155795055:A:T	I581N	0.999
1:155795122:A:G	Y559H	0.999
1:155805068:A:G	L509S	0.999

dbSNP variants (sampled 300 via entrez): RS1000069795 (1:155806121 G>A), RS1000085655 (1:155790699 A>C), RS1000091600 (1:155843794 T>C), RS1000122370 (1:155800094 G>T), RS1000160186 (1:155776012 G>A), RS1000171831 (1:155816477 G>T), RS1000248383 (1:155799224 T>C), RS1000312479 (1:155854061 A>G,T), RS1000314943 (1:155824068 G>C,T), RS1000316990 (1:155850482 C>T), RS1000333089 (1:155810248 C>A), RS1000346562 (1:155748837 T>C), RS1000479027 (1:155767987 A>G,T), RS1000520410 (1:155858768 G>A,C), RS1000588592 (1:155860292 C>A,T)

Disease associations

OMIM: gene MIM:610393 | disease phenotypes: MIM:621212

GenCC curated gene-disease

Disease	Classification	Inheritance
complex neurodevelopmental disorder	Strong	Autosomal recessive
neurodevelopmental disorder	Limited	Autosomal recessive

Mondo (4): Li-Takada-Miyake syndrome (MONDO:0978303), ependymoma (MONDO:0016698), complex neurodevelopmental disorder (MONDO:0100038), neurodevelopmental disorder (MONDO:0700092)

Orphanet (1): Ependymoma (Orphanet:251636)

HPO phenotypes

63 total (30 of 63 shown, HPO-id order):

HPO	Term
HP:0000007	Autosomal recessive inheritance
HP:0000179	Thick lower lip vermilion
HP:0000232	Everted lower lip vermilion
HP:0000276	Long face
HP:0000293	Full cheeks
HP:0000307	Pointed chin
HP:0000322	Short philtrum
HP:0000324	Facial asymmetry
HP:0000343	Long philtrum
HP:0000348	High forehead
HP:0000369	Low-set ears
HP:0000396	Overfolded helix
HP:0000414	Bulbous nose
HP:0000431	Wide nasal bridge
HP:0000444	Convex nasal ridge
HP:0000445	Wide nose
HP:0000486	Strabismus
HP:0000494	Downslanted palpebral fissures
HP:0000568	Microphthalmia
HP:0000574	Thick eyebrow
HP:0000582	Upslanted palpebral fissure
HP:0000729	Autistic behavior
HP:0000750	Delayed speech and language development
HP:0000752	Hyperactivity
HP:0000805	Enuresis
HP:0001250	Seizure
HP:0001252	Hypotonia
HP:0001256	Mild intellectual disability
HP:0001260	Dysarthria
HP:0001263	Global developmental delay

GWAS associations

22 associations (top):

Study	Trait	p-value
GCST002591_8	Lewy body disease	5.000000e-06
GCST004131_70	Inflammatory bowel disease	6.000000e-08
GCST004132_44	Crohn’s disease	2.000000e-07
GCST004904_219	Body mass index	9.000000e-11
GCST007294_124	Body fat distribution (trunk fat ratio)	8.000000e-35
GCST007294_3	Body fat distribution (trunk fat ratio)	6.000000e-21
GCST007294_50	Body fat distribution (trunk fat ratio)	1.000000e-15
GCST007295_17	Body fat distribution (leg fat ratio)	3.000000e-13
GCST007295_37	Body fat distribution (leg fat ratio)	7.000000e-17
GCST007295_72	Body fat distribution (leg fat ratio)	1.000000e-28
GCST008062_50	Blood urea nitrogen levels	2.000000e-22
GCST008822_1	Neuritic plaque	5.000000e-06
GCST008972_258	Urate levels	6.000000e-20
GCST010696_19	Cortical thickness (min-P)	2.000000e-10
GCST010697_10	Cortical surface area (min-P)	3.000000e-10
GCST010698_59	Subcortical volume (min-P)	9.000000e-10
GCST010699_20	Brain morphology (min-P)	7.000000e-10
GCST010700_5	Cortical thickness (MOSTest)	8.000000e-17
GCST010701_66	Cortical surface area (MOSTest)	1.000000e-09
GCST010702_43	Subcortical volume (MOSTest)	3.000000e-10
GCST010703_253	Brain morphology (MOSTest)	4.000000e-14
GCST010726_2	Periventricular white matter hyperintensities	6.000000e-06

EFO canonical traits (8, from GWAS)

EFO ID	Trait name
EFO:0006799	Lewy body dementia measurement
EFO:0004340	body mass index
EFO:0004341	body fat distribution
EFO:0006798	neuritic plaque measurement
EFO:0004531	urate measurement
EFO:0004346	neuroimaging measurement
EFO:0004840	cortical thickness
EFO:0005665	white matter hyperintensity measurement

MeSH disease descriptors (2)

Descriptor	Name	Tree numbers
D004806	Ependymoma	C04.557.465.625.600.380.290; C04.557.470.670.380.290; C04.557.580.625.600.380.290
D065886	Neurodevelopmental Disorders	F03.625

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
methacrylaldehyde	affects cotreatment, increases oxidation, increases abundance	2
Acrolein	affects cotreatment, increases oxidation, increases abundance	2
Ozone	affects cotreatment, increases oxidation, increases abundance	2
FR900359	affects phosphorylation	1
dicrotophos	increases expression	1
methylmercuric chloride	increases expression	1
triphenyl phosphate	affects expression	1
alpha-pinene	affects cotreatment, increases oxidation, increases abundance	1
bisphenol A	increases expression	1
beta-lapachone	increases expression	1
arsenite	affects binding, decreases reaction	1
sodium arsenite	increases expression	1
benzo(e)pyrene	decreases methylation	1
beta-methylcholine	affects expression	1
di-n-butylphosphoric acid	affects expression	1
CGP 52608	affects binding, increases reaction	1
(+)-JQ1 compound	decreases expression	1
Sunitinib	increases expression	1
Vorinostat	decreases expression	1
Air Pollutants	affects cotreatment, increases abundance, increases oxidation	1
Amiodarone	increases expression	1
Benzo(a)pyrene	increases methylation	1
Cadmium	increases abundance, decreases expression	1
Caffeine	decreases phosphorylation	1
Demecolcine	increases expression	1
Dinitrochlorobenzene	affects binding	1
Doxorubicin	decreases expression	1
Hydrogen Peroxide	affects expression	1
Methapyrilene	decreases methylation	1
Methyl Methanesulfonate	increases expression	1

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT04586348	PHASE4	UNKNOWN	Prenatal Iodine Supplementation and Early Childhood Neurodevelopment
NCT04873115	PHASE4	UNKNOWN	Double-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,
NCT02559102	PHASE3	COMPLETED	Dexmedetomidine Sedation Versus General Anaesthesia for Inguinal Hernia Surgery in Infants
NCT02757079	PHASE3	COMPLETED	Study of the Efficacy and Safety of NPC-15 for Sleep Disorders of Children With Neurodevelopmental Disorders
NCT06915480	PHASE3	RECRUITING	Reducing Missed Appointments
NCT07377032	PHASE3	RECRUITING	TAP-GRIN: Interventional Study on Patients With GRIN-related Neurodevelopmental Disorders
NCT00517959	PHASE3	UNKNOWN	SCRT Versus Conventional RT in Children and Young Adults With Low Grade and Benign Brain Tumors
NCT01096368	PHASE3	COMPLETED	Maintenance Chemotherapy or Observation Following Induction Chemotherapy and Radiation Therapy in Treating Patients With Newly Diagnosed Ependymoma
NCT02909959	PHASE2	COMPLETED	Sulforaphane for the Treatment of Young Men With Autism Spectrum Disorder
NCT06081348	PHASE2	RECRUITING	Sertraline vs. Placebo in the Treatment of Anxiety in Children and AdoLescents With NeurodevelopMental Disorders
NCT06352372	PHASE2	COMPLETED	Safety and Efficacy of tPBM for Epileptiform Activity in Autism
NCT00003479	PHASE2	TERMINATED	Antineoplaston Therapy in Treating Patients With Ependymoma
NCT00520936	PHASE2	COMPLETED	A Study of Pemetrexed in Children With Recurrent Cancer
NCT00840047	PHASE2	ACTIVE_NOT_RECRUITING	Methionine PET/CT Studies In Patients With Cancer
NCT01088035	PHASE2	TERMINATED	Carboplatin as a Radiosensitizer in Treating Childhood Ependymoma
NCT01247922	PHASE2	TERMINATED	Single-agent Erlotinib in Patients Previously Treated With Oral Etoposide in Protocol OSI-774-205
NCT01288235	PHASE2	COMPLETED	Proton Radiotherapy for Pediatric Brain Tumors Requiring Partial Brain Irradiation
NCT01295944	PHASE2	COMPLETED	Carboplatin and Bevacizumab for Recurrent Ependymoma
NCT01356290	PHASE2	RECRUITING	Antiangiogenic Therapy for Children With Recurrent Medulloblastoma, Ependymoma, ATRT and Rare CNS Tumors
NCT01836549	PHASE2	TERMINATED	Imetelstat Sodium in Treating Younger Patients With Recurrent or Refractory Brain Tumors
NCT02125786	PHASE2	ACTIVE_NOT_RECRUITING	A Trial of Surgery and Fractionated Re-Irradiation for Recurrent Ependymoma
NCT02689336	PHASE2	WITHDRAWN	Erlotinib in Combination With Temozolomide in Treating Relapsed/Recurrent/Refractory Pediatric Solid Tumors
NCT03095248	PHASE2	TERMINATED	Trial of Selumetinib in Patients With Neurofibromatosis Type II Related Tumors
NCT03155620	PHASE2	ACTIVE_NOT_RECRUITING	Targeted Therapy Directed by Genetic Testing in Treating Pediatric Patients With Relapsed or Refractory Advanced Solid Tumors, Non-Hodgkin Lymphomas, or Histiocytic Disorders (The Pediatric MATCH Screening Trial)
NCT03173950	PHASE2	COMPLETED	Immune Checkpoint Inhibitor Nivolumab in People With Recurrent Select Rare CNS Cancers
NCT03194906	PHASE2	COMPLETED	Memantine for Prevention of Cognitive Late Effects in Pediatric Patients Receiving Cranial Radiation Therapy for Localized Brain Tumors
NCT03210714	PHASE2	ACTIVE_NOT_RECRUITING	Erdafitinib in Treating Patients With Relapsed or Refractory Advanced Solid Tumors, Non-Hodgkin Lymphoma, or Histiocytic Disorders With FGFR Mutations (A Pediatric MATCH Treatment Trial)
NCT03213652	PHASE2	ACTIVE_NOT_RECRUITING	Ensartinib in Treating Patients With Relapsed or Refractory Advanced Solid Tumors, Non-Hodgkin Lymphoma, or Histiocytic Disorders With ALK or ROS1 Genomic Alterations (A Pediatric MATCH Treatment Trial)
NCT03213665	PHASE2	COMPLETED	Tazemetostat in Treating Patients With Relapsed or Refractory Advanced Solid Tumors, Non-Hodgkin Lymphoma, or Histiocytic Disorders With EZH2, SMARCB1, or SMARCA4 Gene Mutations (A Pediatric MATCH Treatment Trial)
NCT03213678	PHASE2	COMPLETED	Samotolisib in Treating Patients With Relapsed or Refractory Advanced Solid Tumors, Non-Hodgkin Lymphoma, or Histiocytic Disorders With TSC or PI3K/MTOR Mutations (A Pediatric MATCH Treatment Trial)
NCT03213704	PHASE2	ACTIVE_NOT_RECRUITING	Larotrectinib in Treating Patients With Relapsed or Refractory Advanced Solid Tumors, Non-Hodgkin Lymphoma, or Histiocytic Disorders With NTRK Fusions (A Pediatric MATCH Treatment Trial)
NCT03220035	PHASE2	COMPLETED	Vemurafenib in Treating Patients With Relapsed or Refractory Advanced Solid Tumors, Non-Hodgkin Lymphoma, or Histiocytic Disorders With BRAF V600 Mutations (A Pediatric MATCH Treatment Trial)
NCT03233204	PHASE2	COMPLETED	Olaparib in Treating Patients With Relapsed or Refractory Advanced Solid Tumors, Non-Hodgkin Lymphoma, or Histiocytic Disorders With Defects in DNA Damage Repair Genes (A Pediatric MATCH Treatment Trial)
NCT03526250	PHASE2	COMPLETED	Palbociclib in Treating Patients With Relapsed or Refractory Rb Positive Advanced Solid Tumors, Non-Hodgkin Lymphoma, or Histiocytic Disorders With Activating Alterations in Cell Cycle Genes (A Pediatric MATCH Treatment Trial)
NCT03698994	PHASE2	ACTIVE_NOT_RECRUITING	Ulixertinib in Treating Patients With Advanced Solid Tumors, Non-Hodgkin Lymphoma, or Histiocytic Disorders With MAPK Pathway Mutations (A Pediatric MATCH Treatment Trial)
NCT03727841	PHASE2	TERMINATED	Marizomib for Recurrent Low-Grade and Anaplastic Supratentorial, Infratentorial, and Spinal Cord Ependymoma
NCT04049669	PHASE2	ACTIVE_NOT_RECRUITING	Pediatric Trial of Indoximod With Chemotherapy and Radiation for Relapsed Brain Tumors or Newly Diagnosed DIPG
NCT04195555	PHASE2	ACTIVE_NOT_RECRUITING	Ivosidenib in Treating Patients With Advanced Solid Tumors, Lymphoma, or Histiocytic Disorders With IDH1 Mutations (A Pediatric MATCH Treatment Trial)
NCT04284774	PHASE2	ACTIVE_NOT_RECRUITING	Tipifarnib for the Treatment of Advanced Solid Tumors, Lymphoma, or Histiocytic Disorders With HRAS Gene Alterations, a Pediatric MATCH Treatment Trial
NCT04320888	PHASE2	ACTIVE_NOT_RECRUITING	Selpercatinib for the Treatment of Advanced Solid Tumors, Lymphomas, or Histiocytic Disorders With Activating RET Gene Alterations, a Pediatric MATCH Treatment Trial