LSAMP

Summary

LSAMP (limbic system associated membrane protein, HGNC:6705) is a protein-coding gene on chromosome 3q13.31, encoding Limbic system-associated membrane protein (Q13449). Mediates selective neuronal growth and axon targeting.

This gene encodes a member of the immunoglobulin LAMP, OBCAM and neurotrimin (IgLON) family of proteins. The encoded preproprotein is proteolytically processed to generate a neuronal surface glycoprotein. This protein may act as a selective homophilic adhesion molecule during axon guidance and neuronal growth in the developing limbic system. The encoded protein may also function as a tumor suppressor and may play a role in neuropsychiatric disorders. Alternative splicing results in multiple transcript variants, at least one of which encodes a preproprotein that is proteolytically processed.

Source: NCBI Gene 4045 — RefSeq curated summary.

At a glance

• GWAS associations: 18
• Clinical variants (ClinVar): 44 total
• MANE Select transcript: NM_002338

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:6705
Approved symbol	LSAMP
Name	limbic system associated membrane protein
Location	3q13.31
Locus type	gene with protein product
Status	Approved
Aliases	LAMP, IGLON3
Ensembl gene	ENSG00000185565
Ensembl biotype	protein_coding
OMIM	603241
Entrez	4045

Gene structure

Transcript identifiers

Ensembl transcripts: 7 — 3 protein_coding, 3 protein_coding_CDS_not_defined, 1 retained_intron

ENST00000333617, ENST00000473171, ENST00000474851, ENST00000475403, ENST00000490035, ENST00000498645, ENST00000717962

RefSeq mRNA: 2 — MANE Select: NM_002338 NM_001318915, NM_002338

CCDS: CCDS2982

Canonical transcript exons

ENST00000490035 — 7 exons

Exon	Start	End
ENSE00001296901	116086324	116086556
ENSE00001882134	116444877	116445487
ENSE00001905972	115802374	115810414
ENSE00003511178	115841845	115841993
ENSE00003519070	115842458	115842578
ENSE00003635808	115852483	115852617
ENSE00003789311	116019515	116019640

Expression profiles

Bgee: expression breadth ubiquitous, 216 present calls, max score 98.01.

FANTOM5 (CAGE): breadth broad, TPM avg 8.4301 / max 302.5444, expressed in 655 samples.

FANTOM5 promoters (7 alternative TSS)

Promoter ID	TPM avg	Samples expressed
43943	5.0493	606
43942	2.9492	407
43940	0.1258	61
43929	0.1186	40
43934	0.1015	28
43941	0.0469	17
43930	0.0387	17

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
postcentral gyrus	UBERON:0002581	98.01	gold quality
parietal lobe	UBERON:0001872	97.69	gold quality
entorhinal cortex	UBERON:0002728	97.61	gold quality
Brodmann (1909) area 23	UBERON:0013554	96.80	gold quality
lateral nuclear group of thalamus	UBERON:0002736	96.30	gold quality
superior frontal gyrus	UBERON:0002661	95.92	gold quality
ventral tegmental area	UBERON:0002691	95.90	gold quality
pons	UBERON:0000988	95.53	gold quality
substantia nigra pars compacta	UBERON:0001965	95.34	gold quality
superior vestibular nucleus	UBERON:0007227	95.26	gold quality
primary visual cortex	UBERON:0002436	94.86	gold quality
cerebellar vermis	UBERON:0004720	94.69	gold quality
substantia nigra pars reticulata	UBERON:0001966	94.49	gold quality
middle temporal gyrus	UBERON:0002771	94.49	gold quality
temporal lobe	UBERON:0001871	94.28	gold quality
medial globus pallidus	UBERON:0002477	93.87	gold quality
globus pallidus	UBERON:0001875	93.84	gold quality
occipital lobe	UBERON:0002021	93.74	gold quality
lateral globus pallidus	UBERON:0002476	93.58	gold quality
caudate nucleus	UBERON:0001873	93.50	gold quality
corpus callosum	UBERON:0002336	93.06	gold quality
nucleus accumbens	UBERON:0001882	92.86	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	92.75	gold quality
amygdala	UBERON:0001876	92.62	gold quality
Ammon’s horn	UBERON:0001954	92.51	gold quality
telencephalon	UBERON:0001893	92.32	gold quality
cerebral cortex	UBERON:0000956	91.98	gold quality
anterior cingulate cortex	UBERON:0009835	91.90	gold quality
cingulate cortex	UBERON:0003027	91.88	gold quality
prefrontal cortex	UBERON:0000451	91.74	gold quality

Single-cell (SCXA)

Detected in 11 experiment(s), a significant marker in 10.

Experiment	Marker?	Max mean expression
E-HCAD-35	yes	10396.94
E-HCAD-30	yes	9256.58
E-GEOD-180759	yes	6655.87
E-ANND-2	yes	4929.30
E-GEOD-100618	yes	305.17
E-MTAB-7407	yes	290.56
E-HCAD-25	yes	21.31
E-HCAD-5	yes	16.03
E-MTAB-7316	yes	14.93
E-ANND-3	yes	8.44
E-MTAB-6108	no	192.81

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

351 targeting LSAMP, 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-6873-3P	100.00	71.42	2626
HSA-MIR-7110-3P	100.00	73.18	2486
HSA-MIR-6833-3P	100.00	70.63	3197
HSA-MIR-4768-5P	100.00	69.49	2861
HSA-MIR-8485	100.00	77.57	4731
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-656-3P	100.00	72.15	2788
HSA-MIR-1252-5P	100.00	69.80	2774
HSA-MIR-6867-5P	100.00	82.21	3464
HSA-MIR-4476	100.00	68.18	2030
HSA-MIR-6876-5P	100.00	67.68	2126
HSA-MIR-6127	100.00	66.76	2188
HSA-MIR-4510	100.00	66.60	2050
HSA-MIR-4533	100.00	69.48	2758
HSA-MIR-4283	100.00	66.42	2097
HSA-MIR-6129	100.00	66.46	2080
HSA-MIR-6130	100.00	66.69	2012
HSA-MIR-6133	100.00	66.48	2064
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-4795-3P	100.00	74.62	4024
HSA-MIR-3120-5P	100.00	65.56	965
HSA-MIR-126-5P	100.00	72.71	3180
HSA-MIR-4668-3P	100.00	68.74	2635
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-6748-5P	100.00	65.81	1057
HSA-MIR-5692B	100.00	71.32	2622
HSA-MIR-5692C	100.00	71.32	2622
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-4262	100.00	73.26	3931

Literature-anchored findings (GeneRIF, showing 12)

• proteomic assessments of membrane microdomains in prefrontal cortex and validation in two brain series, strongly implicates LAMP, STXBP1 and BASP1 in schizophreina and supports the view of a neuritic and synaptic dysfunction in the neuropathology (PMID:18268500)
• Single nucleotide polymorphisms of LSAMP is associated with the pathogenesis of coronary artery disease. (PMID:18318786)
• LSAMP might play a role in pathoaetiology of suicidal behaviour but further studies are needed to understand its exact contribution (PMID:18433483)
• results show that LSAMP is a novel candidate tumor suppressor gene in osteosarcomas (PMID:19441093)
• Identification of chromosomal aberrations associated with disease progression and a novel 3q13.31 deletion involving LSAMP gene in osteosarcoma. (PMID:19724913)
• This study presents the first evidence of a possible role of LSAMP gene in mood and anxiety disorders in humans. (PMID:22892717)
• The results showed significant allelic and haplotypic associations between LSAMP gene and schizophrenia. (PMID:24491686)
• The tumor suppressor function of LSAMP is most likely exerted by reducing the proliferation rate of the tumor cells, possibly by indirectly upregulating one or more of the genes HES1, CTAG2 or KLF10. (PMID:24885297)
• A novel genomic alteration of LSAMP associates with aggressive prostate cancer in African American men (PMID:26844274)
• We detected African-specific SNPs at ZNF649 and LSAMP, with associations of genome-wide significance for ulcerative colitis. (PMID:27693347)
• Limbic System Associated Membrane Protein Mutation in an Iranian Family Diagnosed with Meniere’s Disease. (PMID:32383616)
• Identification of recurrent 3q13.31 chromosomal rearrangement indicates LSAMP as a tumor suppressor gene in neuroblastoma. (PMID:36601748)

Cross-species orthologs

16 orthologs

Organism	Symbol	Gene ID
danio_rerio		ENSDARG00000103069
mus_musculus	Lsamp	ENSMUSG00000061080
rattus_norvegicus	Lsamp	ENSRNOG00000031852
drosophila_melanogaster	Ama	FBGN0000071
drosophila_melanogaster	Lac	FBGN0010238
drosophila_melanogaster	klg	FBGN0017590
drosophila_melanogaster	fipi	FBGN0031627
drosophila_melanogaster	DIP-eta	FBGN0031725
drosophila_melanogaster	DIP-iota	FBGN0031837
drosophila_melanogaster	CG13506	FBGN0034723
drosophila_melanogaster	DIP-zeta	FBGN0051708
drosophila_melanogaster	DIP-kappa	FBGN0051814
drosophila_melanogaster	CG33543	FBGN0053543
drosophila_melanogaster	DIP-beta	FBGN0259245
drosophila_melanogaster	DIP-epsilon	FBGN0259714
caenorhabditis_elegans	rig-5	WBGENE00004372

Paralogs (5): IGLON5 (ENSG00000142549), NEGR1 (ENSG00000172260), NTM (ENSG00000182667), IGSF5 (ENSG00000183067), OPCML (ENSG00000183715)

Protein

Protein identifiers

Limbic system-associated membrane protein — Q13449 (reviewed: Q13449)

Alternative names: IgLON family member 3

All UniProt accessions (3): Q13449, C9J5G3, H3BLU2

UniProt curated annotations — full annotation on UniProt →

Function. Mediates selective neuronal growth and axon targeting. Contributes to the guidance of developing axons and remodeling of mature circuits in the limbic system. Essential for normal growth of the hippocampal mossy fiber projection.

Subcellular location. Cell membrane.

Tissue specificity. Expressed on limbic neurons and fiber tracts as well as in single layers of the superior colliculus, spinal cord and cerebellum.

Similarity. Belongs to the immunoglobulin superfamily. IgLON family.

RefSeq proteins (2): NP_001305844, NP_002329* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR003598	Ig_sub2	Domain
IPR003599	Ig_sub	Domain
IPR007110	Ig-like_dom	Domain
IPR013098	Ig_I-set	Domain
IPR013783	Ig-like_fold	Homologous_superfamily
IPR036179	Ig-like_dom_sf	Homologous_superfamily
IPR050876	IgLON_domain	Family

Pfam: PF07679, PF13927

UniProt features (22 total): glycosylation site 8, disulfide bond 3, domain 3, sequence conflict 2, signal peptide 1, chain 1, sequence variant 1, propeptide 1, modified residue 1, lipid moiety-binding region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q13449-F1	83.76	0.70

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 (2): 94, 315

Disulfide bonds (3): 53–111, 153–197, 239–290

Glycosylation sites (8): 136, 148, 279, 287, 300, 315, 40, 66

Function

Pathways and Gene Ontology

Reactome pathways

3 pathways

ID	Pathway
R-HSA-163125	Post-translational modification: synthesis of GPI-anchored proteins
R-HSA-392499	Metabolism of proteins
R-HSA-597592	Post-translational protein modification

MSigDB gene sets: 205 (showing top): GOBP_HETEROPHILIC_CELL_CELL_ADHESION, GOBP_SYNAPSE_ASSEMBLY, GOBP_REGULATION_OF_CELL_JUNCTION_ASSEMBLY, GOBP_REGULATION_OF_CELLULAR_COMPONENT_BIOGENESIS, CHANDRAN_METASTASIS_DN, GOBP_CELL_CELL_ADHESION, GOBP_CELL_JUNCTION_ORGANIZATION, GOBP_REGULATION_OF_SYNAPSE_ASSEMBLY, GATA6_01, GATA1_01, GRE_C, GOBP_REGULATION_OF_SYNAPSE_STRUCTURE_OR_ACTIVITY, RICKMAN_HEAD_AND_NECK_CANCER_A, AACTTT_UNKNOWN, GOBP_CELL_JUNCTION_ASSEMBLY

GO Biological Process (2): cell adhesion (GO:0007155), nervous system development (GO:0007399)

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (5): extracellular region (GO:0005576), cytosol (GO:0005829), plasma membrane (GO:0005886), side of membrane (GO:0098552), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-2 pathways:

Category	Pathways
Post-translational protein modification	1
Metabolism of proteins	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	4
membrane	2
cellular process	1
system development	1
binding	1
cytoplasm	1
cell periphery	1
leaflet of membrane bilayer	1

Protein interactions and networks

STRING

1592 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
LSAMP	VSTM4	Q8IW00	497
LSAMP	PRNP	P04156	463
LSAMP	NTMT2	Q5VVY1	428
LSAMP	CAMKV	Q8NCB2	427
LSAMP	LGALS12	Q96DT0	420
LSAMP	SLC1A3	P43003	416
LSAMP	SYP	P08247	397
LSAMP	NPAS3	Q8IXF0	393
LSAMP	ZNF649	Q9BS31	392
LSAMP	THY1	P04216	388
LSAMP	CDH9	Q9ULB4	365
LSAMP	DIRC1	Q969H9	357
LSAMP	NTS	P30990	353
LSAMP	NRCAM	Q92823	345
LSAMP	NTMT1	Q9BV86	343

IntAct

69 interactions, top by confidence:

A	B	Type	Score
ELK3	LSAMP	psi-mi:“MI:0915”(physical association)	0.560
PCDHGC3	LSAMP	psi-mi:“MI:0915”(physical association)	0.560
SMARCD1	LSAMP	psi-mi:“MI:0915”(physical association)	0.560
STAM	LSAMP	psi-mi:“MI:0915”(physical association)	0.560
LSAMP	BECN1	psi-mi:“MI:0915”(physical association)	0.560
MED21	LSAMP	psi-mi:“MI:0915”(physical association)	0.560
DELE1	LSAMP	psi-mi:“MI:0915”(physical association)	0.560
ITGB3BP	LSAMP	psi-mi:“MI:0915”(physical association)	0.560
	LSAMP	psi-mi:“MI:0915”(physical association)	0.560
CD248	LSAMP	psi-mi:“MI:0915”(physical association)	0.560
LRRC61	LSAMP	psi-mi:“MI:0915”(physical association)	0.560
LSAMP	THAP3	psi-mi:“MI:0915”(physical association)	0.560
PLB1	LSAMP	psi-mi:“MI:0915”(physical association)	0.560
LSAMP	METTL27	psi-mi:“MI:0915”(physical association)	0.560
LSAMP	CENPV	psi-mi:“MI:0915”(physical association)	0.560
H3-5	LSAMP	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (17): LSAMP (Affinity Capture-MS), LSAMP (Affinity Capture-MS), LSAMP (Affinity Capture-MS), LSAMP (Affinity Capture-MS), LSAMP (Affinity Capture-MS), LSAMP (Affinity Capture-MS), LSAMP (Affinity Capture-MS), LSAMP (Affinity Capture-MS), LSAMP (Affinity Capture-MS), SPCS3 (Co-fractionation), LSAMP (Affinity Capture-MS), LSAMP (Affinity Capture-MS), LSAMP (Reconstituted Complex), NTM (Reconstituted Complex), LSAMP (Reconstituted Complex)

ESM2 similar proteins: A4IFA6, A6NGN9, B1AUH1, B3N666, B4Q599, O09127, O73791, P00545, P07333, P11834, P13369, P29322, P32736, P35590, P35916, P35917, Q06805, Q06806, Q13308, Q13449, Q14982, Q2EY13, Q2EY14, Q2EY15, Q2VWP9, Q58DA5, Q5IS61, Q5JZY3, Q5R412, Q62718, Q62813, Q6GU68, Q7Z3B1, Q80Z24, Q8BKG3, Q8BLK3, Q8BYG9, Q8HW98, Q8TDY8, Q90773

Diamond homologs: A0A087WV53, A1KZ92, A2AJ76, A4IFW2, A4IGL7, A6NDA9, B0BNK7, B0V2N1, D2HFT7, D3YXG0, D4A1J9, D4ABX8, F1NWE3, G5EG78, O15146, O73775, O75325, O94898, P07722, P15364, P20916, P20917, P23468, P43146, P48960, P53813, P70193, P70211, Q03142, Q08761, Q08879, Q13332, Q13449, Q1ENI8, Q1RMS4, Q1WIM1, Q21038, Q24372, Q26474, Q2Q421

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	40
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

4608 predictions. Top by Δscore:

Variant	Effect	Δscore
3:115841837:ATAC:A	donor_loss	1.0000
3:115841838:TACT:T	donor_loss	1.0000
3:115841839:ACTT:A	donor_loss	1.0000
3:115841840:CTTA:C	donor_gain	1.0000
3:115841841:TTAC:T	donor_loss	1.0000
3:115841842:TACTG:T	donor_loss	1.0000
3:115841843:A:AC	donor_gain	1.0000
3:115841844:C:CG	donor_gain	1.0000
3:115841844:CT:C	donor_gain	1.0000
3:115841844:CTG:C	donor_gain	1.0000
3:115841844:CTGA:C	donor_gain	1.0000
3:115841844:CTGAA:C	donor_gain	1.0000
3:115841989:TTATC:T	acceptor_gain	1.0000
3:115841990:TATC:T	acceptor_gain	1.0000
3:115841992:TC:T	acceptor_gain	1.0000
3:115841992:TCC:T	acceptor_loss	1.0000
3:115841993:CC:C	acceptor_gain	1.0000
3:115841993:CCT:C	acceptor_loss	1.0000
3:115841994:C:CC	acceptor_gain	1.0000
3:115842000:G:GC	acceptor_gain	1.0000
3:115842003:C:CT	acceptor_gain	1.0000
3:115842004:A:T	acceptor_gain	1.0000
3:115842453:CATA:C	donor_loss	1.0000
3:115842454:ATAC:A	donor_loss	1.0000
3:115842456:A:AC	donor_gain	1.0000
3:115842456:A:AT	donor_loss	1.0000
3:115842457:C:CC	donor_gain	1.0000
3:115842457:C:CG	donor_loss	1.0000
3:115842575:GGAT:G	acceptor_gain	1.0000
3:115842576:GATC:G	acceptor_loss	1.0000

AlphaMissense

2172 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
3:115842475:C:A	W251C	1.000
3:115842475:C:G	W251C	1.000
3:115842477:A:G	W251R	1.000
3:115842477:A:T	W251R	1.000
3:116019534:C:A	W165C	1.000
3:116019534:C:G	W165C	1.000
3:115841882:G:C	N294K	0.999
3:115841882:G:T	N294K	0.999
3:115841940:A:G	L275P	0.999
3:115852542:C:G	C197S	0.999
3:115852543:A:T	C197S	0.999
3:115852548:T:C	Y195C	0.999
3:115852549:A:C	Y195D	0.999
3:116019535:C:G	W165S	0.999
3:116019536:A:G	W165R	0.999
3:116019536:A:T	W165R	0.999
3:116019570:G:C	C153W	0.999
3:116019572:A:G	C153R	0.999
3:116019577:A:G	L151P	0.999
3:116086335:A:G	L126S	0.999
3:116086380:C:G	C111S	0.999
3:116086381:A:G	C111R	0.999
3:116086381:A:T	C111S	0.999
3:116086387:A:C	Y109D	0.999
3:116086398:T:A	D105V	0.999
3:116086425:A:G	L96P	0.999
3:116086520:C:A	W64C	0.999
3:116086520:C:G	W64C	0.999
3:116086522:A:G	W64R	0.999
3:116086522:A:T	W64R	0.999

dbSNP variants (sampled 300 via entrez): RS1000008790 (3:115941653 T>C), RS1000010352 (3:116359527 T>C), RS1000017130 (3:116118246 T>C), RS1000020803 (3:115825371 G>C), RS1000023525 (3:116202454 C>A,T), RS1000025165 (3:116250575 A>G,T), RS1000027105 (3:115964759 G>A), RS1000033792 (3:116118513 T>C), RS1000035760 (3:115844158 T>C,G), RS1000036336 (3:116420653 T>C), RS1000046897 (3:115856445 C>G), RS1000047041 (3:116219013 C>T), RS1000048257 (3:116227385 C>T), RS1000052679 (3:115897979 C>A,T), RS1000055674 (3:116290998 T>G)

Disease associations

OMIM: gene MIM:603241 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

18 associations (top):

Study	Trait	p-value
GCST002682_5	Tourette’s syndrome or obsessive-compulsive disorder	2.000000e-06
GCST002945_7	Emphysema imaging phenotypes	9.000000e-07
GCST003208_13	Colorectal or endometrial cancer	4.000000e-07
GCST004865_71	Itch intensity from mosquito bite adjusted by bite size	9.000000e-07
GCST006585_50	Blood protein levels	1.000000e-12
GCST006943_35	Feeling miserable	6.000000e-09
GCST006944_36	Experiencing mood swings	2.000000e-08
GCST007576_329	Chronotype	2.000000e-10
GCST007576_383	Chronotype	2.000000e-10
GCST007709_15	General factor of neuroticism	3.000000e-08
GCST008162_49	Hip circumference	6.000000e-06
GCST008887_1	Systemising	3.000000e-08
GCST010142_33	Fish- and plant-related diet	7.000000e-09
GCST010396_287	Gut microbiota (bacterial taxa, hurdle binary method)	3.000000e-08
GCST012048_8	Triglyceride levels	1.000000e-06
GCST012326_4	BMI x SSRI defined daily dose interaction in schizophrenia or bipolar disorder	2.000000e-07
GCST012488_37	L1-L4 bone mineral density x serum urate levels interaction	9.000000e-07
GCST90000047_56	Age at first sexual intercourse	5.000000e-08

EFO canonical traits (17, from GWAS)

EFO ID	Trait name
EFO:0007626	emphysema imaging measurement
EFO:0004230	endometrial neoplasm
EFO:0008377	mosquito bite reaction itch intensity measurement
EFO:0008378	mosquito bite reaction size measurement
EFO:0009598	feeling miserable measurement
EFO:0008475	mood instability measurement
EFO:0008328	chronotype measurement
EFO:0007660	neuroticism measurement
EFO:0010221	systemising measurement
EFO:0008111	diet measurement
EFO:0007874	gut microbiome measurement
EFO:0004530	triglyceride measurement
EFO:0004340	body mass index
EFO:0005658	response to selective serotonin reuptake inhibitor
EFO:0004531	urate measurement
EFO:0007701	spine bone mineral density
EFO:0009749	age at first sexual intercourse measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, decreases expression, affects expression	4
mercuric bromide	affects cotreatment, decreases expression	2
entinostat	decreases expression, affects cotreatment	2
Benzo(a)pyrene	affects methylation, decreases methylation, increases methylation	2
Nickel	decreases expression	2
Phenylmercuric Acetate	affects cotreatment, decreases expression	2
Tretinoin	decreases expression, increases expression	2
aristolochic acid I	decreases expression	1
methylmercuric chloride	decreases expression	1
bisphenol A	affects cotreatment, decreases methylation	1
tris(1,3-dichloro-2-propyl)phosphate	increases expression	1
sodium arsenite	affects methylation	1
butyraldehyde	decreases expression	1
benzo(e)pyrene	increases methylation	1
aflatoxin B2	affects methylation	1
CGP 52608	affects binding, increases reaction	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, decreases expression	1
abrine	increases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
bisphenol S	increases methylation	1
(+)-JQ1 compound	decreases expression	1
Dasatinib	increases expression	1
Arsenic Trioxide	decreases expression	1
Fulvestrant	affects cotreatment, decreases methylation	1
Arsenic	affects methylation	1
Daunorubicin	affects response to substance	1
Diethylhexyl Phthalate	decreases expression	1
Doxorubicin	decreases expression	1
Formaldehyde	decreases expression	1

Clinical trials (associated diseases)

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