CNTN6

Summary

CNTN6 (contactin 6, HGNC:2176) is a protein-coding gene on chromosome 3p26.3, encoding Contactin-6 (Q9UQ52). Contactins mediate cell surface interactions during nervous system development.

The protein encoded by this gene is a member of the immunoglobulin superfamily. It is a glycosylphosphatidylinositol (GPI)-anchored neuronal membrane protein that functions as a cell adhesion molecule. It may play a role in the formation of axon connections in the developing nervous system. Alternative splicing results in multiple transcript variants.

Source: NCBI Gene 27255 — RefSeq curated summary.

At a glance

• Gene–disease (curated): Tourette syndrome (Limited, GenCC) — +1 more curated relationship
• GWAS associations: 22
• Clinical variants (ClinVar): 376 total — 1 pathogenic, 7 likely-pathogenic
• Phenotypes (HPO): 2
• Dosage sensitivity (ClinGen): haploinsufficiency no evidence, triplosensitivity no evidence
• MANE Select transcript: NM_001289080

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:2176
Approved symbol	CNTN6
Name	contactin 6
Location	3p26.3
Locus type	gene with protein product
Status	Approved
Aliases	NB-3
Ensembl gene	ENSG00000134115
Ensembl biotype	protein_coding
OMIM	607220
Entrez	27255

Gene structure

Transcript identifiers

Ensembl transcripts: 12 — 8 protein_coding, 3 nonsense_mediated_decay, 1 retained_intron

ENST00000350110, ENST00000394261, ENST00000397479, ENST00000413210, ENST00000446702, ENST00000485257, ENST00000861156, ENST00000861157, ENST00000947275, ENST00000947276, ENST00000947277, ENST00000947278

RefSeq mRNA: 16 — MANE Select: NM_001289080 NM_001289080, NM_001289081, NM_001349350, NM_001349351, NM_001349352, NM_001349353, NM_001349354, NM_001349355, NM_001349356, NM_001349357, NM_001349358, NM_001349359, NM_001349360, NM_001349361, NM_001349362, NM_014461

CCDS: CCDS2557

Canonical transcript exons

ENST00000446702 — 23 exons

Exon	Start	End
ENSE00001704784	1093024	1093120
ENSE00001765793	1403318	1404217
ENSE00003459215	1321650	1321834
ENSE00003459997	1402318	1402486
ENSE00003468750	1297889	1297991
ENSE00003471152	1373604	1373762
ENSE00003482505	1327457	1327586
ENSE00003521780	1373924	1374073
ENSE00003523562	1401433	1401545
ENSE00003533144	1329785	1329935
ENSE00003537746	1295601	1295804
ENSE00003537891	1325815	1325951
ENSE00003542198	1372299	1372474
ENSE00003548622	1385611	1385797
ENSE00003548943	1383293	1383408
ENSE00003555559	1220687	1220813
ENSE00003560125	1147927	1148063
ENSE00003563236	1227818	1227993
ENSE00003580089	1377005	1377075
ENSE00003626693	1382942	1383176
ENSE00003663443	1372838	1372955
ENSE00003669050	1352324	1352451
ENSE00003680524	1278413	1278508

Expression profiles

Bgee: expression breadth ubiquitous, 164 present calls, max score 82.12.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.7894 / max 125.9712, expressed in 169 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter ID	TPM avg	Samples expressed
34991	0.4036	123
34990	0.1887	71
34989	0.0786	38
202652	0.0681	23
34987	0.0297	9
34988	0.0208	10

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
cerebellar hemisphere	UBERON:0002245	82.12	gold quality
cerebellar cortex	UBERON:0002129	81.99	gold quality
cerebellum	UBERON:0002037	81.03	gold quality
right hemisphere of cerebellum	UBERON:0014890	80.97	gold quality
endothelial cell	CL:0000115	78.18	silver quality
right adrenal gland cortex	UBERON:0035827	77.82	gold quality
hair follicle	UBERON:0002073	77.42	silver quality
left adrenal gland cortex	UBERON:0035825	76.85	gold quality
left adrenal gland	UBERON:0001234	76.84	gold quality
right adrenal gland	UBERON:0001233	76.14	gold quality
adrenal cortex	UBERON:0001235	76.02	gold quality
left lobe of thyroid gland	UBERON:0001120	74.86	gold quality
adrenal gland	UBERON:0002369	74.38	gold quality
thyroid gland	UBERON:0002046	74.22	gold quality
right lobe of thyroid gland	UBERON:0001119	73.88	gold quality
adrenal tissue	UBERON:0018303	73.17	gold quality
buccal mucosa cell	CL:0002336	73.06	gold quality
cerebellar vermis	UBERON:0004720	72.18	gold quality
right lung	UBERON:0002167	71.99	gold quality
Brodmann (1909) area 23	UBERON:0013554	71.87	silver quality
prefrontal cortex	UBERON:0000451	71.19	gold quality
secondary oocyte	CL:0000655	71.15	silver quality
orbitofrontal cortex	UBERON:0004167	68.36	silver quality
upper lobe of left lung	UBERON:0008952	68.05	gold quality
lung	UBERON:0002048	67.85	gold quality
upper lobe of lung	UBERON:0008948	67.85	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	67.80	gold quality
cingulate cortex	UBERON:0003027	67.43	gold quality
frontal cortex	UBERON:0001870	67.27	gold quality
anterior cingulate cortex	UBERON:0009835	67.16	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	5.68

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

22 targeting CNTN6, 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-4282	99.99	75.36	6408
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-548AJ-3P	99.96	73.38	5345
HSA-MIR-548X-3P	99.96	73.38	5345
HSA-MIR-548J-3P	99.94	72.61	4881
HSA-MIR-548AE-3P	99.93	72.66	4867
HSA-MIR-548AH-3P	99.93	72.54	4872
HSA-MIR-548AM-3P	99.93	72.54	4872
HSA-MIR-548AQ-3P	99.93	72.66	4867
HSA-MIR-6844	99.82	70.69	2423
HSA-MIR-4306	99.72	70.50	3630
HSA-MIR-1290	99.59	69.90	2079
HSA-MIR-6882-5P	99.35	71.13	1206
HSA-MIR-185-5P	99.35	68.60	2497
HSA-MIR-4644	99.35	69.12	2514
HSA-MIR-3145-3P	98.85	69.07	2031
HSA-MIR-4742-3P	98.73	69.82	1803
HSA-MIR-592	96.59	67.59	817

Functional genomics

ClinGen dosage: haploinsufficiency 0 (no evidence), triplosensitivity 0 (no evidence). ClinGen Gene Dosage Map

Literature-anchored findings (GeneRIF, showing 6)

• results do not support the candidacy of CHL1, CNTN6, and CNTN4 as tumor suppressor genes in the 3p26-pter region in ovarian cancer (PMID:19509545)
• Clinical investigations of the patients carrying CNTN5 or CNTN6 variants showed that they were hypersensitive to sounds (a condition called hyperacusis) and displayed changes in wave latency within the auditory pathway. (PMID:27166760)
• CNTN6 copy number variants (duplications) were associated with increased risk of Tourette syndrome. (PMID:28641109)
• this study describes of 2 boys with intellectual disability, attention-deficit hyperactivity disorder harboring a 3p26.3 microdeletion and a 3p26.3 microduplication, which are both paternally inherited and include only the CNTN6 gene. (PMID:30508811)
• CNTN6 copy number variations: Uncertain clinical significance in individuals with neurodevelopmental disorders. (PMID:30836150)
• Contactin 6, A Novel Causative Gene for Congenital Hypothyroidism, Mediates Thyroid Hormone Biosynthesis Through Notch Signaling. (PMID:38183624)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Cntn6	ENSMUSG00000030092
rattus_norvegicus	Cntn6	ENSRNOG00000032517

Paralogs (36): CNTN1 (ENSG00000018236), CDON (ENSG00000064309), NEO1 (ENSG00000067141), SDK2 (ENSG00000069188), IGSF9B (ENSG00000080854), IGSF9 (ENSG00000085552), NRCAM (ENSG00000091129), MXRA5 (ENSG00000101825), IGDCC4 (ENSG00000103742), CNTN3 (ENSG00000113805), IGSF21 (ENSG00000117154), CHL1 (ENSG00000134121), PTPRQ (ENSG00000139304), CNTN4 (ENSG00000144619), BOC (ENSG00000144857), SDK1 (ENSG00000146555), HMCN2 (ENSG00000148357), NCAM1 (ENSG00000149294), CNTN5 (ENSG00000149972), IGSF10 (ENSG00000152580), ROBO4 (ENSG00000154133), ROBO3 (ENSG00000154134), NCAM2 (ENSG00000154654), VCAM1 (ENSG00000162692), NFASC (ENSG00000163531), PRTG (ENSG00000166450), ROBO1 (ENSG00000169855), DSCAM (ENSG00000171587), IGDCC3 (ENSG00000174498), VSIG10 (ENSG00000176834), DSCAML1 (ENSG00000177103), CNTN2 (ENSG00000184144), ROBO2 (ENSG00000185008), VSIG10L (ENSG00000186806), DCC (ENSG00000187323), L1CAM (ENSG00000198910)

Protein

Protein identifiers

Contactin-6 — Q9UQ52 (reviewed: Q9UQ52)

Alternative names: Neural recognition molecule NB-3

All UniProt accessions (3): Q9UQ52, F8VWS7, F8WDQ0

UniProt curated annotations — full annotation on UniProt →

Function. Contactins mediate cell surface interactions during nervous system development. Participates in oligodendrocytes generation by acting as a ligand of NOTCH1. Its association with NOTCH1 promotes NOTCH1 activation through the released notch intracellular domain (NICD) and subsequent translocation to the nucleus. Involved in motor coordination.

Subunit / interactions. Interacts with PTPRG.

Subcellular location. Cell membrane.

Tissue specificity. Expressed in nervous system. Highly expressed in cerebellum. Expressed at intermediate level in thalamus, subthalamic nucleus. Weakly expressed in corpus callosum, caudate nucleus and spinal cord.

Similarity. Belongs to the immunoglobulin superfamily. Contactin family.

RefSeq proteins (16): NP_001276009, NP_001276010, NP_001336279, NP_001336280, NP_001336281, NP_001336282, NP_001336283, NP_001336284, NP_001336285, NP_001336286, NP_001336287, NP_001336288, NP_001336289, NP_001336290, NP_001336291, NP_055276 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR003598	Ig_sub2	Domain
IPR003599	Ig_sub	Domain
IPR003961	FN3_dom	Domain
IPR007110	Ig-like_dom	Domain
IPR013098	Ig_I-set	Domain
IPR013783	Ig-like_fold	Homologous_superfamily
IPR036116	FN3_sf	Homologous_superfamily
IPR036179	Ig-like_dom_sf	Homologous_superfamily

Pfam: PF00041, PF07679, PF13927

UniProt features (43 total): glycosylation site 13, domain 10, sequence variant 7, disulfide bond 6, signal peptide 1, chain 1, region of interest 1, compositionally biased region 1, modified residue 1, lipid moiety-binding region 1, propeptide 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9UQ52-F1	86.19	0.57

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): 882, 999

Disulfide bonds (6): 50–100, 144–196, 249–297, 339–386, 431–479, 521–577

Glycosylation sites (13): 65, 193, 368, 377, 468, 659, 765, 860, 865, 895, 931, 956, 957

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-447041	CHL1 interactions

MSigDB gene sets: 151 (showing top): GOBP_NEURON_RECOGNITION, CAR_TNFRSF25, LU_IL4_SIGNALING, RORA1_01, GCANCTGNY_MYOD_Q6, MODULE_45, GOBP_POSITIVE_REGULATION_OF_NOTCH_SIGNALING_PATHWAY, GOBP_NEUROGENESIS, TGACCTY_ERR1_Q2, GGGTGGRR_PAX4_03, GGAMTNNNNNTCCY_UNKNOWN, CAGCTG_AP4_Q5, MORF_RAD51L3, GOBP_CELL_CELL_ADHESION, PAX8_B

GO Biological Process (8): cell adhesion (GO:0007155), homophilic cell-cell adhesion (GO:0007156), Notch signaling pathway (GO:0007219), axon guidance (GO:0007411), central nervous system development (GO:0007417), positive regulation of Notch signaling pathway (GO:0045747), synapse organization (GO:0050808), dendrite self-avoidance (GO:0070593)

GO Molecular Function (2): cell-cell adhesion mediator activity (GO:0098632), protein binding (GO:0005515)

GO Cellular Component (8): plasma membrane (GO:0005886), axon (GO:0030424), presynaptic membrane (GO:0042734), synapse (GO:0045202), side of membrane (GO:0098552), parallel fiber to Purkinje cell synapse (GO:0098688), membrane (GO:0016020), presynapse (GO:0098793)

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
L1CAM interactions	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	3
cell-cell adhesion	2
membrane	2
cellular process	1
cell surface receptor signaling pathway	1
axonogenesis	1
neuron projection guidance	1
nervous system development	1
system development	1
Notch signaling pathway	1
regulation of Notch signaling pathway	1
positive regulation of signal transduction	1
cell junction organization	1
neuron recognition	1
cell adhesion mediator activity	1
binding	1
cell periphery	1
neuron projection	1
synaptic membrane	1
presynapse	1
cell junction	1
leaflet of membrane bilayer	1
excitatory synapse	1
synapse	1

Protein interactions and networks

STRING

1688 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CNTN6	CD177	Q8N6Q3	843
CNTN6	ALCAM	Q13740	802
CNTN6	BCAM	P50895	788
CNTN6	CD6	P30203	773
CNTN6	PTPRG	P23470	692
CNTN6	CHL1	O00533	691
CNTN6	SCN2B	O60939	589
CNTN6	PTPRA	P18433	556
CNTN6	PDZD4	Q76G19	549
CNTN6	NOTCH1	P46531	542
CNTN6	ADGRL2	O95490	538
CNTN6	DNER	Q8NFT8	533
CNTN6	NRXN1	Q9ULB1	524
CNTN6	ADGRL1	O94910	523
CNTN6	L1CAM	P32004	508

IntAct

0 interactions, top by confidence:

BioGRID (4): CNTN6 (Affinity Capture-Western), CHL1 (Affinity Capture-Western), CNTN6 (Synthetic Lethality), CNTN6 (Affinity Capture-MS)

ESM2 similar proteins: B0KW95, B2KI42, B4USZ0, O00222, O18926, O55075, O60245, O94779, P10288, P15116, P19022, P19534, P24503, P33145, P33150, P35400, P39038, P47743, P55283, P55290, P58365, P68500, P70579, P97527, Q07409, Q0E9H9, Q0ZM14, Q14831, Q3B7N0, Q5H8C1, Q5R5W6, Q5R9X1, Q5RDQ8, Q62682, Q62845, Q63149, Q68ED2, Q69Z26, Q8IWV2, Q90275

Diamond homologs: A0A452E9Y6, A1KZ92, A2ASS6, A4IGL7, A5JUY8, A8WQH2, B0V2N1, B3A0P3, B3A0Q8, D3YXG0, G5EG78, O15146, O42414, O60469, O61213, O94779, P05164, P07202, P09933, P11247, P11678, P13591, P13595, P13596, P14650, P14781, P20241, P22063, P22079, P23468, P29533, P29534, P31836, P35419, P49290, P68500, P80025, P90820, P97528, P98160

SIGNOR signaling

2 interactions.

A	Effect	B	Mechanism
CNTN6	up-regulates	NOTCH1	relocalization
CNTN6	up-regulates	NOTCH	relocalization

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	7
Uncertain significance	303
Likely benign	27
Benign	22

Top pathogenic / likely-pathogenic (8)

Variant ID	HGVS	Classification
562722	GRCh37/hg19 3p26.3(chr3:1368769-2263514)x1	Pathogenic
1802251	NM_001289080.2(CNTN6):c.1492+1G>T	Likely pathogenic
545285	NC_000003.12:g.(?1133359)(1192637_?)del	Likely pathogenic
545286	NC_000003.12:g.(?1185337)(1255844_?)del	Likely pathogenic
545287	NC_000003.12:g.(?1204527)(1310468_?)del	Likely pathogenic
545288	NC_000003.12:g.(?1247669)(1285156_?)del	Likely pathogenic
545289	NC_000003.12:g.(?1264992)(1295956_?)del	Likely pathogenic
548950	NM_001289080.2(CNTN6):c.566C>A (p.Ser189Ter)	Likely pathogenic

SpliceAI

5233 predictions. Top by Δscore:

Variant	Effect	Δscore
3:1147922:TTCA:T	acceptor_loss	1.0000
3:1147923:TCA:T	acceptor_loss	1.0000
3:1147925:A:AG	acceptor_gain	1.0000
3:1147925:A:C	acceptor_loss	1.0000
3:1147926:G:GA	acceptor_gain	1.0000
3:1147926:GA:G	acceptor_gain	1.0000
3:1147926:GAC:G	acceptor_gain	1.0000
3:1147926:GACT:G	acceptor_gain	1.0000
3:1147926:GACTC:G	acceptor_gain	1.0000
3:1148061:CAG:C	donor_loss	1.0000
3:1148062:AG:A	donor_loss	1.0000
3:1148063:GG:G	donor_loss	1.0000
3:1148064:G:GC	donor_loss	1.0000
3:1148065:T:G	donor_loss	1.0000
3:1148786:G:A	acceptor_gain	1.0000
3:1227990:GCAT:G	donor_gain	1.0000
3:1227991:CATGT:C	donor_loss	1.0000
3:1227993:TGTGA:T	donor_loss	1.0000
3:1227994:G:GG	donor_gain	1.0000
3:1227994:GTGA:G	donor_loss	1.0000
3:1227995:T:G	donor_loss	1.0000
3:1227996:G:GT	donor_loss	1.0000
3:1278402:T:TA	acceptor_gain	1.0000
3:1278408:CCAAG:C	acceptor_loss	1.0000
3:1278409:CAAGA:C	acceptor_loss	1.0000
3:1278410:A:AG	acceptor_gain	1.0000
3:1278410:AAG:A	acceptor_loss	1.0000
3:1278411:A:C	acceptor_loss	1.0000
3:1278411:A:G	acceptor_gain	1.0000
3:1278412:G:GA	acceptor_loss	1.0000

AlphaMissense

6737 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
3:1321671:G:C	W261C	1.000
3:1321671:G:T	W261C	1.000
3:1373999:G:C	R674P	1.000
3:1227819:T:A	W62R	0.999
3:1227819:T:C	W62R	0.999
3:1227821:G:C	W62C	0.999
3:1227821:G:T	W62C	0.999
3:1295615:T:A	W157R	0.999
3:1295615:T:C	W157R	0.999
3:1295617:G:C	W157C	0.999
3:1295617:G:T	W157C	0.999
3:1295726:T:G	Y194D	0.999
3:1295732:T:C	C196R	0.999
3:1295734:C:G	C196W	0.999
3:1297975:T:C	C249R	0.999
3:1297977:T:G	C249W	0.999
3:1321669:T:A	W261R	0.999
3:1321669:T:C	W261R	0.999
3:1321670:G:C	W261S	0.999
3:1321733:T:C	L282P	0.999
3:1321771:T:G	Y295D	0.999
3:1321777:T:C	C297R	0.999
3:1321779:C:G	C297W	0.999
3:1321791:C:A	N301K	0.999
3:1321791:C:G	N301K	0.999
3:1325828:G:C	W320C	0.999
3:1325828:G:T	W320C	0.999
3:1325919:T:A	W351R	0.999
3:1325919:T:C	W351R	0.999
3:1325921:G:C	W351C	0.999

dbSNP variants (sampled 300 via entrez): RS1000010155 (3:1299756 G>A), RS1000017167 (3:1261591 A>C,G), RS1000028079 (3:1199380 A>T), RS1000054173 (3:1241438 T>C), RS1000054878 (3:1161052 C>T), RS1000056590 (3:1330324 C>G), RS1000066335 (3:1160199 A>AT), RS1000083020 (3:1299006 C>G), RS1000091642 (3:1192774 C>T), RS1000091680 (3:1388310 C>A,T), RS1000105959 (3:1375830 A>C), RS1000112153 (3:1312597 A>C), RS1000113108 (3:1316124 C>A), RS1000141858 (3:1241269 A>C,T), RS1000153192 (3:1126685 T>A,C)

Disease associations

OMIM: gene MIM:607220 | disease phenotypes: MIM:209850, MIM:181500

GenCC curated gene-disease

Disease	Classification	Inheritance
Tourette syndrome	Limited	Unknown

ClinGen Gene-Disease Validity (1)

Expert-panel classifications — Definitive > Strong > Moderate > Limited > Disputed > Refuted.

Disease	Classification	Inheritance
complex neurodevelopmental disorder	Disputed	AD

Mondo (4): autism spectrum disorder (MONDO:0005258), autism (MONDO:0005260), schizophrenia (MONDO:0005090), Tourette syndrome (MONDO:0007661)

Orphanet (2): NON RARE IN EUROPE: Autism (Orphanet:106), 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

22 associations (top):

Study	Trait	p-value
GCST000635_14	Response to statin therapy	9.000000e-07
GCST000635_29	Response to statin therapy	8.000000e-06
GCST001524_3	Visceral adipose tissue/subcutaneous adipose tissue ratio	9.000000e-06
GCST002012_5	Venous thromboembolism	2.000000e-06
GCST002279_60	PR interval in Tripanosoma cruzi seropositivity	4.000000e-07
GCST002463_13	Systemic lupus erythematosus	1.000000e-07
GCST003771_9	Loneliness	2.000000e-06
GCST003835_4	Depressive symptoms (stressful life events interaction)	6.000000e-06
GCST003875_36	Gut microbiota (bacterial taxa)	3.000000e-10
GCST003875_37	Gut microbiota (bacterial taxa)	3.000000e-10
GCST004203_1	Diastolic blood pressure	5.000000e-08
GCST004406_3	Neurocognitive impairment in HIV-1 infection (continuous)	1.000000e-06
GCST005359_9	Disease progression in age-related macular degeneration	4.000000e-06
GCST005915_1	Fasting blood insulin	3.000000e-07
GCST007743_41	Iris color (L* coordinate)	4.000000e-07
GCST009391_855	Metabolite levels	9.000000e-07
GCST009391_970	Metabolite levels	6.000000e-06
GCST009509_1	High density lipoprotein cholesterol levels	3.000000e-07
GCST010396_117	Gut microbiota (bacterial taxa, hurdle binary method)	7.000000e-07
GCST010994_4	High myopia	6.000000e-09
GCST012049_2	High density lipoprotein cholesterol levels	8.000000e-08
GCST012071_2	Response to selenium supplementation (change in plasma selenium concentration)	3.000000e-06

EFO canonical traits (14, from GWAS)

EFO ID	Trait name
EFO:0004767	visceral:subcutaneous adipose tissue ratio
EFO:0004462	PR interval
EFO:0007865	loneliness measurement
EFO:0007006	depressive symptom measurement
EFO:0007781	stressful life event measurement
EFO:0007874	gut microbiome measurement
EFO:0007883	taxonomic microbiome measurement
EFO:0006336	diastolic blood pressure
EFO:0007998	cognitive impairment measurement
EFO:0008336	disease progression measurement
EFO:0009764	eye colour measurement
EFO:0010533	sorbitol measurement
EFO:0004612	high density lipoprotein cholesterol measurement
EFO:0600021	response to dietary selenium supplementation

MeSH disease descriptors (2)

Descriptor	Name	Tree numbers
D001321	Autistic Disorder	F03.625.164.113.500
D005879	Tourette Syndrome	C10.228.140.079.898; C10.228.662.825.800; C10.574.500.850; C16.320.400.820; F03.625.992.850

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

16 total (human), top 16 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	affects methylation, decreases methylation	2
Phenylmercuric Acetate	affects cotreatment, increases expression	2
Valproic Acid	decreases expression	2
aristolochic acid I	decreases expression	1
trichostatin A	decreases expression	1
sodium arsenite	increases expression	1
CGP 52608	affects binding, increases reaction	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	increases expression, affects cotreatment	1
dorsomorphin	affects cotreatment, increases expression	1
bisphenol S	increases expression	1
Folic Acid	decreases expression	1
Tetradecanoylphorbol Acetate	affects cotreatment, affects expression	1
Thiram	increases expression	1
Tretinoin	decreases expression	1
Zinc	affects cotreatment, affects expression	1
Aflatoxin B1	decreases methylation	1

Cellosaurus cell lines

4 cell lines: 4 induced pluripotent stem cell

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

Cellosaurus	Name	Category	Sex
CVCL_WP98	ICGi009-A	Induced pluripotent stem cell	Male
CVCL_WU28	ICGi009-B	Induced pluripotent stem cell	Male
CVCL_WU29	ICGi013-A	Induced pluripotent stem cell	Female
CVCL_WU30	ICGi013-B	Induced pluripotent stem cell	Female

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT00152750	PHASE4	UNKNOWN	Study of Clonidine on Sleep Architecture in Children With Tourette’s Syndrome (TS) and Comorbid ADHD
NCT00226824	PHASE4	TERMINATED	Safety Study of Galantamine in Tic Disorders
NCT00241176	PHASE4	COMPLETED	Open Label Trial of Aripiprazole in Children and Adolescents With Tourette’s Disorder
NCT00370838	PHASE4	COMPLETED	Comparison of Keppra and Clonidine in the Treatment of Tics
NCT01018056	PHASE4	COMPLETED	Developing New Treatments for Tourette Syndrome: Therapeutic Trials With Modulators of Glutamatergic Neurotransmission
NCT01547000	PHASE4	COMPLETED	Guanfacine in Children With Tic Disorders
NCT03239210	PHASE4	COMPLETED	Effects of Ondansetron in Obsessive-compulsive and Tic Disorders
NCT00391261	PHASE4	COMPLETED	An Open-label Trial of Metformin for Weight Control of Pediatric Patients on Antipsychotic Medications.
NCT01028820	PHASE4	COMPLETED	FMRI Brain Activation of Aripiprazole Treatment in 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
NCT02096952	PHASE4	COMPLETED	Methylphenidate ER Liquid Formulation in Adults With ASD and ADHD
NCT02235467	PHASE4	COMPLETED	Multisite Study: Parental Training Using Video Modelling to Develop Social Skills in Children With Autism
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
NCT00004376	PHASE3	COMPLETED	Phase III Randomized, Double-Blind, Placebo-Controlled Study of Guanfacine for Tourette Syndrome and Attention Deficit Hyperactivity Disorder
NCT00206323	PHASE3	COMPLETED	A Randomized, Placebo-controlled, Tourette Syndrome Study.
NCT00206336	PHASE3	COMPLETED	An Open-label Study to Determine the Efficacy and Safety of Topiramate in the Treatment of Tourette Syndrome.
NCT00478842	PHASE3	COMPLETED	Pallidal Stimulation and Gilles de la Tourette Syndrome
NCT00681863	PHASE3	TERMINATED	Open-label Extension Study of Pramipexole in the Treatment of Children and Adolescents With Tourette Syndrome
NCT01501695	PHASE3	COMPLETED	Phase III Study of 5LGr to Treat Tic Disorder
NCT03087201	PHASE3	COMPLETED	CANNAbinoids in the Treatment of TICS (CANNA-TICS)
NCT03487783	PHASE3	COMPLETED	Aripiprazole Oral Solution in the Treatment of Children and Adolescents With Tourette’s Syndrome
NCT03567291	PHASE3	TERMINATED	Evaluation of Safety and Tolerability of Long-term TEV-50717 (Deutetrabenazine) for Treatment of Tourette Syndrome in Children and Adolescents
NCT03571256	PHASE3	COMPLETED	A Study to Test if TEV-50717 is Effective in Relieving Tics Associated With Tourette Syndrome (TS)
NCT06021522	PHASE3	ACTIVE_NOT_RECRUITING	A Study to Evaluate Long-term Safety of Ecopipam Tablets in Children, Adolescents and Adults With Tourette’s Disorder
NCT01302964	PHASE3	COMPLETED	Mirtazapine Treatment of Anxiety in Children and Adolescents With Pervasive Developmental Disorders