CLTRN

Summary

CLTRN (collectrin, amino acid transport regulator, HGNC:29437) is a protein-coding gene on chromosome Xp22.2, encoding Collectrin (Q9HBJ8). Plays an important role in amino acid transport by acting as binding partner of amino acid transporters SLC6A18 and SLC6A19, regulating their trafficking on the cell surface and their amino acid transporter activity.

This gene encodes a type 1 transmembrane protein that is important for trafficking amino acid transporters to the apical brush border of proximal tubules. The encoded protein binds to amino acid transporters and regulates their expression on the plasma membrane. It also plays a role in controlling insulin exocytosis by regulating formation of the SNARE (soluble N-ethylmaleimide-sensitive-factor attachment protein receptor) complex in pancreatic beta cells. The extracellular domain of the encoded protein may be cleaved and shed from the plasma membrane specifically in pancreatic beta cells.

Source: NCBI Gene 57393 — RefSeq curated summary.

At a glance

• Gene–disease (curated): Hartnup disease (Supportive, GenCC)
• Clinical variants (ClinVar): 54 total — 2 pathogenic
• Phenotypes (HPO): 30
• MANE Select transcript: NM_020665

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:29437
Approved symbol	CLTRN
Name	collectrin, amino acid transport regulator
Location	Xp22.2
Locus type	gene with protein product
Status	Approved
Aliases	NX17
Ensembl gene	ENSG00000147003
Ensembl biotype	protein_coding
OMIM	300631
Entrez	57393

Gene structure

Transcript identifiers

Ensembl transcripts: 7 — 7 protein_coding

ENST00000380342, ENST00000650271, ENST00000869716, ENST00000869717, ENST00000918250, ENST00000918251, ENST00000953963

RefSeq mRNA: 1 — MANE Select: NM_020665 NM_020665

CCDS: CCDS14170

Canonical transcript exons

ENST00000380342 — 6 exons

Exon	Start	End
ENSE00000978329	15664337	15664395
ENSE00000978331	15644916	15645029
ENSE00000978332	15639562	15639756
ENSE00001202097	15659016	15659101
ENSE00001484603	15627318	15628127
ENSE00001484615	15664718	15664805

Expression profiles

Bgee: expression breadth ubiquitous, 172 present calls, max score 99.71.

FANTOM5 (CAGE): breadth broad, TPM avg 2.1641 / max 926.8794, expressed in 611 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
198542	1.0507	550
198538	0.8020	87
198539	0.2884	45
198541	0.0167	3
198540	0.0064	2

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
kidney epithelium	UBERON:0004819	99.71	gold quality
adult mammalian kidney	UBERON:0000082	97.35	gold quality
pigmented layer of retina	UBERON:0001782	95.35	gold quality
kidney	UBERON:0002113	93.37	gold quality
renal medulla	UBERON:0000362	93.10	gold quality
adult organism	UBERON:0007023	92.13	gold quality
cortex of kidney	UBERON:0001225	90.94	gold quality
metanephros cortex	UBERON:0010533	89.31	gold quality
islet of Langerhans	UBERON:0000006	85.33	gold quality
right lobe of liver	UBERON:0001114	85.10	gold quality
epithelial cell of pancreas	CL:0000083	84.99	silver quality
liver	UBERON:0002107	84.61	gold quality
oocyte	CL:0000023	83.30	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	83.26	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	82.42	gold quality
metanephros	UBERON:0000081	80.31	gold quality
secondary oocyte	CL:0000655	76.70	gold quality
caput epididymis	UBERON:0004358	75.21	gold quality
pancreas	UBERON:0001264	74.60	gold quality
decidua	UBERON:0002450	72.14	gold quality
body of pancreas	UBERON:0001150	71.09	gold quality
gall bladder	UBERON:0002110	70.53	gold quality
amniotic fluid	UBERON:0000173	67.78	gold quality
ventricular zone	UBERON:0003053	66.45	gold quality
body of stomach	UBERON:0001161	66.12	gold quality
oviduct epithelium	UBERON:0004804	65.56	silver quality
left ovary	UBERON:0002119	65.29	gold quality
bronchial epithelial cell	CL:0002328	65.06	gold quality
corpus epididymis	UBERON:0004359	64.82	gold quality
ovary	UBERON:0000992	64.32	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): HNF1B

miRNA regulators (miRDB)

63 targeting CLTRN, 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-3613-3P	100.00	76.36	7965
HSA-MIR-4262	100.00	73.26	3931
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-181A-5P	99.99	72.96	2995
HSA-MIR-181B-5P	99.99	72.97	2996
HSA-MIR-181C-5P	99.99	72.95	2996
HSA-MIR-181D-5P	99.99	73.04	2997
HSA-LET-7F-2-3P	99.98	70.98	2588
HSA-MIR-1185-1-3P	99.98	71.04	2593
HSA-MIR-1185-2-3P	99.98	71.04	2593
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-3065-5P	99.97	71.56	3281
HSA-MIR-551B-5P	99.96	71.28	3493
HSA-MIR-185-3P	99.95	67.01	1743
HSA-MIR-205-3P	99.92	69.92	3165
HSA-MIR-515-5P	99.92	69.82	2343
HSA-MIR-519E-5P	99.92	69.62	2358
HSA-MIR-5680	99.91	69.83	3421
HSA-MIR-8063	99.91	69.76	3146
HSA-MIR-7-1-3P	99.91	71.53	4384
HSA-MIR-7-2-3P	99.91	71.40	4394
HSA-MIR-4698	99.84	71.41	4303
HSA-MIR-498-5P	99.76	69.64	1807
HSA-MIR-556-3P	99.74	68.75	1203
HSA-MIR-494-3P	99.70	71.45	2795
HSA-MIR-875-3P	99.63	69.47	2548
HSA-MIR-3616-5P	99.55	67.02	989
HSA-MIR-573	99.55	67.44	955
HSA-MIR-7159-5P	99.53	72.12	2472

Literature-anchored findings (GeneRIF, showing 12)

• Collectrin has a role in amino acid transpor in the kidney [review] (PMID:17693757)
• the first human study of the gene TMEM27 and an attempt to shine a light on genotype-phenotype correlation in Turner syndrome patients. (PMID:19417552)
• No TMEM27 gene mutations were discovered among 26 patients showing a phenotype resembling Dent’s disease (PMID:19582483)
• Data support a role for TMEM27 in glucose-induced insulin secretion but not in cell proliferation. The finding that its cleavage is not specific to beta cells challenges the current support for its use as a potential beta cell mass biomarker. (PMID:20386877)
• Collectrin and ACE2 in renal and intestinal amino acid transport. (PMID:21814048)
• Bace2 specifically targets Tmem27 and cleaves its extracellular domain, which is then shed from the plasma membrane of pancreatic beta cells. (PMID:21907142)
• Tmem27 dimerization is a dynamic process involving Bace2 (PMID:22628310)
• Tmem27 is present in human serum and its levels are significantly lower in subjects with autoimmune diabetes as compared to healthy individuals. (PMID:24693993)
• Lack of expression of the TMEM27 in conventional renal cell carcinoma defines a group of patients at high risk for cancer-related death. (PMID:27417314)
• Maternal serum collectrin levels are significantly lower in patients with preeclampsia than in the control group. There is an inverse correlation between serum collectrin levels and blood pressure. (PMID:28764560)
• Collectrin (Tmem27) deficiency in proximal tubules causes hypertension in mice and a TMEM27 variant associates with blood pressure in males in a Latino cohort. (PMID:36264884)
• TMEM27 expression and clinical characteristics and survival in clear cell renal cell carcinoma. (PMID:36369873)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	cltrn	ENSDARG00000041644
mus_musculus	Cltrn	ENSMUSG00000015401
rattus_norvegicus	Cltrn	ENSRNOG00000003960

Protein

Protein identifiers

Collectrin — Q9HBJ8 (reviewed: Q9HBJ8)

Alternative names: Transmembrane protein 27

All UniProt accessions (2): Q9HBJ8, A0A3B3ITM8

UniProt curated annotations — full annotation on UniProt →

Function. Plays an important role in amino acid transport by acting as binding partner of amino acid transporters SLC6A18 and SLC6A19, regulating their trafficking on the cell surface and their amino acid transporter activity. May also play a role in trafficking of amino acid transporters SLC3A1 and SLC7A9 to the renal cortical cell membrane. Regulator of SNARE complex function. Stimulator of beta cell replication.

Subunit / interactions. Monomer. Homodimer; dimerization prevents CLTRN cleavage by BACE2. Interacts with SLC6A18; this interaction regulates the trafficking of SLC6A18 to the cell membrane and its amino acid transporter activity. Interacts with SLC6A19; this interaction regulates the trafficking of SLC6A19 to the cell membrane and its amino acid transporter activity. Interacts with SNAPIN.

Subcellular location. Cell membrane.

Tissue specificity. Kidney; collecting ducts. Pancreas; beta cells of islets.

Post-translational modifications. Glycosylated. Glycosylation is required for plasma membrane localization and for its cleavage by BACE2. Proteolytically processed in pancreatic beta cells by BACE2 leading to the generation and extracellular release of soluble CLTRN, and a corresponding cell-associated C-terminal fragment which is later cleaved by gamma-secretase. This shedding process inactivates CLTRN. Three cleavage sites have been identified for BACE2, two clustered sites after Phe-116 and Leu-118 and a more membrane proximal site at Phe-125; the preferred BACE2 cleavage site seems to be between Phe-125 and Leu-126, Phe-116 and Leu-118 act as alternative sites.

Disease relevance. An interstitial deletion on chromosome Xp22.2 encompassing CLTRN and a deletion spanning CLTRN exons 1 to 3 have been found in two individuals with a neuropsychiatric disorder characterized by autistic features, anxiety, depression, compulsions, motor tics, and neutral aminoaciduria. Plasma amino acids were normal in both patients.

Domain organisation. The cleavage site containing the double Phe-Phe motif acts as negative regulator of shedding by BACE2.

Similarity. Belongs to the CLTRN family.

RefSeq proteins (1): NP_065716* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR031588	Collectrin_dom	Domain
IPR042944	Collectrin	Family

Pfam: PF16959

UniProt features (18 total): mutagenesis site 7, glycosylation site 2, topological domain 2, modified residue 2, signal peptide 1, chain 1, transmembrane region 1, domain 1, site 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9HBJ8-F1	77.38	0.48

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): 125–126 (cleavage by bace2)

Post-translational modifications (2): 214, 220

Glycosylation sites (2): 93, 76

Mutagenesis-validated functional residues (7):

Position	Phenotype
75	increased dimerization leading to hyperoligomerized. abolishes processing by bace2. abolishes localization to the cell m
76	loss of localization to the cell membrane. abolishes processing by bace2. loss of localization to the cell membrane; whe
93	loss of localization to the cell membrane. abolishes processing by bace2. loss of localization to the cell membrane; whe
115–119	increases processing by bace2. decreases of protein abundance.
123–128	does not affet processing by bace2.
152	does not affect dimerization. does not affect cell membrane localization. abolishes dimerization; when associated with a
186	abolishes dimerization. does not affect cell membrane localization. does not affect processing by bace2. abolishes dimer

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-264876	Insulin processing

MSigDB gene sets: 189 (showing top): BENPORATH_ES_WITH_H3K27ME3, GOBP_REGULATION_OF_ORGANIC_ACID_TRANSPORT, GOBP_VESICLE_ORGANIZATION, GOBP_INSULIN_SECRETION, GOBP_CELLULAR_RESPONSE_TO_CARBOHYDRATE_STIMULUS, GOBP_MEMBRANE_FUSION, GOBP_REGULATION_OF_HORMONE_LEVELS, GOBP_HORMONE_TRANSPORT, GOBP_VESICLE_MEDIATED_TRANSPORT, HNF1_Q6, GOBP_AMINO_ACID_TRANSMEMBRANE_TRANSPORT, AAAYRNCTG_UNKNOWN, GOBP_CELLULAR_RESPONSE_TO_OXYGEN_CONTAINING_COMPOUND, GOBP_POSITIVE_REGULATION_OF_TRANSMEMBRANE_TRANSPORT, GOBP_CELL_CELL_SIGNALING

GO Biological Process (5): calcium-ion regulated exocytosis (GO:0017156), SNARE complex assembly (GO:0035493), insulin secretion involved in cellular response to glucose stimulus (GO:0035773), positive regulation of amino acid transport (GO:0051957), positive regulation of L-proline import across plasma membrane (GO:1905737)

GO Molecular Function (3): protein homodimerization activity (GO:0042803), transporter activator activity (GO:0141109), protein binding (GO:0005515)

GO Cellular Component (5): cytoplasm (GO:0005737), plasma membrane (GO:0005886), brush border membrane (GO:0031526), extracellular exosome (GO:0070062), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
Peptide hormone metabolism	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	2
regulated exocytosis	1
vesicle fusion	1
protein-containing complex assembly	1
insulin secretion	1
establishment of localization in cell	1
cellular response to glucose stimulus	1
amino acid transport	1
positive regulation of amine transport	1
regulation of amino acid transport	1
positive regulation of proline import across plasma membrane	1
L-proline import across plasma membrane	1
regulation of L-proline import across plasma membrane	1
identical protein binding	1
protein dimerization activity	1
transporter activity	1
molecular function activator activity	1
transporter regulator activity	1
binding	1
intracellular anatomical structure	1
membrane	1
cell periphery	1
brush border	1
apical plasma membrane	1
cell projection membrane	1
extracellular vesicle	1

Protein interactions and networks

STRING

712 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CLTRN	SLC6A19	Q695T7	952
CLTRN	ACE	P12821	699
CLTRN	SNAP25	P13795	683
CLTRN	SLC3A1	Q07837	668
CLTRN	BACE2	Q9Y5Z0	627
CLTRN	AGT	P01019	612
CLTRN	REN	P00797	600
CLTRN	TMPRSS2	O15393	592
CLTRN	ANPEP	P15144	584
CLTRN	ADAM17	P78536	561
CLTRN	AGTR2	P50052	539
CLTRN	KNG1	P01042	538
CLTRN	CLEC4M	Q9H2X3	533
CLTRN	FURIN	P09958	511
CLTRN	SLC6A18	Q96N87	485

IntAct

14 interactions, top by confidence:

A	B	Type	Score
OLFM4	CLTRN	psi-mi:“MI:0915”(physical association)	0.560
CLTRN	UBE2J1	psi-mi:“MI:0915”(physical association)	0.560
CLTRN	SMCO4	psi-mi:“MI:0915”(physical association)	0.560
RBM18	CLTRN	psi-mi:“MI:0915”(physical association)	0.370
CLTRN		psi-mi:“MI:0915”(physical association)	0.370
	SHTN1	psi-mi:“MI:0914”(association)	0.350
SLC6A19	TMEM129	psi-mi:“MI:0914”(association)	0.350
UBE2J1	CLTRN	psi-mi:“MI:0915”(physical association)	0.000
SMCO4	CLTRN	psi-mi:“MI:0915”(physical association)	0.000
OLFM4	CLTRN	psi-mi:“MI:0915”(physical association)	0.000
CLTRN	UBE2J1	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (7): TMEM27 (Two-hybrid), SMCO4 (Two-hybrid), UBE2J1 (Two-hybrid), TMEM27 (Affinity Capture-MS), TMEM27 (Two-hybrid), TMEM27 (Affinity Capture-MS), TMEM27 (Two-hybrid)

ESM2 similar proteins: A1A4K5, A7E2Z9, A8MWY0, A8WCC4, C0H9B6, C6KFA3, F1QR43, F1R520, O13097, O18756, O73874, O94923, O94985, P07224, P07225, P0C152, P13612, P19218, P24387, P24668, P26009, P53813, P98118, Q00651, Q08761, Q0VCT4, Q13822, Q16819, Q28CF8, Q3UZV7, Q5HYA8, Q64610, Q66IR0, Q6AY20, Q6BEA0, Q6F3F9, Q6Q0N0, Q86SQ4, Q8BGZ8, Q8TCW7

Diamond homologs: Q0VCT4, Q56H28, Q56NL1, Q58DD0, Q5EGZ1, Q5RFN1, Q8R0I0, Q9BYF1, Q9ESG3, Q9ESG4, Q9HBJ8, D0G895, F1RRW5, P09470, P12820, P12821, P12822, P47820, Q10714, Q10715, Q10751, Q50JE5, Q6Q4G4, Q9GLN7, Q9VLJ6

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (2)

Variant ID	HGVS	Classification
632559	Single allele	Pathogenic
691618	Single allele	Pathogenic

SpliceAI

735 predictions. Top by Δscore:

Variant	Effect	Δscore
X:15659014:A:AC	donor_gain	1.0000
X:15659015:C:CC	donor_gain	1.0000
X:15659015:CT:C	donor_gain	1.0000
X:15664335:A:AC	donor_gain	1.0000
X:15664336:C:CC	donor_gain	1.0000
X:15664336:CTG:C	donor_gain	1.0000
X:15628124:CTTT:C	acceptor_gain	0.9900
X:15628125:TTT:T	acceptor_gain	0.9900
X:15628127:TC:T	acceptor_loss	0.9900
X:15628128:C:CC	acceptor_gain	0.9900
X:15628128:CTAAA:C	acceptor_loss	0.9900
X:15628129:T:C	acceptor_loss	0.9900
X:15659010:GCTTA:G	donor_loss	0.9900
X:15659011:CT:C	donor_loss	0.9900
X:15659012:TTA:T	donor_loss	0.9900
X:15659013:TACTC:T	donor_loss	0.9900
X:15659015:C:T	donor_loss	0.9900
X:15659015:CTCT:C	donor_gain	0.9900
X:15659015:CTCTG:C	donor_gain	0.9900
X:15659098:CATA:C	acceptor_gain	0.9900
X:15659099:ATA:A	acceptor_gain	0.9900
X:15659100:TA:T	acceptor_gain	0.9900
X:15659102:C:CC	acceptor_gain	0.9900
X:15664323:G:C	donor_gain	0.9900
X:15659014:ACT:A	donor_gain	0.9800
X:15659015:CTC:C	donor_gain	0.9800
X:15659097:GCATA:G	acceptor_gain	0.9800
X:15659098:CATAC:C	acceptor_gain	0.9800
X:15664335:ACTG:A	donor_gain	0.9800
X:15664336:CT:C	donor_gain	0.9800

AlphaMissense

1476 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
X:15639699:A:C	F125L	0.985
X:15639699:A:T	F125L	0.985
X:15639701:A:G	F125L	0.985
X:15659093:C:A	W42C	0.983
X:15659093:C:G	W42C	0.983
X:15659095:A:G	W42R	0.979
X:15659095:A:T	W42R	0.979
X:15639700:A:G	F125S	0.977
X:15644984:G:C	F83L	0.975
X:15644984:G:T	F83L	0.975
X:15644986:A:G	F83L	0.975
X:15659051:G:C	F56L	0.974
X:15659051:G:T	F56L	0.974
X:15659053:A:G	F56L	0.974
X:15659065:C:G	A52P	0.970
X:15659070:A:G	F50S	0.968
X:15639700:A:C	F125C	0.966
X:15644973:A:T	V87D	0.962
X:15659069:G:C	F50L	0.960
X:15659069:G:T	F50L	0.960
X:15659071:A:G	F50L	0.960
X:15644979:A:G	F85S	0.959
X:15644978:A:C	F85L	0.957
X:15644978:A:T	F85L	0.957
X:15644980:A:G	F85L	0.957
X:15645018:A:T	V72D	0.956
X:15644923:C:G	A104P	0.944
X:15644919:A:T	I105K	0.942
X:15644985:A:G	F83S	0.942
X:15659070:A:C	F50C	0.942

dbSNP variants (sampled 300 via entrez): RS1000013860 (X:15672246 G>A), RS1000036474 (X:15669492 G>A), RS1000122135 (X:15662898 C>G,T), RS1000243344 (X:15663319 T>C), RS1000364220 (X:15631516 G>A,C), RS1000577659 (X:15677320 A>C), RS1000724863 (X:15648925 C>T), RS1000755595 (X:15629917 C>A), RS1000796589 (X:15636397 A>T), RS1000914847 (X:15636695 G>C), RS1000928601 (X:15676972 T>A), RS1000954335 (X:15655429 C>G,T), RS1000965565 (X:15648382 T>C), RS1001044142 (X:15672622 G>A), RS1001162370 (X:15648186 G>T)

Disease associations

OMIM: gene MIM:300631 | disease phenotypes: MIM:209850

GenCC curated gene-disease

Disease	Classification	Inheritance
Hartnup disease	Supportive	Autosomal recessive

Mondo (2): autism (MONDO:0005260), Hartnup disease (MONDO:0009324)

Orphanet (0):

HPO phenotypes

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

HPO	Term
HP:0000206	Glossitis
HP:0000230	Gingivitis
HP:0000486	Strabismus
HP:0000504	Abnormality of vision
HP:0000613	Photophobia
HP:0000639	Nystagmus
HP:0000709	Psychosis
HP:0000712	Emotional lability
HP:0000738	Hallucinations
HP:0000739	Anxiety
HP:0000988	Skin rash
HP:0000992	Cutaneous photosensitivity
HP:0001053	Hypopigmented skin patches
HP:0001249	Intellectual disability
HP:0001250	Seizure
HP:0001251	Ataxia
HP:0001252	Hypotonia
HP:0001263	Global developmental delay
HP:0001337	Tremor
HP:0001347	Hyperreflexia
HP:0002024	Malabsorption
HP:0002076	Migraine
HP:0002353	EEG abnormality
HP:0002383	Infectious encephalitis
HP:0004322	Short stature
HP:0007400	Irregular hyperpigmentation
HP:0008066	Abnormal blistering of the skin
HP:0008353	Neutral hyperaminoaciduria
HP:0012086	Abnormal urinary color
HP:6000130	Elevated urinary indican level

GWAS associations

0 associations (top):

MeSH disease descriptors (2)

Descriptor	Name	Tree numbers
D001321	Autistic Disorder	F03.625.164.113.500
D006250	Hartnup Disease	C10.228.140.163.100.355; C12.050.351.968.419.815.885.625; C12.200.777.419.815.885.457; C12.950.419.815.885.625; C16.320.565.151.355; C16.320.565.189.355; C16.320.831.885.457; C18.452.132.100.355; C18.452.648.151.355; C18.452.648.189.355

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, affects cotreatment, decreases expression	7
Aflatoxin B1	affects expression, decreases methylation, increases expression	5
trichostatin A	affects cotreatment, decreases expression	3
Estradiol	affects cotreatment, decreases expression	3
Cyclosporine	decreases expression	3
sodium arsenite	decreases expression	2
Panobinostat	affects cotreatment, decreases expression	2
Benzo(a)pyrene	increases expression	2
bisphenol F	affects cotreatment, decreases methylation	1
aminomethylphosphonic acid (AMPA)	increases expression	1
propionaldehyde	increases expression	1
tris(2-butoxyethyl) phosphate	affects expression	1
beta-lapachone	decreases expression	1
arsenite	affects binding, increases reaction	1
butyraldehyde	increases expression	1
benzo(e)pyrene	decreases methylation	1
perfluorooctane sulfonic acid	decreases expression	1
monomethylarsonous acid	increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	increases expression, affects cotreatment, decreases expression	1
dorsomorphin	decreases expression, increases expression, affects cotreatment	1
jinfukang	affects cotreatment, increases expression, decreases expression	1
Fulvestrant	affects cotreatment, decreases methylation	1
Acetaminophen	increases expression	1
Cadmium	decreases expression	1
Calcitriol	increases expression	1
Cisplatin	affects cotreatment, increases expression	1
Coumestrol	decreases expression	1
Methapyrilene	decreases methylation	1
Mustard Gas	increases expression	1
Nickel	decreases expression	1

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
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
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
NCT00346736	PHASE3	COMPLETED	Use of Acupuncture In Children With Autistic Spectrum Disorder
NCT00352248	PHASE3	COMPLETED	Randomized Controlled Trial of Acupuncture Versus Sham Acupuncture in Autistic Spectrum Disorder
NCT00352352	PHASE3	COMPLETED	Use of Acupuncture In Children With Autistic Spectrum Disorder
NCT00355329	PHASE3	COMPLETED	Randomized Control Trial of Using Tongue Acupuncture in Autistic Spectrum Disorder Using PET Scan for Clinical Correlation
NCT00498173	PHASE3	COMPLETED	Effectiveness of Atomoxetine in Treating ADHD Symptoms in Children and Adolescents With Autism
NCT00541346	PHASE3	COMPLETED	A Pilot Study of Daytrana TM in Children With Autism Co-Morbid for Attention Deficit Hyperactivity Disorder (ADHD) Symptoms