BDH1

Summary

BDH1 (3-hydroxybutyrate dehydrogenase 1, HGNC:1027) is a protein-coding gene on chromosome 3q29, encoding D-beta-hydroxybutyrate dehydrogenase, mitochondrial (Q02338).

This gene encodes a member of the short-chain dehydrogenase/reductase gene family. The encoded protein forms a homotetrameric lipid-requiring enzyme of the mitochondrial membrane and has a specific requirement for phosphatidylcholine for optimal enzymatic activity. The encoded protein catalyzes the interconversion of acetoacetate and (R)-3-hydroxybutyrate, the two major ketone bodies produced during fatty acid catabolism. Alternatively spliced transcript variants encoding the same protein have been described.

Source: NCBI Gene 622 — RefSeq curated summary.

At a glance

• Gene–disease (curated): neurodevelopmental disorder (Limited, GenCC)
• GWAS associations: 3
• Clinical variants (ClinVar): 139 total — 32 pathogenic, 2 likely-pathogenic
• Phenotypes (HPO): 2
• MANE Select transcript: NM_203314

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:1027
Approved symbol	BDH1
Name	3-hydroxybutyrate dehydrogenase 1
Location	3q29
Locus type	gene with protein product
Status	Approved
Aliases	SDR9C1
Ensembl gene	ENSG00000161267
Ensembl biotype	protein_coding
OMIM	603063
Entrez	622

Gene structure

Transcript identifiers

Ensembl transcripts: 38 — 30 protein_coding, 4 retained_intron, 3 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay

ENST00000358186, ENST00000392378, ENST00000392379, ENST00000431056, ENST00000432819, ENST00000434143, ENST00000441275, ENST00000445160, ENST00000446746, ENST00000455876, ENST00000468710, ENST00000476764, ENST00000477015, ENST00000479425, ENST00000483920, ENST00000492681, ENST00000495285, ENST00000651856, ENST00000903995, ENST00000903996, ENST00000903997, ENST00000903998, ENST00000903999, ENST00000904000, ENST00000904001, ENST00000904002, ENST00000904003, ENST00000904004, ENST00000904005, ENST00000904006, ENST00000904007, ENST00000904008, ENST00000904009, ENST00000922416, ENST00000922417, ENST00000922418, ENST00000942956, ENST00000942957

RefSeq mRNA: 3 — MANE Select: NM_203314 NM_004051, NM_203314, NM_203315

CCDS: CCDS3328

Canonical transcript exons

ENST00000392379 — 8 exons

Exon	Start	End
ENSE00001511624	197554562	197554713
ENSE00003529729	197514264	197514416
ENSE00003531632	197522640	197522781
ENSE00003555828	197533489	197533561
ENSE00003633643	197546361	197546486
ENSE00003646322	197532412	197532522
ENSE00003841770	197555781	197555968
ENSE00003889211	197509783	197512364

Expression profiles

Bgee: expression breadth ubiquitous, 134 present calls, max score 98.62.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 10.6102 / max 243.3312, expressed in 1481 samples.

FANTOM5 promoters (7 alternative TSS)

Promoter ID	TPM avg	Samples expressed
46441	9.8675	1461
46443	0.3584	22
46440	0.2397	119
46444	0.0569	9
46445	0.0401	9
46442	0.0257	9
46439	0.0218	7

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right lobe of liver	UBERON:0001114	98.62	gold quality
liver	UBERON:0002107	98.20	gold quality
mucosa of transverse colon	UBERON:0004991	97.76	gold quality
cerebellar hemisphere	UBERON:0002245	97.53	gold quality
cerebellar cortex	UBERON:0002129	97.52	gold quality
right hemisphere of cerebellum	UBERON:0014890	97.52	gold quality
cerebellum	UBERON:0002037	97.49	gold quality
rectum	UBERON:0001052	96.61	gold quality
lower esophagus mucosa	UBERON:0035834	96.54	gold quality
esophagus mucosa	UBERON:0002469	94.88	gold quality
duodenum	UBERON:0002114	94.34	gold quality
right frontal lobe	UBERON:0002810	93.96	gold quality
apex of heart	UBERON:0002098	93.69	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	93.69	gold quality
heart left ventricle	UBERON:0002084	93.63	gold quality
nucleus accumbens	UBERON:0001882	93.58	gold quality
Brodmann (1909) area 9	UBERON:0013540	93.32	gold quality
transverse colon	UBERON:0001157	93.19	gold quality
primary visual cortex	UBERON:0002436	93.07	gold quality
superior frontal gyrus	UBERON:0002661	93.06	gold quality
frontal cortex	UBERON:0001870	92.99	gold quality
caudate nucleus	UBERON:0001873	92.88	gold quality
skin of leg	UBERON:0001511	92.81	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	92.78	gold quality
small intestine Peyer’s patch	UBERON:0003454	92.42	gold quality
right uterine tube	UBERON:0001302	92.38	gold quality
prefrontal cortex	UBERON:0000451	92.33	gold quality
zone of skin	UBERON:0000014	92.32	gold quality
putamen	UBERON:0001874	92.19	gold quality
small intestine	UBERON:0002108	92.19	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	7.86
E-GEOD-125970	no	140.15

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): E2F1

miRNA regulators (miRDB)

39 targeting BDH1, 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-6867-5P	100.00	82.21	3464
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-493-5P	99.96	72.47	2382
HSA-MIR-548AA	99.96	70.64	3753
HSA-MIR-548AP-3P	99.96	70.64	3753
HSA-MIR-548T-3P	99.96	70.64	3753
HSA-MIR-4493	99.90	66.48	977
HSA-MIR-9902	99.89	69.15	2250
HSA-MIR-605-3P	99.88	69.22	1833
HSA-MIR-4319	99.76	69.83	2586
HSA-MIR-6752-3P	99.72	66.71	1587
HSA-MIR-5004-5P	99.68	66.63	1294
HSA-MIR-6892-3P	99.68	66.40	1178
HSA-MIR-519A-3P	99.67	71.67	1868
HSA-MIR-519B-3P	99.67	71.67	1868
HSA-MIR-519C-3P	99.67	71.67	1870
HSA-MIR-3177-5P	99.65	70.38	1174
HSA-MIR-875-3P	99.63	69.47	2548
HSA-MIR-6126	99.62	68.09	996
HSA-MIR-642A-5P	99.51	65.10	1152
HSA-MIR-125A-5P	99.36	70.59	1640
HSA-MIR-125B-5P	99.36	70.36	1662
HSA-MIR-324-3P	99.26	66.31	1034
HSA-MIR-3611	98.76	68.76	1290
HSA-MIR-4763-5P	98.75	63.89	854
HSA-MIR-583	98.71	67.44	1791
HSA-MIR-3650	97.88	64.89	693
HSA-MIR-7154-3P	97.65	65.02	985
HSA-MIR-3173-5P	97.35	65.82	1282
HSA-MIR-6799-3P	97.35	65.60	1302

Literature-anchored findings (GeneRIF, showing 4)

• Data show that the ketone body metabolizing enzymes BDH1, BDH2, OXCT1 and ACAT1 were expressed at the mRNA and protein level in all glioma cell lines. (PMID:21791085)
• MTA2 triggered R-loop trans-regulates BDH1-mediated beta-hydroxybutyrylation and potentiates propagation of hepatocellular carcinoma stem cells. (PMID:33795651)
• Expression and clinical significance of BDH1 in liver cancer. (PMID:35049211)
• D-beta-Hydroxybutyrate Dehydrogenase Mitigates Diabetes-Induced Atherosclerosis through the Activation of Nrf2. (PMID:37399841)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	bdh1	ENSDARG00000059388
mus_musculus	Bdh1	ENSMUSG00000046598
rattus_norvegicus	Bdh1	ENSRNOG00000001736

Paralogs (25): HSD17B6 (ENSG00000025423), RDH11 (ENSG00000072042), HSD17B10 (ENSG00000072506), DHRS9 (ENSG00000073737), HSD17B2 (ENSG00000086696), HSD17B14 (ENSG00000087076), DHRS12 (ENSG00000102796), HSDL1 (ENSG00000103160), HSD17B1 (ENSG00000108786), RDH10 (ENSG00000121039), HSD17B3 (ENSG00000130948), HSD17B7 (ENSG00000132196), HSD17B4 (ENSG00000133835), RDH5 (ENSG00000135437), RDH16 (ENSG00000139547), RDH12 (ENSG00000139988), HSD17B12 (ENSG00000149084), DHRS3 (ENSG00000162496), SDR9C7 (ENSG00000170426), HSD17B13 (ENSG00000170509), SDR16C5 (ENSG00000170786), HSD11B2 (ENSG00000176387), WWOX (ENSG00000186153), HSD17B11 (ENSG00000198189), HSD17B8 (ENSG00000204228)

Protein

Protein identifiers

D-beta-hydroxybutyrate dehydrogenase, mitochondrial — Q02338 (reviewed: Q02338)

Alternative names: 3-hydroxybutyrate dehydrogenase, Short chain dehydrogenase/reductase family 9C member 1

All UniProt accessions (10): A0A384MTY4, A0A494C1C0, C9JB83, C9JEB9, C9JM78, C9JQ90, C9K0G7, E9PCG9, H7C2W1, Q02338

UniProt curated annotations — full annotation on UniProt →

Subunit / interactions. Homotetramer.

Subcellular location. Mitochondrion inner membrane. Mitochondrion matrix.

Activity regulation. Requires phosphatidylcholine as an allosteric activator for enzymatic activity.

Similarity. Belongs to the short-chain dehydrogenases/reductases (SDR) family.

RefSeq proteins (3): NP_004042, NP_976059, NP_976060 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR002347	SDR_fam	Family
IPR020904	Sc_DH/Rdtase_CS	Conserved_site
IPR036291	NAD(P)-bd_dom_sf	Homologous_superfamily

Pfam: PF00106

Catalyzed reactions (Rhea), 1 shown:

• (R)-3-hydroxybutanoate + NAD(+) = acetoacetate + NADH + H(+) (RHEA:20521)

UniProt features (19 total): modified residue 10, sequence conflict 3, binding site 2, transit peptide 1, chain 1, glycosylation site 1, active site 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q02338-F1	87.23	0.78

Functional residue map

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

Catalytic / active sites (1): 208 (proton acceptor)

Ligand- & substrate-binding residues (2): 59–83; 195

Post-translational modifications (10): 246, 258, 259, 259, 280, 73, 97, 132, 177, 212

Glycosylation sites (1): 219

Function

Pathways and Gene Ontology

Reactome pathways

7 pathways

ID	Pathway
R-HSA-77108	Utilization of Ketone Bodies
R-HSA-77111	Synthesis of Ketone Bodies
R-HSA-9837999	Mitochondrial protein degradation
R-HSA-1430728	Metabolism
R-HSA-392499	Metabolism of proteins
R-HSA-556833	Metabolism of lipids
R-HSA-74182	Ketone body metabolism

MSigDB gene sets: 255 (showing top): BUYTAERT_PHOTODYNAMIC_THERAPY_STRESS_DN, HNF3ALPHA_Q6, PID_HNF3B_PATHWAY, RIZKI_TUMOR_INVASIVENESS_3D_DN, MODULE_16, GCM_RING1, HOSHIDA_LIVER_CANCER_SUBCLASS_S3, HSIAO_LIVER_SPECIFIC_GENES, FOXJ2_01, SCHAEFFER_PROSTATE_DEVELOPMENT_48HR_UP, GOCC_MITOCHONDRIAL_ENVELOPE, GOBP_LIPID_METABOLIC_PROCESS, HFH1_01, MODULE_88, GOMF_OXIDOREDUCTASE_ACTIVITY_ACTING_ON_CH_OH_GROUP_OF_DONORS

GO Biological Process (2): steroid metabolic process (GO:0008202), lipid metabolic process (GO:0006629)

GO Molecular Function (4): 3-hydroxybutyrate dehydrogenase activity (GO:0003858), catalytic activity (GO:0003824), oxidoreductase activity (GO:0016491), oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor (GO:0016616)

GO Cellular Component (5): mitochondrion (GO:0005739), mitochondrial matrix (GO:0005759), matrix side of mitochondrial inner membrane (GO:0099617), mitochondrial inner membrane (GO:0005743), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-4 pathways:

Category	Pathways
Ketone body metabolism	2
Metabolism of proteins	1
Metabolism	1
Metabolism of lipids	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
lipid metabolic process	1
primary metabolic process	1
oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor	1
molecular_function	1
catalytic activity	1
oxidoreductase activity, acting on CH-OH group of donors	1
cytoplasm	1
intracellular membrane-bounded organelle	1
mitochondrion	1
intracellular organelle lumen	1
mitochondrial inner membrane	1
lumenal side of membrane	1
organelle inner membrane	1
mitochondrial membrane	1
cellular anatomical structure	1

Protein interactions and networks

STRING

1172 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
BDH1	OXCT1	P55809	824
BDH1	HMGCL	P35914	745
BDH1	HMGCS2	P54868	741
BDH1	ACAT1	P24752	735
BDH1	BDH2	Q9BUT1	731
BDH1	WDR53	Q7Z5U6	588
BDH1	FBXO45	P0C2W1	560
BDH1	ACAA2	P42765	556
BDH1	OXCT2	Q9BYC2	545
BDH1	HMGCS1	Q01581	538
BDH1	PIGZ	Q86VD9	527
BDH1	ZDHHC19	Q8WVZ1	504
BDH1	NCBP2	P52298	500
BDH1	PCYT1A	P49585	493
BDH1	UBXN7	O94888	460

IntAct

55 interactions, top by confidence:

A	B	Type	Score
LPAR4	POTEF	psi-mi:“MI:0914”(association)	0.530
CD79A	METTL15	psi-mi:“MI:0914”(association)	0.530
APLNR	METTL15	psi-mi:“MI:0914”(association)	0.530
SLC15A1	METTL15	psi-mi:“MI:0914”(association)	0.530
IL13RA2	METTL15	psi-mi:“MI:0914”(association)	0.530
SPACA1	GOLIM4	psi-mi:“MI:0914”(association)	0.530
SLC39A9	B4GALT5	psi-mi:“MI:0914”(association)	0.530
NPTN	TNPO2	psi-mi:“MI:0914”(association)	0.530
ESR1	ESYT2	psi-mi:“MI:0914”(association)	0.350
ERGIC3	TMEM223	psi-mi:“MI:0914”(association)	0.350
GLMP	RTL8C	psi-mi:“MI:0914”(association)	0.350
LAMP2	HSPA12A	psi-mi:“MI:0914”(association)	0.350
SLC18A1	LIMK2	psi-mi:“MI:0914”(association)	0.350
TNF	NRP1	psi-mi:“MI:0914”(association)	0.350
COQ9	NDUFS8	psi-mi:“MI:0914”(association)	0.350
ELK1	TPP1	psi-mi:“MI:0914”(association)	0.350
ELK1	PPP6C	psi-mi:“MI:0914”(association)	0.350
ATG16L1	ESYT2	psi-mi:“MI:0914”(association)	0.350
ATG16L1		psi-mi:“MI:0914”(association)	0.350
MGARP	BTAF1	psi-mi:“MI:0914”(association)	0.350
HCST	TMEM120B	psi-mi:“MI:0914”(association)	0.350
P2RY10	POTEF	psi-mi:“MI:0914”(association)	0.350
CD80	POTEF	psi-mi:“MI:0914”(association)	0.350

BioGRID (70): BDH1 (Affinity Capture-MS), BDH1 (Affinity Capture-MS), BDH1 (Affinity Capture-MS), BDH1 (Affinity Capture-MS), BDH1 (Affinity Capture-MS), BDH1 (Affinity Capture-MS), BDH1 (Affinity Capture-MS), BDH1 (Affinity Capture-MS), BDH1 (Affinity Capture-MS), BDH1 (Affinity Capture-MS), BDH1 (Affinity Capture-MS), BDH1 (Affinity Capture-MS), BDH1 (Affinity Capture-MS), BDH1 (Affinity Capture-MS), BDH1 (Affinity Capture-MS)

ESM2 similar proteins: A0A059TC02, A0A072VDF2, A0A0B6VQ48, A0A1Y0BRF3, A0AAW1NHX6, A4UHT7, B2X050, D7U6G6, G3XMB9, G7IYC1, G7JEE5, I3PLR3, O22133, O94563, P14720, P29147, P51102, P51103, P51104, P51105, P51106, P51107, P51108, P51109, P51110, P53111, P53183, Q02337, Q02338, Q03049, Q071N0, Q40316, Q500U8, Q5FB34, Q5XLY0, Q67ZE1, Q6K9A2, Q6QA32, Q6WAU1, Q7PCC4

Diamond homologs: A0A017SE81, A0A0E3D8L9, A0A0U1LQE2, A0A140JWS5, A0A2G0QDN4, A0A3R5XUE6, A0A5B8YU68, A0A8F5XX49, A7LB60, D2WKD9, F1QLP1, G4N286, G9N4A9, N4WE73, O05730, O14756, O16881, O54753, O55240, O67610, O74628, O75452, P0A2D1, P0A2D2, P0AFP4, P0AFP5, P0CU71, P0DKC5, P0DKC6, P15047, P16152, P25970, P29147, P37059, P37959, P39577, P40471, P50170, P54554, P66778

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	32
Likely pathogenic	2
Uncertain significance	74
Likely benign	9
Benign	10

Top pathogenic / likely-pathogenic (30)

Variant ID	HGVS	Classification
148016	GRCh38/hg38 3q29(chr3:195711798-198110178)x3	Pathogenic
148628	GRCh38/hg38 3q29(chr3:195974291-197597912)x1	Pathogenic
149576	GRCh38/hg38 3q29(chr3:196013531-197590232)x1	Pathogenic
149940	GRCh38/hg38 3q29(chr3:195955711-197597912)x1	Pathogenic
152467	GRCh38/hg38 3q29(chr3:196013486-197612399)x1	Pathogenic
153972	GRCh38/hg38 3q29(chr3:195976744-197629463)x1	Pathogenic
154986	GRCh38/hg38 3q29(chr3:196013486-197597912)x1	Pathogenic
160885	GRCh38/hg38 3q29(chr3:196013486-197590232)x1	Pathogenic
160933	GRCh38/hg38 3q29(chr3:196013486-197590232)x3	Pathogenic
1703655	GRCh37/hg19 3q29(chr3:195703615-197386180)	Pathogenic
1808666	GRCh37/hg19 3q29(chr3:195690228-197356334)x1	Pathogenic
2499658	GRCh38/hg38 3q29(chr3:195950438-197629463)	Pathogenic
253577	GRCh37/hg19 3q29(chr3:195690241-197299811)x1	Pathogenic
2685951	GRCh37/hg19 3q29(chr3:196190723-197605588)x3	Pathogenic
3148878	GRCh37/hg19 3q29(chr3:195739427-197340833)x1	Pathogenic
34369	GRCh38/hg38 3q29(chr3:196013486-197590232)x1	Pathogenic
394253	GRCh37/hg19 3q29(chr3:195780280-197299752)x1	Pathogenic
4082236	Single allele	Pathogenic
4277371	Single allele	Pathogenic
443234	GRCh37/hg19 3q29(chr3:195725290-197344176)x1	Pathogenic
443988	GRCh37/hg19 3q29(chr3:195690227-197356334)x1	Pathogenic
545294	NC_000003.12:g.(?195990063)(197617301_?)del	Pathogenic
562865	GRCh37/hg19 3q29(chr3:195703615-197356334)x3	Pathogenic
562867	GRCh37/hg19 3q29(chr3:195725290-197339848)x3	Pathogenic
562868	GRCh37/hg19 3q29(chr3:195725290-197356334)x3	Pathogenic
59289	GRCh38/hg38 3q29(chr3:196035777-197625573)x1	Pathogenic
59981	GRCh38/hg38 3q29(chr3:195755702-197583580)x3	Pathogenic
59982	GRCh38/hg38 3q29(chr3:195965316-197625573)x3	Pathogenic
59983	GRCh38/hg38 3q29(chr3:195972720-197658495)x3	Pathogenic
59984	GRCh38/hg38 3q29(chr3:195997494-197662231)x3	Pathogenic

SpliceAI

1525 predictions. Top by Δscore:

Variant	Effect	Δscore
3:197514412:CATGC:C	acceptor_gain	1.0000
3:197514417:C:CC	acceptor_gain	1.0000
3:197522634:CCCTA:C	donor_loss	1.0000
3:197522635:CCTAC:C	donor_loss	1.0000
3:197522636:CTA:C	donor_loss	1.0000
3:197522637:TA:T	donor_loss	1.0000
3:197522639:CCTTT:C	donor_gain	1.0000
3:197533559:CGT:C	acceptor_gain	1.0000
3:197533562:C:CC	acceptor_gain	1.0000
3:197512361:CGGC:C	acceptor_gain	0.9900
3:197512362:GGC:G	acceptor_gain	0.9900
3:197512364:CCTAC:C	acceptor_loss	0.9900
3:197512365:C:CC	acceptor_gain	0.9900
3:197514413:ATGC:A	acceptor_gain	0.9900
3:197514414:TGC:T	acceptor_gain	0.9900
3:197514415:GC:G	acceptor_gain	0.9900
3:197514416:CC:C	acceptor_gain	0.9900
3:197514416:CCTG:C	acceptor_loss	0.9900
3:197514417:C:CG	acceptor_loss	0.9900
3:197514422:C:CT	acceptor_gain	0.9900
3:197514423:A:T	acceptor_gain	0.9900
3:197522781:CCTGG:C	acceptor_loss	0.9900
3:197522782:CTGG:C	acceptor_loss	0.9900
3:197522783:T:A	acceptor_loss	0.9900
3:197533484:C:CG	donor_loss	0.9900
3:197533485:TCA:T	donor_loss	0.9900
3:197533486:C:CG	donor_loss	0.9900
3:197533487:A:AC	donor_gain	0.9900
3:197533488:C:CC	donor_gain	0.9900
3:197533488:CCGG:C	donor_gain	0.9900

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000039835 (3:197536143 T>C), RS1000070049 (3:197561177 C>A), RS1000115054 (3:197529871 T>C), RS1000123170 (3:197541043 T>A), RS1000204530 (3:197561406 C>T), RS1000239337 (3:197563487 G>C), RS1000264423 (3:197530571 C>T), RS1000294557 (3:197519613 G>A), RS1000300397 (3:197524474 C>T), RS1000321838 (3:197566839 T>A), RS1000324114 (3:197530419 T>C), RS1000327807 (3:197524777 A>G), RS1000375964 (3:197535928 C>T), RS1000419003 (3:197557386 A>G), RS1000427321 (3:197516800 T>C)

Disease associations

OMIM: gene MIM:603063 | disease phenotypes: MIM:609425, MIM:612528, MIM:209850, MIM:181500

GenCC curated gene-disease

Disease	Classification	Inheritance
neurodevelopmental disorder	Limited	Autosomal recessive

Mondo (5): chromosome 3q29 microdeletion syndrome (MONDO:0012269), Diamond-Blackfan anemia 5 (MONDO:0012925), autism (MONDO:0005260), schizophrenia (MONDO:0005090), neurodevelopmental disorder (MONDO:0700092)

Orphanet (3): 3q29 microdeletion syndrome (Orphanet:65286), Diamond-Blackfan anemia (Orphanet:124), NON RARE IN EUROPE: Schizophrenia (Orphanet:3140)

HPO phenotypes

2 total (2 of 2 shown, HPO-id order):

HPO	Term
HP:0000717	Autism
HP:0100753	Schizophrenia

GWAS associations

3 associations (top):

Study	Trait	p-value
GCST004253_6	Accelerated cognitive decline after conversion of mild cognitive impairment to Alzheimer’s disease (Alzhiemer’s diagnosis trajectory interaction)	3.000000e-06
GCST006148_7	Frontotemporal dementia with GRN mutation	1.000000e-06
GCST008155_76	Waist-hip ratio	5.000000e-06

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0007710	cognitive decline measurement
EFO:0004343	waist-hip ratio

MeSH disease descriptors (4)

Descriptor	Name	Tree numbers
D001321	Autistic Disorder	F03.625.164.113.500
D065886	Neurodevelopmental Disorders	F03.625
C567184	Chromosome 3q29 Deletion Syndrome (supp.)
C567280	Diamond-Blackfan Anemia 5 (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	decreases expression, increases abundance, increases expression	5
Cyclosporine	decreases expression	4
(+)-JQ1 compound	decreases expression	3
Benzo(a)pyrene	affects methylation, decreases expression, increases methylation	3
entinostat	increases expression, affects cotreatment	2
Acetaminophen	decreases expression	2
Fluorouracil	decreases expression	2
Tetrachlorodibenzodioxin	decreases reaction, affects cotreatment, decreases expression	2
Valproic Acid	decreases methylation, affects expression, decreases expression	2
Aflatoxin B1	affects expression, decreases expression	2
Cadmium Chloride	decreases expression, increases abundance, increases expression	2
aristolochic acid I	decreases expression	1
bufotalin	decreases expression	1
lasiocarpine	decreases expression	1
methyleugenol	decreases expression	1
bisphenol A	affects cotreatment, decreases methylation	1
tris(2-butoxyethyl) phosphate	affects expression	1
beta-lapachone	increases expression	1
butyraldehyde	decreases expression	1
zinc chromate	decreases expression, increases abundance	1
benzo(e)pyrene	increases methylation	1
nickel sulfate	decreases expression	1
ciglitazone	affects binding, increases expression	1
phenethyl isothiocyanate	decreases expression	1
chromium hexavalent ion	decreases expression, increases abundance	1
CGP 52608	affects binding, increases reaction	1
perfluoro-n-nonanoic acid	decreases expression	1
2-palmitoylglycerol	increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	1
abrine	decreases expression	1

Cellosaurus cell lines

2 cell lines: 1 transformed cell line, 1 cancer cell line

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

Cellosaurus	Name	Category	Sex
CVCL_D9A3	Ubigene HEK293 BDH1 KO	Transformed cell line	Female
CVCL_E1S3	HAP1 BDH1 (-)	Cancer cell line	Male

Clinical trials (associated diseases)

498 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,
NCT00211796	PHASE4	COMPLETED	Divalproex Sodium ER in Adult Autism
NCT00391261	PHASE4	COMPLETED	An Open-label Trial of Metformin for Weight Control of Pediatric Patients on Antipsychotic Medications.
NCT00409747	PHASE4	COMPLETED	Minocycline to Treat Childhood Regressive Autism
NCT00576732	PHASE4	COMPLETED	A Study of the Effectiveness and Safety of Two Doses of Risperidone in the Treatment of Children and Adolescents With Autistic Disorder
NCT00844753	PHASE4	COMPLETED	Atomoxetine, Placebo and Parent Management Training in Autism
NCT01028820	PHASE4	COMPLETED	FMRI Brain Activation of Aripiprazole Treatment in Autism Spectrum Disorders
NCT01098383	PHASE4	UNKNOWN	Treatment With Acetyl-Choline Esterase Inhibitors in Children With Autism Spectrum Disorders
NCT01333865	PHASE4	COMPLETED	A Study of Memantine Hydrochloride (Namenda®) for Cognitive and Behavioral Impairment in Adults With Autism Spectrum Disorders
NCT01337700	PHASE4	COMPLETED	Milnacipran in Autism and the Functional Locus Coeruleus and Noradrenergic Model of Autism
NCT01695200	PHASE4	COMPLETED	Omega-3 Fatty Acids in Autism Spectrum Disorders
NCT02069977	PHASE4	UNKNOWN	Study to Evaluate the Efficacy and Safety of Aripiprazole
NCT02096952	PHASE4	COMPLETED	Methylphenidate ER Liquid Formulation in Adults With ASD and ADHD
NCT02199925	PHASE4	UNKNOWN	An Open-Label Study to Evaluate the Efficacy of High-Dose Gammaplex in Children on the Autism Spectrum
NCT02235467	PHASE4	COMPLETED	Multisite Study: Parental Training Using Video Modelling to Develop Social Skills in Children With Autism
NCT02255565	PHASE4	COMPLETED	Dose Response Effects of Quillivant XR in Children With ADHD and Autism: A Pilot Study
NCT02940574	PHASE4	COMPLETED	Neural and Behavioral Effects of Oxytocin in Autism Spectrum Disorders
NCT03333629	PHASE4	COMPLETED	Promoting Positive Outcomes for Individuals With ASD: Linking Early Detection, Treatment, and Long-term Outcomes
NCT03337646	PHASE4	COMPLETED	Evaluation of the Effect and Safety of Lisdexamfetamine in Children Aged 6-12 With ADHD and Autism
NCT03538431	PHASE4	COMPLETED	Improving Driving in Young People With Autism Spectrum Disorders
NCT03757585	PHASE4	COMPLETED	Natural Treatments for the Management of Emotional Dysregulation in Youth With Non-verbal Learning Disability (NVLD) and/or Autism Spectrum Disorders (ASD)
NCT04903353	PHASE4	COMPLETED	Pragmatic Trial Comparing Weight Gain in Children With Autism Taking Risperidone Versus Aripiprazole
NCT05063656	PHASE4	COMPLETED	Biomarker-Driven Pharmacological Treatment of Adolescents With Autism Spectrum Disorder With Gabapentin
NCT05146245	PHASE4	UNKNOWN	Safety and Pharmacokinetics of Antipsychotics in Children 2: Studying TDM in an RCT
NCT05916339	PHASE4	RECRUITING	AWARE: Management of ADHD in Autism Spectrum Disorder
NCT05954052	PHASE4	TERMINATED	A Study of Glutathione in Children With Autism Spectrum Disorder
NCT06853665	PHASE4	RECRUITING	The TEAM Study - Treatment Efficacy for Autism/Attention Using Mixed Amphetamine
NCT07054697	PHASE4	COMPLETED	Pilot-RCT With Individualized Homeopathic Treatment in the Children With Autism Spectrum Disorder
NCT07161804	PHASE4	COMPLETED	Pilot RCT Using Homeopathic Medicines in ASD
NCT07439042	PHASE4	NOT_YET_RECRUITING	Buspirone for Anxiety in Autistic Youth
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
NCT00036231	PHASE3	TERMINATED	Synthetic Human Secretin in Children With Autism and Gastrointestinal Dysfunction
NCT00036244	PHASE3	COMPLETED	Synthetic Human Secretin in Children With Autism
NCT00065884	PHASE3	UNKNOWN	Valproate Response in Aggressive Autistic Adolescents
NCT00065962	PHASE3	COMPLETED	Secretin for the Treatment of Autism
NCT00252603	PHASE3	COMPLETED	Galantamine Versus Placebo in Childhood Autism