OTX1

Summary

OTX1 (orthodenticle homeobox 1, HGNC:8521) is a protein-coding gene on chromosome 2p15, encoding Homeobox protein OTX1 (P32242). Probably plays a role in the development of the brain and the sense organs.

This gene encodes a member of the bicoid sub-family of homeodomain-containing transcription factors. The encoded protein acts as a transcription factor and may play a role in brain and sensory organ development. A similar protein in mouse is required for proper brain and sensory organ development and can cause epilepsy. Alternative splicing results in multiple transcript variants.

Source: NCBI Gene 5013 — RefSeq curated summary.

At a glance

• GWAS associations: 4
• Clinical variants (ClinVar): 40 total
• MANE Select transcript: NM_014562

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:8521
Approved symbol	OTX1
Name	orthodenticle homeobox 1
Location	2p15
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000115507
Ensembl biotype	protein_coding
OMIM	600036
Entrez	5013

Gene structure

Transcript identifiers

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

ENST00000282549, ENST00000366671, ENST00000405984, ENST00000476383, ENST00000477348, ENST00000484066, ENST00000946233

RefSeq mRNA: 2 — MANE Select: NM_014562 NM_001199770, NM_014562

CCDS: CCDS1873

Canonical transcript exons

ENST00000282549 — 5 exons

Exon	Start	End
ENSE00001006365	63050830	63050897
ENSE00001006366	63051249	63051317
ENSE00001070038	63052880	63053087
ENSE00001632038	63054047	63054198
ENSE00003846107	63055501	63057831

Expression profiles

Bgee: expression breadth broad, 82 present calls, max score 92.61.

FANTOM5 (CAGE): breadth broad, TPM avg 7.0762 / max 470.7754, expressed in 774 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
20523	4.8193	699
20524	1.6938	351
20521	0.3423	63
20522	0.2208	120

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
olfactory segment of nasal mucosa	UBERON:0005386	92.61	gold quality
ventricular zone	UBERON:0003053	89.77	gold quality
ganglionic eminence	UBERON:0004023	85.94	gold quality
minor salivary gland	UBERON:0001830	85.08	gold quality
mouth mucosa	UBERON:0003729	79.34	gold quality
skin of leg	UBERON:0001511	78.36	gold quality
skin of abdomen	UBERON:0001416	76.86	gold quality
saliva-secreting gland	UBERON:0001044	76.83	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	75.57	silver quality
cortical plate	UBERON:0005343	74.81	gold quality
tibialis anterior	UBERON:0001385	74.09	silver quality
kidney epithelium	UBERON:0004819	73.43	gold quality
zone of skin	UBERON:0000014	73.40	gold quality
nasal cavity epithelium	UBERON:0005384	72.65	silver quality
ileal mucosa	UBERON:0000331	71.08	silver quality
nasal cavity mucosa	UBERON:0001826	70.19	gold quality
cardiac muscle of right atrium	UBERON:0003379	68.70	gold quality
left ventricle myocardium	UBERON:0006566	68.49	gold quality
lower esophagus mucosa	UBERON:0035834	68.22	gold quality
amygdala	UBERON:0001876	64.57	gold quality
anterior cingulate cortex	UBERON:0009835	64.25	gold quality
right frontal lobe	UBERON:0002810	63.48	gold quality
prefrontal cortex	UBERON:0000451	63.30	gold quality
Brodmann (1909) area 9	UBERON:0013540	62.37	gold quality
pancreatic ductal cell	CL:0002079	61.24	silver quality
neocortex	UBERON:0001950	60.42	gold quality
blood	UBERON:0000178	59.98	gold quality
putamen	UBERON:0001874	59.50	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	59.23	gold quality
quadriceps femoris	UBERON:0001377	59.12	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	7.39

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

3 targets.

Target	Regulation
BEST1	Activation
CGA	Activation
GH1	Activation

JASPAR motifs

Motif	Name	Family
MA0711.1	OTX1	Paired-related HD factors
MA0711.2	OTX1	Paired-related HD factors

JASPAR matrix evidence (PMIDs): PMID:18585360

Upstream regulators (CollecTRI, top): TP53

miRNA regulators (miRDB)

104 targeting OTX1, 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-190A-3P	100.00	80.35	5520
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-4510	100.00	66.60	2050
HSA-MIR-3924	100.00	72.09	2394
HSA-MIR-6127	100.00	66.76	2188
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-196A-5P	100.00	68.16	684
HSA-MIR-196B-5P	100.00	68.16	681
HSA-MIR-511-3P	99.99	68.85	1467
HSA-MIR-4531	99.99	69.70	3181
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-8068	99.98	73.85	2376
HSA-MIR-548AJ-3P	99.96	73.38	5345
HSA-MIR-548X-3P	99.96	73.38	5345
HSA-MIR-9983-3P	99.94	71.48	3631
HSA-MIR-6845-3P	99.94	66.88	1439
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-497-5P	99.92	71.83	2674
HSA-MIR-6768-5P	99.92	67.36	1942
HSA-MIR-1305	99.91	71.43	3443
HSA-MIR-15A-5P	99.90	72.80	2787
HSA-MIR-15B-5P	99.90	72.78	2798
HSA-MIR-16-5P	99.90	72.80	2780

Literature-anchored findings (GeneRIF, showing 25)

• Fine mapping of the chromosome 2p12-16 dyslexia susceptibility locus candidate gene (PMID:11901358)
• OTR1, OTX2 and CRX act as positive modulators of the BEST1 promoter in the retinal pigment epithelium. (PMID:18849347)
• In the human fetal eye, OTX1 expression was confined to anterior retina. (PMID:19414065)
• This study identifies OTX1 as a molecular marker for high-grade germinal center derived Non-Hodgkin Lymphoma (PMID:19893048)
• The early expression of OTX1 in proliferative cell layers of the human fetal brain supports the concept that this homeobox gene is important in neuronal cell development and differentiation. (PMID:20354145)
• established that the p53 protein directly induces OTX1 expression by acting on its promoter (PMID:21478910)
• XPO1 and OXT1 may contribute to ASD in 2p15-p16.1 deletion cases and non-deletion cases of ASD mapping to this chromosome region. (PMID:21750575)
• overexpression of OTX1 results in accumulation of colorectal cancer (CRC) cell proliferation and invasion in vitro and tumor growth in vivo, whereas ablation of OTX1 expression inhibits the proliferative and invasive capability of CRC cell lines (PMID:24388989)
• Genitalia defects in these patients could result from the effect of OTX1. (PMID:25203062)
• OTX1 and OTX2 genes might have a role in the pathogenesis of different types of sinonasal neoplasms. (PMID:28348423)
• We speculate that ACTR2 and MEIS1 might respectively play a role in the pathogenesis of the observed deafness and cardiomyopathy…the patient carrying a 2p14p15 deletion including OTX1 had normal kidneys and genitalia, thus confirming that OTX1 haploinsufficiency is not invariably associated with genitourinary defects. (PMID:28599093)
• High OTX1 expression is associated with gastric cancer. (PMID:30066897)
• The OTX1 gene was expressed in 52% of 60 Brazilian medulloblastoma patients. Expression varied with age (higher in adults), location (predominantly by hemisphere), and histological type (desmoplastic). (PMID:30797919)
• Long non-coding RNA HNF1A-AS1 upregulates OTX1 to enhance angiogenesis in colon cancer via the binding of transcription factor PBX3. (PMID:32325080)
• miR-3196 acts as a Tumor Suppressor and Predicts Survival Outcomes in Patients With Gastric Cancer. (PMID:32419651)
• MicroRNA-4516 suppresses pancreatic cancer development via negatively regulating orthodenticle homeobox 1. (PMID:32549762)
• OTX1 exerts an oncogenic role and is negatively regulated by miR129-5p in laryngeal squamous cell carcinoma. (PMID:32838760)
• OTX1 is a novel regulator of proliferation, migration, invasion and apoptosis in lung adenocarcinoma. (PMID:33015792)
• Long noncoding RNA MAFG-AS1 facilitates the progression of hepatocellular carcinoma via targeting miR-3196/OTX1 axis. (PMID:33336731)
• Orthodenticle homeobox OTX1 is a potential prognostic biomarker for bladder cancer. (PMID:34559577)
• Overexpression of OTX1 promotes tumorigenesis in patients with esophageal squamous cell carcinoma. (PMID:35303522)
• Knockdown of circMYOF inhibits cell growth, metastasis, and glycolysis through miR-145-5p/OTX1 regulatory axis in laryngeal squamous cell carcinoma. (PMID:35474406)
• MiR-195-5p suppresses gastric adenocarcinoma cell progression via targeting OTX1. (PMID:36093844)
• OTX1 promotes tumorigenesis and progression of cervical cancer by regulating the Wnt signaling pathway. (PMID:36177903)
• OTX1 regulates tumorigenesis and metastasis in glioma. (PMID:38218040)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	otx1	ENSDARG00000094992
mus_musculus	Otx1	ENSMUSG00000005917
rattus_norvegicus	Otx1	ENSRNOG00000065081

Paralogs (50): ARX (ENSG00000004848), PAX6 (ENSG00000007372), PAX7 (ENSG00000009709), ALX4 (ENSG00000052850), GSC2 (ENSG00000063515), PITX1 (ENSG00000069011), PAX2 (ENSG00000075891), RHOXF1 (ENSG00000101883), CRX (ENSG00000105392), EVX1 (ENSG00000106038), PAX4 (ENSG00000106331), NOBOX (ENSG00000106410), PITX3 (ENSG00000107859), PHOX2B (ENSG00000109132), PRRX1 (ENSG00000116132), VSX2 (ENSG00000119614), ESX1 (ENSG00000123576), PAX8 (ENSG00000125618), PAX1 (ENSG00000125813), RHOXF2 (ENSG00000131721), GSC (ENSG00000133937), RAX (ENSG00000134438), PAX3 (ENSG00000135903), ALX3 (ENSG00000156150), HESX1 (ENSG00000163666), PITX2 (ENSG00000164093), UNCX (ENSG00000164853), PHOX2A (ENSG00000165462), OTX2 (ENSG00000165588), DRGX (ENSG00000165606), PRRX2 (ENSG00000167157), SHOX2 (ENSG00000168779), OTP (ENSG00000171540), RAX2 (ENSG00000173976), EVX2 (ENSG00000174279), PROP1 (ENSG00000175325), ISX (ENSG00000175329), ALX1 (ENSG00000180318), MIXL1 (ENSG00000185155), SHOX (ENSG00000185960)

Protein

Protein identifiers

Homeobox protein OTX1 — P32242 (reviewed: P32242)

Alternative names: Orthodenticle homolog 1

All UniProt accessions (2): B5MC54, P32242

UniProt curated annotations — full annotation on UniProt →

Function. Probably plays a role in the development of the brain and the sense organs. Can bind to the BCD target sequence (BTS): 5’-TCTAATCCC-3'.

Subcellular location. Nucleus.

Tissue specificity. Expressed in brain. Detected in the anterior part of the neural fetal retina (at protein level).

Similarity. Belongs to the paired homeobox family. Bicoid subfamily.

RefSeq proteins (2): NP_001186699, NP_055377* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001356	HD	Domain
IPR003025	Otx_TF	Family
IPR003026	Otx1_TF	Family
IPR009057	Homeodomain-like_sf	Homologous_superfamily
IPR013851	Otx_TF_C	Domain
IPR017970	Homeobox_CS	Conserved_site

Pfam: PF00046, PF03529

UniProt features (9 total): compositionally biased region 4, region of interest 2, chain 1, DNA-binding region 1, cross-link 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P32242-F1	58.01	0.18

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 (1): 344

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 157 (showing top): GOBP_HINDBRAIN_DEVELOPMENT, ACTACCT_MIR196A_MIR196B, GOBP_METENCEPHALON_DEVELOPMENT, BENPORATH_ES_WITH_H3K27ME3, WWTAAGGC_UNKNOWN, GOBP_FOREBRAIN_MORPHOGENESIS, TGCTGCT_MIR15A_MIR16_MIR15B_MIR195_MIR424_MIR497, TGACCTY_ERR1_Q2, BONCI_TARGETS_OF_MIR15A_AND_MIR16_1, GOBP_FOREBRAIN_DEVELOPMENT, AACWWCAANK_UNKNOWN, SRF_Q5_01, GOBP_ANIMAL_ORGAN_MORPHOGENESIS, GOBP_EAR_DEVELOPMENT, GOBP_ANTERIOR_POSTERIOR_PATTERN_SPECIFICATION

GO Biological Process (10): regulation of transcription by RNA polymerase II (GO:0006357), anterior/posterior pattern specification (GO:0009952), metencephalon development (GO:0022037), midbrain development (GO:0030901), inner ear morphogenesis (GO:0042472), positive regulation of transcription by RNA polymerase II (GO:0045944), diencephalon morphogenesis (GO:0048852), regulation of DNA-templated transcription (GO:0006355), multicellular organism development (GO:0007275), forebrain development (GO:0030900)

GO Molecular Function (7): RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978), DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981), DNA-binding transcription activator activity, RNA polymerase II-specific (GO:0001228), sequence-specific double-stranded DNA binding (GO:1990837), DNA binding (GO:0003677), DNA-binding transcription factor activity (GO:0003700), protein binding (GO:0005515)

GO Cellular Component (2): chromatin (GO:0000785), nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
anatomical structure development	4
RNA polymerase II transcription regulatory region sequence-specific DNA binding	3
regulation of DNA-templated transcription	2
transcription by RNA polymerase II	2
brain development	2
regulation of transcription by RNA polymerase II	2
regionalization	1
hindbrain development	1
ear morphogenesis	1
embryonic morphogenesis	1
inner ear development	1
positive regulation of DNA-templated transcription	1
anatomical structure morphogenesis	1
diencephalon development	1
forebrain morphogenesis	1
DNA-templated transcription	1
regulation of gene expression	1
regulation of RNA biosynthetic process	1
multicellular organismal process	1
cis-regulatory region sequence-specific DNA binding	1
chromatin	1
DNA-binding transcription factor activity	1
DNA-binding transcription factor activity, RNA polymerase II-specific	1
DNA-binding transcription activator activity	1
positive regulation of transcription by RNA polymerase II	1
double-stranded DNA binding	1
sequence-specific DNA binding	1
nucleic acid binding	1
transcription cis-regulatory region binding	1
transcription regulator activity	1
binding	1
chromosome	1
cellular anatomical structure	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

1216 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
OTX1	PAX2	Q02962	796
OTX1	FOXG1	P55315	613
OTX1	NEUROG1	Q92886	603
OTX1	EBF1	Q9UH73	602
OTX1	FGF8	P55075	562
OTX1	TBR1	Q16650	556
OTX1	HLTF	Q14527	552
OTX1	TERT	O14746	543
OTX1	FGF3	P11487	540
OTX1	ONECUT2	O95948	521
OTX1	LMX1A	Q8TE12	510
OTX1	SIX3	O95343	508
OTX1	LHX2	P50458	504
OTX1	FEZF2	Q8TBJ5	492
OTX1	ACTR1B	P42025	490

IntAct

584 interactions, top by confidence:

A	B	Type	Score
OTX1	MDFI	psi-mi:“MI:0915”(physical association)	0.860
MDFI	OTX1	psi-mi:“MI:0915”(physical association)	0.860
GRN	OTX1	psi-mi:“MI:0915”(physical association)	0.850
OTX1	GRN	psi-mi:“MI:0915”(physical association)	0.850
OTX1	COMP	psi-mi:“MI:0915”(physical association)	0.780
KRTAP4-12	OTX1	psi-mi:“MI:0915”(physical association)	0.780
OTX1	KRTAP3-2	psi-mi:“MI:0915”(physical association)	0.780
COMP	OTX1	psi-mi:“MI:0915”(physical association)	0.780
OTX1	KRTAP4-12	psi-mi:“MI:0915”(physical association)	0.780
KRTAP3-2	OTX1	psi-mi:“MI:0915”(physical association)	0.780
RGS20	OTX1	psi-mi:“MI:0915”(physical association)	0.740
OTX1	KRTAP10-9	psi-mi:“MI:0915”(physical association)	0.740
OTX1	LCE1B	psi-mi:“MI:0915”(physical association)	0.740
OTX1	RGS20	psi-mi:“MI:0915”(physical association)	0.740
KRTAP10-9	OTX1	psi-mi:“MI:0915”(physical association)	0.740
LCE1B	OTX1	psi-mi:“MI:0915”(physical association)	0.740

BioGRID (192): OTX1 (Two-hybrid), OTX1 (Two-hybrid), OTX1 (Two-hybrid), OTX1 (Two-hybrid), SMARCC1 (Two-hybrid), RGS20 (Two-hybrid), CHRD (Two-hybrid), SPRY1 (Two-hybrid), SPRY2 (Two-hybrid), RBPMS (Two-hybrid), RGS17 (Two-hybrid), KRTAP4-12 (Two-hybrid), KCNK16 (Two-hybrid), KRTAP3-2 (Two-hybrid), KRTAP9-2 (Two-hybrid)

ESM2 similar proteins: A2TED3, O00570, O57401, O95409, P06602, P07548, P09085, P14734, P16241, P20264, P22544, P23441, P23757, P31361, P32027, P32182, P32242, P35583, P39768, P40764, P41225, P43241, P43698, P43699, P48430, P48431, P48432, P50220, P53783, P53784, P54231, P54269, P56224, P80205, Q04649, Q07687, Q24255, Q24533, Q2PG84, Q2Z1R2

Diamond homologs: A0A1W2PPF3, A1YEY5, A1YFI3, A1YG57, A2T733, A2T7P4, A6NLW8, A6NNA5, F1NEA7, G5EBU4, G5EDS1, O18381, O35137, O35160, O42250, O43186, O43316, O43812, O54751, O70137, O73917, O75360, O75364, O95076, P09088, P0CJ85, P0CJ86, P0CJ87, P0CJ88, P0CJ89, P0CJ90, P21711, P22810, P26367, P26630, P29454, P32242, P32243, P34764, P34765

SIGNOR signaling

1 interactions.

A	Effect	B	Mechanism
OTX1	“up-regulates quantity by expression”	BEST1	“transcriptional regulation”

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 68 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
Keratinization	34	35.1×	5e-45
Formation of the cornified envelope	9	14.6×	2e-07

GO biological processes:

GO term	Partners	Fold	FDR
hair cycle	5	104.0×	1e-07
keratinization	9	46.8×	6e-11

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	33
Likely benign	0
Benign	3

Top pathogenic / likely-pathogenic (0)

SpliceAI

888 predictions. Top by Δscore:

Variant	Effect	Δscore
2:63050149:GCAG:G	donor_gain	1.0000
2:63050150:CAGG:C	donor_loss	1.0000
2:63050152:GGT:G	donor_loss	1.0000
2:63054045:A:AG	acceptor_gain	1.0000
2:63054046:G:GG	acceptor_gain	1.0000
2:63054046:GCC:G	acceptor_gain	1.0000
2:63054157:G:GT	donor_gain	1.0000
2:63054199:G:GG	donor_gain	1.0000
2:63054199:GTGC:G	donor_loss	1.0000
2:63055488:C:CA	acceptor_gain	1.0000
2:63055489:G:A	acceptor_gain	1.0000
2:63055496:T:A	acceptor_gain	1.0000
2:63055498:CA:C	acceptor_loss	1.0000
2:63055500:GGTCT:G	acceptor_gain	1.0000
2:63050153:G:GG	donor_gain	0.9900
2:63052878:A:AG	acceptor_gain	0.9900
2:63052879:G:GG	acceptor_gain	0.9900
2:63052879:GGCCA:G	acceptor_gain	0.9900
2:63053084:CCGGG:C	donor_loss	0.9900
2:63053086:GG:G	donor_gain	0.9900
2:63053087:GG:G	donor_gain	0.9900
2:63053088:GTGAG:G	donor_loss	0.9900
2:63053089:T:TC	donor_loss	0.9900
2:63053090:G:GT	donor_loss	0.9900
2:63054041:CCGCA:C	acceptor_loss	0.9900
2:63054045:A:C	acceptor_loss	0.9900
2:63054046:GC:G	acceptor_gain	0.9900
2:63054046:GCCA:G	acceptor_gain	0.9900
2:63054194:TCCAG:T	donor_gain	0.9900
2:63055485:ATCC:A	acceptor_gain	0.9900

AlphaMissense

2292 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
2:63054058:A:G	K37E	1.000
2:63054060:G:C	K37N	1.000
2:63054060:G:T	K37N	1.000
2:63054067:C:T	R40W	1.000
2:63054068:G:A	R40Q	1.000
2:63054070:G:A	E41K	1.000
2:63054073:C:A	R42S	1.000
2:63054073:C:G	R42G	1.000
2:63054073:C:T	R42C	1.000
2:63054074:G:A	R42H	1.000
2:63054074:G:T	R42L	1.000
2:63054076:A:G	T43A	1.000
2:63054076:A:T	T43S	1.000
2:63054077:C:A	T43N	1.000
2:63054077:C:G	T43S	1.000
2:63054077:C:T	T43I	1.000
2:63054082:T:A	F45I	1.000
2:63054082:T:C	F45L	1.000
2:63054082:T:G	F45V	1.000
2:63054083:T:C	F45S	1.000
2:63054083:T:G	F45C	1.000
2:63054084:C:A	F45L	1.000
2:63054084:C:G	F45L	1.000
2:63054095:A:C	Q49P	1.000
2:63054095:A:G	Q49R	1.000
2:63054096:G:C	Q49H	1.000
2:63054096:G:T	Q49H	1.000
2:63054098:T:A	L50Q	1.000
2:63054098:T:C	L50P	1.000
2:63054106:C:T	L53F	1.000

dbSNP variants (sampled 300 via entrez): RS1000098505 (2:63051245 G>T), RS1000553781 (2:63048373 C>G), RS1000792320 (2:63052631 C>G,T), RS1001051355 (2:63054436 C>G), RS1001625233 (2:63053164 G>A), RS1001666489 (2:63047775 G>A), RS1002061074 (2:63049190 C>A), RS1002440576 (2:63052501 C>T), RS1002557487 (2:63054879 T>C), RS1002891990 (2:63054523 C>T), RS1002909221 (2:63049977 AAGAG>A,AAG), RS1003005947 (2:63049703 G>A), RS1003224172 (2:63056069 C>G,T), RS1003244757 (2:63048665 G>C), RS1003681478 (2:63050540 C>T)

Disease associations

OMIM: gene MIM:600036 | disease phenotypes: MIM:209900

GenCC curated gene-disease

Mondo (1): Bardet-Biedl syndrome (MONDO:0015229)

Orphanet (1): Bardet-Biedl syndrome (Orphanet:110)

HPO phenotypes

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

GWAS associations

4 associations (top):

Study	Trait	p-value
GCST006922_6	Regular attendance at a religious group	4.000000e-08
GCST006940_104	Neurociticism	2.000000e-08
GCST007323_63	Risk-taking tendency (4-domain principal component model)	1.000000e-12
GCST010136_10	Fruit consumption	1.000000e-08

EFO canonical traits (4, from GWAS)

EFO ID	Trait name
EFO:0009592	social interaction measurement
EFO:0007660	neuroticism measurement
EFO:0008579	risk-taking behaviour
EFO:0008111	diet measurement

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
D020788	Bardet-Biedl Syndrome	C10.228.140.617.200; C11.270.684.624; C16.131.077.245.125; C16.320.184.125

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, decreases expression	3
sodium arsenite	decreases expression, increases abundance, increases expression	2
Arsenic	affects methylation, increases abundance, increases expression	2
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamide	decreases expression	1
dicrotophos	increases expression	1
ethylbenzene	decreases expression, increases methylation, affects cotreatment	1
bisphenol A	affects cotreatment, increases expression	1
kojic acid	increases expression	1
trichostatin A	decreases expression	1
tris(2-butoxyethyl) phosphate	affects expression	1
ferrous chloride	decreases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	decreases expression, affects cotreatment	1
abrine	decreases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
(+)-JQ1 compound	decreases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Leflunomide	decreases expression	1
Acetaminophen	decreases expression	1
Air Pollutants	affects methylation, increases abundance	1
Air Pollutants, Occupational	decreases expression, increases methylation	1
Arbutin	decreases expression	1
Benzo(a)pyrene	decreases methylation	1
Diethylhexyl Phthalate	decreases expression	1
Enzyme Inhibitors	decreases activity, increases O-linked glycosylation	1
Formaldehyde	increases expression	1
Methotrexate	decreases expression	1
Nitrogen Dioxide	affects methylation, increases abundance	1
Plant Extracts	affects cotreatment, decreases expression	1
Silicon Dioxide	decreases expression	1
Smoke	decreases expression	1

Cellosaurus cell lines

3 cell lines: 3 embryonic stem cell

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

Cellosaurus	Name	Category	Sex
CVCL_A5B1	SEES3-1V human OTX1, clone1	Embryonic stem cell	Male
CVCL_A5B2	SEES3-1V human OTX1, clone2	Embryonic stem cell	Male
CVCL_A5B3	SEES3-1V human OTX1, clone3	Embryonic stem cell	Male

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT03746522	PHASE3	COMPLETED	Setmelanotide (RM-493), Melanocortin-4 Receptor (MC4R) Agonist, in Bardet-Biedl Syndrome (BBS) and Alström Syndrome (AS) Participants With Moderate to Severe Obesity
NCT04966741	PHASE3	COMPLETED	Setmelanotide in Pediatric Participants With Rare Genetic Diseases of Obesity
NCT05194124	PHASE3	COMPLETED	Phase 3 Crossover Trial of Two Formulations of Setmelanotide in Participants With Specific Gene Defects in the MC4R Pathway
NCT03490019	PHASE2	WITHDRAWN	Treatment of Bardet-Biedl-Syndrome With Metformin for Evaluation of a Possible Visual Improvement
NCT00078091	Not specified	TERMINATED	Genetics and Clinical Characteristics of Bardet-Biedl Syndrome
NCT00213811	Not specified	COMPLETED	Bardet-Biedl Syndrome Study: Clinical and Genetic Epidemiology Study in Adults
NCT01401998	Not specified	RECRUITING	ARPKD Database Study
NCT02329210	Not specified	RECRUITING	Clinical Registry Investigating Bardet-Biedl Syndrome
NCT02435940	Not specified	RECRUITING	Inherited Retinal Degenerative Disease Registry
NCT04461444	Not specified	RECRUITING	COhort for Bardet-Bield Syndrome and Alström Syndrome for Translational Research Monocentric Interventional Study
NCT04463316	Not specified	RECRUITING	GROWing Up With Rare GENEtic Syndromes
NCT04874909	Not specified	COMPLETED	Classification, Functional Stratification and Biomarkers in Ciliopathy (CILLICORIRCM)
NCT05183802	Not specified	APPROVED_FOR_MARKETING	An Expanded Access Protocol for Setmelanotide for Treatment of Bardet-Biedl Syndrome (BBS)
NCT05400278	Not specified	COMPLETED	Characterizing the Genotype and Phenotype in Adults With Bardet-Biedl Syndrome
NCT06239064	Not specified	ACTIVE_NOT_RECRUITING	Early Genetic Identification of Obesity
NCT06615011	Not specified	NOT_YET_RECRUITING	Bardet Beidle Syndrome in a Syrian Adolescent : a Rare Case Report
NCT07602803	Not specified	COMPLETED	The Effect of GLP1 Agonists on Weight Loss in BBS Cohort in the UK