CHD9

Summary

CHD9 (chromodomain helicase DNA binding protein 9, HGNC:25701) is a protein-coding gene on chromosome 16q12.2, encoding ATP-dependent chromatin remodeler CHD9 (Q3L8U1). Probable ATP-dependent chromatin-remodeling factor.

Predicted to enable several functions, including ATP binding activity; ATP hydrolysis activity; and DNA helicase activity. Predicted to be involved in chromatin organization. Located in cytosol and nucleoplasm.

Source: NCBI Gene 80205 — RefSeq curated summary.

At a glance

• GWAS associations: 23
• Clinical variants (ClinVar): 385 total
• Druggable target: yes — 1 molecules with ChEMBL bioactivity
• MANE Select transcript: NM_001308319

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:25701
Approved symbol	CHD9
Name	chromodomain helicase DNA binding protein 9
Location	16q12.2
Locus type	gene with protein product
Status	Approved
Aliases	FLJ12178, KIAA0308, BC022889
Ensembl gene	ENSG00000177200
Ensembl biotype	protein_coding
OMIM	616936
Entrez	80205

Gene structure

Transcript identifiers

Ensembl transcripts: 21 — 10 protein_coding, 5 protein_coding_CDS_not_defined, 4 retained_intron, 2 nonsense_mediated_decay

ENST00000219084, ENST00000398510, ENST00000447540, ENST00000561869, ENST00000562785, ENST00000562791, ENST00000562806, ENST00000563410, ENST00000564255, ENST00000564582, ENST00000564600, ENST00000564641, ENST00000564845, ENST00000565119, ENST00000565442, ENST00000565803, ENST00000565832, ENST00000566029, ENST00000569225, ENST00000569794, ENST00000615216

RefSeq mRNA: 9 — MANE Select: NM_001308319 NM_001308319, NM_001352127, NM_001352156, NM_001352157, NM_001352158, NM_001382353, NM_001382354, NM_001382355, NM_025134

CCDS: CCDS45485, CCDS76865, CCDS92161

Canonical transcript exons

ENST00000447540 — 39 exons

Exon	Start	End
ENSE00000684097	53307681	53307953
ENSE00001653868	53155926	53157541
ENSE00003483304	53314377	53314516
ENSE00003485529	53231419	53231505
ENSE00003500972	53321526	53321630
ENSE00003503550	53285596	53285699
ENSE00003520945	53235185	53235306
ENSE00003532365	53318212	53318340
ENSE00003545240	53274213	53274302
ENSE00003558314	53247293	53247503
ENSE00003562156	53209482	53209813
ENSE00003562870	53303720	53304625
ENSE00003563602	53249871	53250066
ENSE00003566856	53267927	53268126
ENSE00003569793	53291725	53291767
ENSE00003573438	53255600	53255779
ENSE00003575813	53227396	53227464
ENSE00003579157	53231647	53231784
ENSE00003586906	53296956	53297158
ENSE00003598816	53292833	53293052
ENSE00003604893	53262987	53263097
ENSE00003616526	53287957	53288014
ENSE00003619355	53314823	53315044
ENSE00003620917	53273626	53273785
ENSE00003626972	53286226	53286343
ENSE00003627181	53306237	53306397
ENSE00003629646	53254438	53254605
ENSE00003634185	53267294	53267490
ENSE00003641177	53245336	53245479
ENSE00003650690	53308686	53308854
ENSE00003652228	53242840	53243016
ENSE00003653314	53245595	53245850
ENSE00003662900	53228983	53229100
ENSE00003683283	53238343	53238586
ENSE00003689365	53226366	53226512
ENSE00003691299	53227548	53227603
ENSE00003785586	53222644	53222755
ENSE00003918336	53324020	53327497
ENSE00003921581	53054991	53055077

Expression profiles

Bgee: expression breadth ubiquitous, 299 present calls, max score 98.81.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 42.0158 / max 1010.8031, expressed in 1811 samples.

FANTOM5 promoters (14 alternative TSS)

Promoter ID	TPM avg	Samples expressed
154060	10.8391	1732
154072	9.7456	1363
154066	6.8294	1599
154065	3.8785	993
154070	3.6914	979
154071	1.7818	644
154067	1.7568	1069
154073	1.4952	632
154064	0.6025	301
154075	0.5660	270

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
calcaneal tendon	UBERON:0003701	98.81	gold quality
tendon	UBERON:0000043	97.76	gold quality
tibia	UBERON:0000979	97.47	gold quality
mucosa of paranasal sinus	UBERON:0005030	97.11	gold quality
tendon of biceps brachii	UBERON:0008188	97.07	gold quality
skin of hip	UBERON:0001554	97.01	gold quality
renal medulla	UBERON:0000362	96.52	gold quality
visceral pleura	UBERON:0002401	96.52	gold quality
tongue squamous epithelium	UBERON:0006919	96.51	gold quality
urethra	UBERON:0000057	96.34	gold quality
pylorus	UBERON:0001166	96.15	gold quality
hair follicle	UBERON:0002073	96.04	gold quality
corpus callosum	UBERON:0002336	96.04	gold quality
parietal pleura	UBERON:0002400	96.01	gold quality
mammalian vulva	UBERON:0000997	96.00	gold quality
colonic epithelium	UBERON:0000397	95.90	gold quality
mammary duct	UBERON:0001765	95.85	gold quality
seminal vesicle	UBERON:0000998	95.83	gold quality
pleura	UBERON:0000977	95.79	gold quality
nipple	UBERON:0002030	95.78	gold quality
superficial temporal artery	UBERON:0001614	95.76	gold quality
cardia of stomach	UBERON:0001162	95.72	gold quality
cervix squamous epithelium	UBERON:0006922	95.68	gold quality
CA1 field of hippocampus	UBERON:0003881	95.67	gold quality
oral cavity	UBERON:0000167	95.65	gold quality
pigmented layer of retina	UBERON:0001782	95.65	gold quality
retina	UBERON:0000966	95.62	gold quality
cranial nerve II	UBERON:0000941	95.60	gold quality
Brodmann (1909) area 23	UBERON:0013554	95.58	gold quality
epithelium of mammary gland	UBERON:0003244	95.57	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-GEOD-137537	yes	19.08
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

277 targeting CHD9, 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-450A-1-3P	100.00	69.33	1837
HSA-MIR-4768-5P	100.00	69.49	2861
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-6833-3P	100.00	70.63	3197
HSA-MIR-1193	100.00	65.93	529
HSA-MIR-3924	100.00	72.09	2394
HSA-MIR-432-3P	100.00	67.86	705
HSA-MIR-4476	100.00	68.18	2030
HSA-MIR-6876-5P	100.00	67.68	2126
HSA-MIR-4533	100.00	69.48	2758
HSA-MIR-656-3P	100.00	72.15	2788
HSA-MIR-4668-3P	100.00	68.74	2635
HSA-MIR-126-5P	100.00	72.71	3180
HSA-MIR-4682	100.00	68.89	1258
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-30A-5P	100.00	76.31	3233
HSA-MIR-30B-5P	100.00	76.29	3248
HSA-MIR-30C-5P	100.00	76.29	3248
HSA-MIR-30D-5P	100.00	76.32	3233
HSA-MIR-30E-5P	100.00	76.32	3242
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-548AW	99.99	72.57	3559
HSA-MIR-6759-5P	99.99	66.54	785
HSA-MIR-433-3P	99.98	69.37	1203
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-32-5P	99.98	75.21	1964
HSA-MIR-92A-3P	99.98	75.21	1960
HSA-MIR-92B-3P	99.98	75.25	1955
HSA-MIR-499A-5P	99.98	70.79	1323

Literature-anchored findings (GeneRIF, showing 4)

• The CHD9 (CReMM) protein is extensively phosphorylated, has DNA-dependent ATPase activity, and binds to A/T-rich DNA. It is also expressed in mesenchymal progenitors. (PMID:16095617)
• CReMM is a chromodomain helicase-DNA-binding protein expressed by osteoprogenitors (PMID:16523501)
• Chromatin immunoprecipitation assay was applied to follow the dynamics of CReMM binding to A/T-rich regions on promoters of genes that play a role in osteoblast maturation. (PMID:16705189)
• Gene expression regulation by the Chromodomain helicase DNA-binding protein 9 (CHD9) chromatin remodeler is dispensable for murine development. (PMID:32453735)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	chd9	ENSDARG00000074498
mus_musculus	Chd9	ENSMUSG00000056608
rattus_norvegicus	Chd9	ENSRNOG00000049302

Paralogs (30): HLTF (ENSG00000071794), SMARCA2 (ENSG00000080503), SRCAP (ENSG00000080603), ATRX (ENSG00000085224), RAD54L (ENSG00000085999), BTAF1 (ENSG00000095564), CHD8 (ENSG00000100888), SMARCA1 (ENSG00000102038), CHD4 (ENSG00000111642), CHD5 (ENSG00000116254), TTF2 (ENSG00000116830), HELLS (ENSG00000119969), ZRANB3 (ENSG00000121988), CHD6 (ENSG00000124177), SMARCA4 (ENSG00000127616), INO80 (ENSG00000128908), CHD1L (ENSG00000131778), SMARCAL1 (ENSG00000138375), SHPRH (ENSG00000146414), SMARCA5 (ENSG00000153147), CHD1 (ENSG00000153922), SMARCAD1 (ENSG00000163104), RAD54L2 (ENSG00000164080), CHD3 (ENSG00000170004), CHD7 (ENSG00000171316), CHD2 (ENSG00000173575), EP400 (ENSG00000183495), ERCC6L (ENSG00000186871), RAD54B (ENSG00000197275), ERCC6 (ENSG00000225830)

Protein

Protein identifiers

ATP-dependent chromatin remodeler CHD9 — Q3L8U1 (reviewed: Q3L8U1)

Alternative names: Chromatin-related mesenchymal modulator, Chromatin-remodeling factor CHROM1, Chromo domain-containing protein 9, Kismet homolog 2, PPAR-alpha-interacting complex protein 320 kDa, Peroxisomal proliferator-activated receptor A-interacting complex 320 kDa protein

All UniProt accessions (9): Q3L8U1, A0A087WU44, H3BRU9, H3BSP3, H3BTW3, H3BV31, I3L340, J3KRH9, J3KSW5

UniProt curated annotations — full annotation on UniProt →

Function. Probable ATP-dependent chromatin-remodeling factor. Acts as a transcriptional coactivator for PPARA and possibly other nuclear receptors. Has DNA-dependent ATPase activity and binds to A/T-rich DNA. Associates with A/T-rich regulatory regions in promoters of genes that participate in the differentiation of progenitors during osteogenesis.

Subunit / interactions. Interacts with PPARA. Probably interacts with ESR1 and NR1I3.

Subcellular location. Cytoplasm. Nucleus.

Tissue specificity. Widely expressed at low levels. In bone marrow, expression is restricted to osteoprogenitor cells adjacent to mature osteoblasts.

Post-translational modifications. Phosphorylated on serine and tyrosine residues.

Similarity. Belongs to the SNF2/RAD54 helicase family.

Isoforms (3)

UniProt ID	Names	Canonical?
Q3L8U1-1	1	yes
Q3L8U1-2	2
Q3L8U1-3	3

RefSeq proteins (9): NP_001295248, NP_001339056, NP_001339085, NP_001339086, NP_001339087, NP_001369282, NP_001369283, NP_001369284, NP_079410 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000330	SNF2_N	Domain
IPR000953	Chromo/chromo_shadow_dom	Domain
IPR001650	Helicase_C-like	Domain
IPR006576	BRK_domain	Domain
IPR014001	Helicase_ATP-bd	Domain
IPR016197	Chromo-like_dom_sf	Homologous_superfamily
IPR023780	Chromo_domain	Domain
IPR027417	P-loop_NTPase	Homologous_superfamily
IPR037259	BRK_sf	Homologous_superfamily
IPR038718	SNF2-like_sf	Homologous_superfamily
IPR049730	SNF2/RAD54-like_C	Domain
IPR051493	CHD	Family
IPR056342	HTH_CHD6-9	Domain

Pfam: PF00176, PF00271, PF00385, PF07533, PF23078

Catalyzed reactions (Rhea), 1 shown:

• ATP + H2O = ADP + phosphate + H(+) (RHEA:13065)

UniProt features (82 total): compositionally biased region 18, sequence conflict 18, cross-link 11, region of interest 10, modified residue 10, short sequence motif 6, domain 4, splice variant 2, chain 1, binding site 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

No AlphaFold model available for Q3L8U1 — AlphaFold DB does not currently provide models for proteins above ~3000 aa.

Functional residue map

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

Ligand- & substrate-binding residues (1): 885–892

Post-translational modifications (21): 499, 550, 611, 1468, 1472, 2026, 2058, 2059, 2075, 2079, 197, 596, 1588, 1738, 1903, 2038, 2074, 2350, 2356, 2361 …

Function

Pathways and Gene Ontology

Reactome pathways

11 pathways

ID	Pathway
R-HSA-1368108	BMAL1:CLOCK,NPAS2 activates circadian expression
R-HSA-1989781	PPARA activates gene expression
R-HSA-2151201	Transcriptional activation of mitochondrial biogenesis
R-HSA-2426168	Activation of gene expression by SREBF (SREBP)
R-HSA-381340	Transcriptional regulation of white adipocyte differentiation
R-HSA-400206	Regulation of lipid metabolism by PPARalpha
R-HSA-9707564	Cytoprotection by HMOX1
R-HSA-9707616	Heme signaling
R-HSA-9931509	Expression of BMAL (ARNTL), CLOCK, and NPAS2
R-HSA-9933387	RORA,B,C and NR1D1 (REV-ERBA) regulate gene expression
R-HSA-9943962	CHD6, CHD7, CHD8, CHD9 subfamily

MSigDB gene sets: 314 (showing top): GSE18804_SPLEEN_MACROPHAGE_VS_BRAIN_TUMORAL_MACROPHAGE_DN, GSE18804_SPLEEN_MACROPHAGE_VS_TUMORAL_MACROPHAGE_DN, REACTOME_TRANSCRIPTIONAL_REGULATION_OF_WHITE_ADIPOCYTE_DIFFERENTIATION, MORF_MSH3, GCM_GSPT1, MODULE_255, TGCACTT_MIR519C_MIR519B_MIR519A, MORF_BRCA1, MORF_ATRX, MODULE_317, LINDGREN_BLADDER_CANCER_CLUSTER_3_DN, MORF_ESR1, CCATCCA_MIR432, MARTINEZ_RB1_TARGETS_UP, MORF_FANCG

GO Biological Process (1): chromatin organization (GO:0006325)

GO Molecular Function (7): DNA binding (GO:0003677), ATP binding (GO:0005524), ATP hydrolysis activity (GO:0016887), nucleotide binding (GO:0000166), helicase activity (GO:0004386), protein binding (GO:0005515), hydrolase activity (GO:0016787)

GO Cellular Component (4): nucleoplasm (GO:0005654), cytosol (GO:0005829), nucleus (GO:0005634), cytoplasm (GO:0005737)

Reactome top-level categories

Rollup of top-9 pathways:

Category	Pathways
Circadian clock	3
Regulation of lipid metabolism by PPARalpha	1
Mitochondrial biogenesis	1
Regulation of cholesterol biosynthesis by SREBP (SREBF)	1
Adipogenesis	1
Metabolism of lipids	1
Cellular response to chemical stress	1
Cellular responses to stress	1
CHD chromatin remodelers	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	3
ATP-dependent activity	2
cellular component organization	1
nucleic acid binding	1
adenyl ribonucleotide binding	1
purine ribonucleoside triphosphate binding	1
ribonucleoside triphosphate phosphatase activity	1
nucleoside phosphate binding	1
heterocyclic compound binding	1
nucleic acid conformation isomerase activity	1
catalytic activity, acting on a nucleic acid	1
binding	1
catalytic activity	1
nuclear lumen	1
cytoplasm	1
intracellular membrane-bounded organelle	1
intracellular anatomical structure	1

Protein interactions and networks

STRING

2750 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CHD9	ESR1	P03372	668
CHD9	CHD1	O14646	642
CHD9	PTK6	Q13882	510
CHD9	NR3C1	P04150	499
CHD9	PPARA	Q07869	498
CHD9	TOX3	O15405	491
CHD9	MED1	Q15648	491
CHD9	H4C16	P02304	470
CHD9	N4BP2	Q86UW6	466
CHD9	RXRA	P19793	463
CHD9	NR1I3	Q14994	461
CHD9	BGLAP	P02818	454
CHD9	H4C7	Q99525	448
CHD9	CHD6	Q8TD26	431
CHD9	PIK3C3	Q8NEB9	410

IntAct

44 interactions, top by confidence:

A	B	Type	Score
MED19	MED19	psi-mi:“MI:0914”(association)	0.730
CAMKV	AP3B1	psi-mi:“MI:0914”(association)	0.640
PIP4K2A	AP3B1	psi-mi:“MI:0914”(association)	0.530
EPB41L3	AP3B1	psi-mi:“MI:0914”(association)	0.530
MDK	SETD1A	psi-mi:“MI:0914”(association)	0.530
EPB41L5	SETD1A	psi-mi:“MI:0914”(association)	0.530
DAXX	TNRC18	psi-mi:“MI:0914”(association)	0.530
EDA	AP3B1	psi-mi:“MI:0914”(association)	0.530
EPB41L1	AP3B1	psi-mi:“MI:0914”(association)	0.530
Crnkl1	PLRG1	psi-mi:“MI:0914”(association)	0.350
Isy1	PFDN6	psi-mi:“MI:0914”(association)	0.350
M		psi-mi:“MI:0914”(association)	0.350
SOX2	DDX39A	psi-mi:“MI:0914”(association)	0.350
HCN1	POTEF	psi-mi:“MI:0914”(association)	0.350
MAD2L1	MED19	psi-mi:“MI:0914”(association)	0.350
SYT2	ARHGAP10	psi-mi:“MI:0914”(association)	0.350
ANKRD36B	CCDC66	psi-mi:“MI:0914”(association)	0.350
SULF2	CCDC85C	psi-mi:“MI:0914”(association)	0.350
FGF11	ZSWIM8	psi-mi:“MI:0914”(association)	0.350
PLCD3	AP3B1	psi-mi:“MI:0914”(association)	0.350
CT45A6	AP3B1	psi-mi:“MI:0914”(association)	0.350
FGF12	SUPT5H	psi-mi:“MI:0914”(association)	0.350
DAXX	SETD1A	psi-mi:“MI:0914”(association)	0.350
NFKBIL1	TNRC18	psi-mi:“MI:0914”(association)	0.350
ADAMTS1	CHD9	psi-mi:“MI:0914”(association)	0.350
MMTAG2	A2ML1	psi-mi:“MI:0914”(association)	0.350
NFKBIL1	AP3B1	psi-mi:“MI:0914”(association)	0.350
ANKRD36B	AHCYL1	psi-mi:“MI:0914”(association)	0.350

BioGRID (95): CHD9 (Co-fractionation), CHD9 (Affinity Capture-MS), CHD9 (Affinity Capture-MS), CHD9 (Affinity Capture-MS), CHD9 (Affinity Capture-MS), CHD9 (Affinity Capture-MS), CHD9 (Affinity Capture-MS), CHD9 (Affinity Capture-MS), CHD9 (Affinity Capture-MS), CHD9 (Affinity Capture-MS), CHD9 (Affinity Capture-MS), CHD9 (Affinity Capture-MS), CHD9 (Affinity Capture-MS), CHD9 (Affinity Capture-MS), CHD9 (Affinity Capture-MS)

ESM2 similar proteins: A2AJK6, A2ICN5, A2VDZ3, F1LYL9, O18896, O94900, P0CB49, P34545, P46936, P46937, P48436, P49750, P55197, P61753, P61754, Q02078, Q03414, Q04887, Q06A37, Q08D57, Q2MJT0, Q3L8U1, Q3TLH4, Q571K4, Q5F3P8, Q5REW7, Q60929, Q66J90, Q66JW3, Q6F2E7, Q6KC79, Q6KCD5, Q6YXY2, Q7YRJ7, Q7ZXH3, Q8BXJ2, Q8BYH8, Q8CHI8, Q8N5C8, Q96EV2

Diamond homologs: A2A8L1, A2AJK6, A3KFM7, A7Z019, A9X4T1, B0R061, B0R0I6, B4KHL5, B5DE69, B6ZLK2, D3Z9Z9, D3ZA12, D3ZD32, E1B7X9, E7F1C4, E9PZM4, F4IHS2, F4IV45, F4IV99, F4J9M5, F4JTF6, F4JY24, F4K128, F4KBP5, F8VPZ5, G5EBZ4, G5EDG2, G5EF53, O14139, O14646, O14647, O16102, O42861, O60264, O74842, O94421, O97159, P22082, P25439, P28370

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	325
Likely benign	12
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

8312 predictions. Top by Δscore:

Variant	Effect	Δscore
16:53075355:T:G	donor_gain	1.0000
16:53132704:A:AG	donor_gain	1.0000
16:53208261:T:TA	acceptor_gain	1.0000
16:53209479:TA:T	acceptor_loss	1.0000
16:53209480:A:AG	acceptor_gain	1.0000
16:53209480:AG:A	acceptor_loss	1.0000
16:53209481:G:GA	acceptor_gain	1.0000
16:53209481:GC:G	acceptor_gain	1.0000
16:53222636:T:TA	acceptor_gain	1.0000
16:53222640:ACAGC:A	acceptor_loss	1.0000
16:53222641:CAGCA:C	acceptor_loss	1.0000
16:53222642:A:AG	acceptor_gain	1.0000
16:53222642:AGCAA:A	acceptor_loss	1.0000
16:53222643:G:GA	acceptor_loss	1.0000
16:53222643:G:GG	acceptor_gain	1.0000
16:53222643:GC:G	acceptor_gain	1.0000
16:53222643:GCA:G	acceptor_gain	1.0000
16:53222643:GCAAA:G	acceptor_gain	1.0000
16:53222754:AAGT:A	donor_loss	1.0000
16:53222755:AGT:A	donor_loss	1.0000
16:53222756:G:GG	donor_gain	1.0000
16:53222756:GT:G	donor_loss	1.0000
16:53222757:T:G	donor_loss	1.0000
16:53222758:GAGTA:G	donor_loss	1.0000
16:53222759:AG:A	donor_loss	1.0000
16:53226353:T:TA	acceptor_gain	1.0000
16:53226354:G:A	acceptor_gain	1.0000
16:53226359:A:AG	acceptor_gain	1.0000
16:53226363:CAGAA:C	acceptor_loss	1.0000
16:53226364:A:AG	acceptor_gain	1.0000

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000004960 (16:53254972 CT>C,CTT), RS1000024295 (16:53129311 T>G), RS1000031390 (16:53093956 A>G), RS1000069863 (16:53076354 C>G,T), RS1000076088 (16:53124191 T>G), RS1000081971 (16:53209921 T>C), RS1000088691 (16:53100555 C>G), RS1000090712 (16:53056704 A>G), RS1000092320 (16:53186753 G>A), RS1000118231 (16:53284037 C>G,T), RS1000128212 (16:53123812 A>T), RS1000130484 (16:53143301 A>C), RS1000134967 (16:53235848 A>G), RS1000142402 (16:53112011 A>C), RS1000144457 (16:53192080 A>G)

Disease associations

OMIM: gene MIM:616936 | disease phenotypes:

GenCC curated gene-disease

Mondo (1): neurodevelopmental disorder (MONDO:0700092)

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

23 associations (top):

Study	Trait	p-value
GCST002147_4	Fibrinogen	1.000000e-10
GCST003194_1	Fibrinogen levels	9.000000e-14
GCST003488_8	Response to fenofibrate (triglyceride levels)	4.000000e-06
GCST004121_7	Fibrinogen levels	8.000000e-11
GCST004122_28	Fibrinogen levels	3.000000e-11
GCST004609_221	Monocyte percentage of white cells	3.000000e-11
GCST005950_1	Body mass index x sex x age interaction (4df test)	2.000000e-187
GCST005951_192	Body mass index	4.000000e-188
GCST005952_1	Body mass index (age>50)	1.000000e-97
GCST007565_81	Morning person	6.000000e-38
GCST007576_288	Chronotype	6.000000e-38
GCST008058_116	Estimated glomerular filtration rate	6.000000e-17
GCST008059_7	Estimated glomerular filtration rate	2.000000e-16
GCST009325_25	Parkinson’s disease or first degree relation to individual with Parkinson’s disease	1.000000e-10
GCST009391_352	Metabolite levels	9.000000e-06
GCST009391_890	Metabolite levels	2.000000e-06
GCST010241_298	Apolipoprotein A1 levels	1.000000e-08
GCST010396_89	Gut microbiota (bacterial taxa, hurdle binary method)	1.000000e-06
GCST90002394_537	Monocyte percentage of white cells	2.000000e-17
GCST90002395_194	Mean platelet volume	2.000000e-14
GCST90002395_195	Mean platelet volume	2.000000e-13
GCST90002398_298	Neutrophil count	4.000000e-09
GCST90002402_459	Platelet count	3.000000e-13

EFO canonical traits (12, from GWAS)

EFO ID	Trait name
EFO:0007681	triglyceride change measurement
EFO:0007989	monocyte percentage of leukocytes
EFO:0004340	body mass index
EFO:0008007	age at assessment
EFO:0008343	sex interaction measurement
EFO:0008328	chronotype measurement
EFO:0010433	triacylglycerol 56:6 measurement
EFO:0010440	triacylglycerol 58:6 measurement
EFO:0004614	apolipoprotein A 1 measurement
EFO:0007874	gut microbiome measurement
EFO:0004833	neutrophil count
EFO:0004309	platelet count

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
D065886	Neurodevelopmental Disorders	F03.625

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL5724783 (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: 1,538 (via chembl_molecule»patent_compound — counts attach to the compound, not the gene–compound relationship, so off-target/promiscuous molecules can dominate).

Molecule	Name	Phase	Patents
CHEMBL1232461	MOLIBRESIB	2	1,538

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

ChEMBL bioactivities

2 potent at pChembl≥5 of 2 total, top 2 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChembl	Type	Value	Unit	Molecule
7.80	Kd	16	nM	MOLIBRESIB
7.52	IC50	30	nM	MOLIBRESIB

PubChem BioAssay actives

2 with measured affinity, of 7 total; 1 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

Compound	Assay	Type	Value	Unit
2-[(4S)-6-(4-chlorophenyl)-8-methoxy-1-methyl-4H-[1,2,4]triazolo[4,3-a][1,4]benzodiazepin-4-yl]-N-ethylacetamide	2179118: Binding affinity against CHD9 (unknown origin) assessed as apparent dissociation constant incubated for 1 hr by colloidal coomassie staining based LC-MS/MS analysis	kd	0.0160	uM

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	increases expression, affects expression, decreases expression, decreases methylation	6
Benzo(a)pyrene	decreases expression, affects methylation	3
methylmercuric chloride	decreases expression, increases expression	2
bisphenol A	decreases expression, affects binding, affects folding, increases reaction, affects cotreatment	2
potassium chromate(VI)	affects cotreatment, decreases expression	2
bisphenol S	decreases expression, affects binding, decreases reaction, affects cotreatment	2
bisphenol AF	affects binding, affects folding, increases reaction, decreases reaction	2
Estradiol	affects binding, decreases reaction, increases expression	2
Tretinoin	increases expression	2
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide	decreases expression	2
p-Chloromercuribenzoic Acid	affects cotreatment, decreases expression	2
Particulate Matter	increases expression, affects cotreatment, decreases expression, increases abundance	2
aristolochic acid I	decreases expression	1
FR900359	increases phosphorylation	1
bisphenol F	affects cotreatment, decreases methylation	1
TAK-243	increases sumoylation	1
urushiol	increases expression	1
triphenyl phosphate	affects expression	1
trichostatin A	increases expression	1
beta-lapachone	decreases expression	1
arsenite	affects binding, decreases reaction	1
sodium arsenite	affects methylation	1
coumarin	decreases phosphorylation	1
isobutyl alcohol	decreases expression, increases abundance, affects cotreatment	1
epigallocatechin gallate	affects cotreatment, decreases expression	1
chromium hexavalent ion	decreases expression	1
perfluorooctane sulfonic acid	decreases expression	1
CGP 52608	increases reaction, affects binding	1
K 7174	increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1

ChEMBL screening assays

7 unique, capped per target: 7 binding

Representative assays (with source publication via chembl_document):

Assay ID	Type	Description	Source paper
CHEMBL5697164	Binding	Inhibition of CHD9 (unknown origin) assessed as fold change at 10 uM incubated for 1 hr by colloidal coomassie staining based LC-MS/MS analysis	Inhibition of BET recruitment to chromatin as an effective treatment for MLL-fusion leukaemia. — Nature

Cellosaurus cell lines

3 cell lines: 3 cancer cell line

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

Cellosaurus	Name	Category	Sex
CVCL_B8DQ	Abcam HCT 116 CHD9 KO	Cancer cell line	Male
CVCL_B8U5	Abcam MCF-7 CHD9 KO	Cancer cell line	Female
CVCL_B9FY	Abcam A-549 CHD9 KO	Cancer cell line	Male

Clinical trials (associated diseases)

202 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
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
NCT00503191	PHASE1	COMPLETED	NeuroModulation Technique Treatment of Autism
NCT04475848	PHASE1	COMPLETED	A Study to Investigate the Safety, Tolerability, Pharmacokinetics, Pharmacodynamics and Food Effect of RO6953958 in Healthy Participants
NCT06300398	PHASE1	COMPLETED	IAMA-6 Oral Dose Study in Healthy Adults
NCT01783041	PHASE2/PHASE3	COMPLETED	Effect of Early L-Carnitine Supplementation on Neurodevelopmental Outcomes in Very Preterm Infants
NCT05767385	PHASE2/PHASE3	RECRUITING	Fetal Cerebrovascular Autoregulation in Congenital Heart Disease and Association With Neonatal Neurobehavior
NCT05675098	EARLY_PHASE1	NOT_YET_RECRUITING	Central Nervous System Stimulants and Physical Function in Children With Cerebral Palsy
NCT00783783	Not specified	COMPLETED	CYP2D6 Pharmacogenetics in Risperidone-Treated Children
NCT01778504	Not specified	RECRUITING	Studying Childhood-onset Behavioral, Psychiatric, and Developmental Disorders
NCT01850784	Not specified	UNKNOWN	High Energy Formula Feeding in Infants With Congenital Heart Disease
NCT01922791	Not specified	COMPLETED	Nutrition and Pregnancy Intervention Study
NCT01942525	Not specified	UNKNOWN	Influence of Intrauterine Growth Restriction on Amplitude-integrated EEG in Preterm Infants
NCT02003170	Not specified	COMPLETED	Etiology and Early Diagnosis of Neurodevelopmental Disorders
NCT02118649	Not specified	ACTIVE_NOT_RECRUITING	Enhancing Behavior and Brain Response to Visual Targets Using a Computer Game
NCT02557191	Not specified	TERMINATED	Biomarkers, Neurodevelopment and Preterm Infants
NCT02690675	Not specified	COMPLETED	Iron Supplement Effect on Child Development
NCT02694003	Not specified	COMPLETED	Better Nights, Better Days for Children With Neurodevelopment Disorders
NCT02792894	Not specified	COMPLETED	Family Networks (FaNs) for Children With Developmental Disorders and Delays
NCT02871674	Not specified	UNKNOWN	Good Night Project: Behavioural Sleep Interventions for Children With ADHD: A Randomised Controlled Trial
NCT02887157	Not specified	COMPLETED	Analyzing Retinal Microanatomy in ROP
NCT02898298	Not specified	COMPLETED	Positive Emotion Regulation Training in Children, Adolescents and Young Adults With and Without Developmental Disorder
NCT02912780	Not specified	UNKNOWN	Introduction of Microsystems in a Level 3 Neonatal Intensive Care Unit
NCT03023293	Not specified	COMPLETED	n-3 PUFAs, Irisin and Maternal Glucose Metabolism From Pregnancy to Postpartum
NCT03023644	Not specified	COMPLETED	Improving Neurodevelopmental Outcomes in Children With Congenital Heart Disease: An Intervention Study
NCT03032991	Not specified	UNKNOWN	Early Biomarkers of Neurodevelopment in Offspring of Diabetic Mothers
NCT03088189	Not specified	TERMINATED	Effect of Parental Peri-conceptional Vitamin B12 Supplementation on Infant Neurocognitive Development in Offspring
NCT03096028	Not specified	COMPLETED	Developmental Origins of Mental Health Disorders
NCT03148782	Not specified	COMPLETED	Brain Plasticity Underlying Acquisition of New Organizational Skills in Children-R61 Phase
NCT03172104	Not specified	COMPLETED	Neurobehavioural Development of Infants Born <30 Weeks Gestational Age Between Birth and Five Years of Age
NCT03222375	Not specified	RECRUITING	SQUED™ Series 28.1 Home-use and Treatment of Autowave Reverberator of Autism
NCT03229928	Not specified	COMPLETED	Clinical Testing of a Real-Time Behavior Measurement Tool: Measuring Outcomes for CHAnge
NCT03232489	Not specified	UNKNOWN	Study for the Evaluation of the Feasibility of Applying Advanced MRI Scanning in Pediatric Clinical Practice