IFT38

Summary

IFT38 (intraflagellar transport 38, HGNC:19009) is a protein-coding gene on chromosome 16p13.3, encoding Clusterin-associated protein 1 (Q96AJ1). Required for cilia biogenesis.

The protein encoded by this gene contains a single coiled-coil region. Alternative splicing results in multiple transcript variants and protein isoforms.

Source: NCBI Gene 23059 — RefSeq curated summary.

At a glance

• Gene–disease (curated): Leber congenital amaurosis (Limited, GenCC)
• GWAS associations: 4
• Clinical variants (ClinVar): 481 total — 1 pathogenic, 2 likely-pathogenic
• Phenotypes (HPO): 1
• MANE Select transcript: NM_015041

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:19009
Approved symbol	IFT38
Name	intraflagellar transport 38
Location	16p13.3
Locus type	gene with protein product
Status	Approved
Aliases	FLJ13297, KIAA0643, FAP22, CFAP22
Ensembl gene	ENSG00000103351
Ensembl biotype	protein_coding
OMIM	616787
Entrez	23059

Gene structure

Transcript identifiers

Ensembl transcripts: 19 — 14 protein_coding, 4 nonsense_mediated_decay, 1 retained_intron

ENST00000341633, ENST00000571025, ENST00000572600, ENST00000572632, ENST00000573370, ENST00000574369, ENST00000574551, ENST00000574592, ENST00000575134, ENST00000575323, ENST00000576117, ENST00000576634, ENST00000910103, ENST00000910104, ENST00000915032, ENST00000969004, ENST00000969005, ENST00000969006, ENST00000969007

RefSeq mRNA: 3 — MANE Select: NM_015041 NM_001330454, NM_015041, NM_024793

CCDS: CCDS32381, CCDS45398, CCDS81942

Canonical transcript exons

ENST00000576634 — 12 exons

Exon	Start	End
ENSE00002645158	3501004	3501089
ENSE00002667147	3536122	3539048
ENSE00003473527	3523158	3523299
ENSE00003476768	3530568	3530675
ENSE00003489632	3532786	3532841
ENSE00003491820	3508289	3508468
ENSE00003538998	3519903	3520036
ENSE00003585723	3515508	3515591
ENSE00003593408	3512383	3512478
ENSE00003650954	3504720	3504831
ENSE00003654981	3506331	3506415
ENSE00003693540	3526412	3526484

Expression profiles

Bgee: expression breadth ubiquitous, 285 present calls, max score 95.86.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 14.7613 / max 459.3157, expressed in 1742 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
152430	10.8619	1721
152431	3.8994	1390

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
bronchial epithelial cell	CL:0002328	95.86	gold quality
calcaneal tendon	UBERON:0003701	95.35	gold quality
epithelium of bronchus	UBERON:0002031	95.30	gold quality
bronchus	UBERON:0002185	94.69	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	94.19	gold quality
ventricular zone	UBERON:0003053	93.29	gold quality
left testis	UBERON:0004533	93.06	gold quality
right uterine tube	UBERON:0001302	92.87	gold quality
right testis	UBERON:0004534	92.66	gold quality
testis	UBERON:0000473	92.47	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	92.38	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	92.19	gold quality
tendon	UBERON:0000043	92.11	gold quality
sperm	CL:0000019	91.92	gold quality
cortical plate	UBERON:0005343	91.21	gold quality
colonic epithelium	UBERON:0000397	90.14	gold quality
ganglionic eminence	UBERON:0004023	90.12	gold quality
male germ cell	CL:0000015	89.72	gold quality
stromal cell of endometrium	CL:0002255	89.14	gold quality
tendon of biceps brachii	UBERON:0008188	89.07	gold quality
endocervix	UBERON:0000458	88.84	gold quality
endothelial cell	CL:0000115	88.83	silver quality
body of uterus	UBERON:0009853	88.44	gold quality
adenohypophysis	UBERON:0002196	88.24	gold quality
endometrium	UBERON:0001295	88.09	gold quality
islet of Langerhans	UBERON:0000006	87.99	gold quality
left ovary	UBERON:0002119	87.99	gold quality
epithelium of nasopharynx	UBERON:0001951	87.54	gold quality
right ovary	UBERON:0002118	87.52	gold quality
right coronary artery	UBERON:0001625	87.41	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

miRNA regulators (miRDB)

73 targeting IFT38, 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-3646	100.00	73.56	5283
HSA-MIR-4262	100.00	73.26	3931
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-3185	99.99	68.12	1959
HSA-MIR-3662	99.99	73.82	5684
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-MIR-5696	99.98	72.36	4487
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-548AA	99.96	70.64	3753
HSA-MIR-548AP-3P	99.96	70.64	3753
HSA-MIR-548T-3P	99.96	70.64	3753
HSA-MIR-651-3P	99.94	73.48	5177
HSA-MIR-6835-3P	99.93	70.49	2904
HSA-MIR-218-5P	99.93	72.22	2103
HSA-MIR-10527-5P	99.91	72.28	3754
HSA-MIR-548E-5P	99.89	72.73	4486
HSA-MIR-3919	99.87	69.45	2489
HSA-MIR-6124	99.87	69.78	3551
HSA-MIR-5003-3P	99.85	69.29	2517
HSA-MIR-4698	99.84	71.41	4303
HSA-MIR-3180-5P	99.82	69.12	2422
HSA-MIR-4420	99.82	70.08	1624
HSA-MIR-181B-2-3P	99.81	70.06	1646
HSA-MIR-181B-3P	99.81	70.06	1646
HSA-MIR-4659A-3P	99.80	72.62	4248

Literature-anchored findings (GeneRIF, showing 5)

• inactivation of CLUAP1 may conceivably serve in the future as a novel therapeutic intervention for treatment of colon cancer (PMID:15480429)
• CLUAP1 (clusterin-associated protein 1) is highly expressed in osteosarcoma, ovarian, colon, and lung cancers (PMID:17203229)
• Consistent with the knowledge that CLUAP1 plays an important role in cilia function and that cilia are critical to photoreceptor function, our results indicate that hypomorphic mutations in CLUAP1 can result in dysfunctional photoreceptors without systemic abnormalities. This is the first report linking mutations in CLUAP1 to human disease and establishes CLUAP1 as a candidate Leber congenital amaurosis gene (PMID:26820066)
• Two variants in CLUAP1 were identified through exome-sequence analysis, Chr16:g.3558407T>G, c.338T>G, p.(Met113Arg) and Chr16:g.3570011C>T, c.688C>T, p.(Arg230Ter). he genetic data show that these variants are present in an affected child, are rare in the population, and result in reduced, but not absent, intraflagellar transport. (PMID:28679688)
• Identification of the primary ciliary proteins IFT38 and IFT144 to enhance serum-mediated YAP activation and cell proliferation. (PMID:37783116)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	cluap1	ENSDARG00000079110
mus_musculus	Cluap1	ENSMUSG00000014232
rattus_norvegicus	Cluap1	ENSRNOG00000007117
drosophila_melanogaster	Cluap1	FBGN0031196
caenorhabditis_elegans		WBGENE00001119

Protein

Protein identifiers

Clusterin-associated protein 1 — Q96AJ1 (reviewed: Q96AJ1)

Alternative names: Qilin

All UniProt accessions (10): Q96AJ1, I3L0L1, I3L121, I3L1J4, I3L257, I3L2E1, I3L3S9, I3L455, I3L487, J3KNW5

UniProt curated annotations — full annotation on UniProt →

Function. Required for cilia biogenesis. Appears to function within the multiple intraflagellar transport complex B (IFT-B). Key regulator of hedgehog signaling.

Subunit / interactions. Interacts with CLU/clusterin. Interacts with UBXN10; the interaction is direct.

Subcellular location. Cell projection. Cilium. Nucleus.

Tissue specificity. Expressed in testis, thyroid and trachea and to a lower extent in spinal cord and adrenal gland. Highly expressed in colon cancer and osteosarcoma cell lines.

Miscellaneous. Associated with a number of cancers such as colon and bone cancer. Possibly involved in polycystic kidney diseases.

Similarity. Belongs to the CLUAP1 family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q96AJ1-1	1	yes
Q96AJ1-2	2

RefSeq proteins (3): NP_001317383, NP_055856, NP_079069 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR019366	Clusterin-associated_protein-1	Family

Pfam: PF10234

UniProt features (12 total): modified residue 4, sequence variant 2, compositionally biased region 2, chain 1, region of interest 1, coiled-coil region 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96AJ1-F1	78.02	0.51

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 (4): 314, 324, 326, 409

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-5620924	Intraflagellar transport

MSigDB gene sets: 191 (showing top): GSE18804_SPLEEN_MACROPHAGE_VS_TUMORAL_MACROPHAGE_DN, GOBP_MORPHOGENESIS_OF_AN_EPITHELIUM, GOBP_EMBRYO_DEVELOPMENT_ENDING_IN_BIRTH_OR_EGG_HATCHING, GOBP_EPITHELIUM_DEVELOPMENT, GOBP_NEURAL_TUBE_DEVELOPMENT, GOBP_MORPHOGENESIS_OF_EMBRYONIC_EPITHELIUM, GOCC_MICROTUBULE_ORGANIZING_CENTER, GOBP_SPECIFICATION_OF_SYMMETRY, GOBP_ANIMAL_ORGAN_MORPHOGENESIS, GOBP_EMBRYONIC_HEART_TUBE_DEVELOPMENT, GOBP_EMBRYONIC_ORGAN_MORPHOGENESIS, GOBP_HEART_MORPHOGENESIS, GOBP_CILIUM_ORGANIZATION, BROWNE_HCMV_INFECTION_14HR_DN, GOCC_CENTROSOME

GO Biological Process (9): neural tube closure (GO:0001843), heart looping (GO:0001947), smoothened signaling pathway (GO:0007224), floor plate formation (GO:0021508), axoneme assembly (GO:0035082), intraciliary anterograde transport (GO:0035720), cilium assembly (GO:0060271), cell projection organization (GO:0030030), left/right pattern formation (GO:0060972)

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

GO Cellular Component (11): nucleoplasm (GO:0005654), centrosome (GO:0005813), microtubule organizing center (GO:0005815), cilium (GO:0005929), actin cytoskeleton (GO:0015629), intraciliary transport particle A (GO:0030991), intraciliary transport particle B (GO:0030992), ciliary tip (GO:0097542), ciliary base (GO:0097546), nucleus (GO:0005634), cell projection (GO:0042995)

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
Assembly of the 9+0 primary cilium	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	5
intraciliary transport particle	3
protein-containing complex	2
cilium	2
primary neural tube formation	1
tube closure	1
embryonic heart tube morphogenesis	1
determination of heart left/right asymmetry	1
cell surface receptor signaling pathway	1
ventral midline development	1
floor plate morphogenesis	1
anatomical structure formation involved in morphogenesis	1
microtubule bundle formation	1
cellular component assembly	1
cilium assembly	1
intraciliary transport	1
axoneme assembly	1
intraciliary transport involved in cilium assembly	1
cilium organization	1
protein localization to cilium	1
organelle assembly	1
trans-Golgi to periciliary membrane compartment transport	1
plasma membrane bounded cell projection assembly	1
ciliary transition zone assembly	1
cellular component organization	1
regionalization	1
binding	1
nuclear lumen	1
centriole	1
microtubule organizing center	1
microtubule cytoskeleton	1
membrane-bounded organelle	1
plasma membrane bounded cell projection	1
cytoskeleton	1
ciliary transition zone	1
ciliary transition fiber	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

1546 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
IFT38	IFT57	Q9NWB7	995
IFT38	IFT54	Q8TDR0	986
IFT38	IFT20	Q8IY31	981
IFT38	IFT52	Q9Y366	980
IFT38	IFT80	Q9P2H3	977
IFT38	IFT172	Q9UG01	969
IFT38	IFT88	Q13099	967
IFT38	IFT22	Q9H7X7	882
IFT38	IFT56	A0AVF1	866
IFT38	IFT25	Q9Y547	859
IFT38	IFT27	Q9BW83	848
IFT38	IFT70B	Q8N4P2	842
IFT38	IFT46	Q9NQC8	835
IFT38	IFT74	Q96LB3	777
IFT38	IFT81	Q8WYA0	757

IntAct

73 interactions, top by confidence:

A	B	Type	Score
IFT57	CORO1A	psi-mi:“MI:0914”(association)	0.790
IFT70A	IFT56	psi-mi:“MI:0914”(association)	0.790
IFT70B	IFT56	psi-mi:“MI:0914”(association)	0.790
MYOG	CLUAP1	psi-mi:“MI:0915”(physical association)	0.780
CLUAP1	MYOG	psi-mi:“MI:0915”(physical association)	0.780
CLUAP1	CINP	psi-mi:“MI:0915”(physical association)	0.740
MAGEA11	CLUAP1	psi-mi:“MI:0915”(physical association)	0.700
CLUAP1	MAGEA11	psi-mi:“MI:0915”(physical association)	0.700
IFT27	IFT56	psi-mi:“MI:0914”(association)	0.690
IFT25	IFT56	psi-mi:“MI:0914”(association)	0.690
IFT88	IFT56	psi-mi:“MI:0914”(association)	0.640
IFT57	IFT56	psi-mi:“MI:0914”(association)	0.640
IFT22	IFT56	psi-mi:“MI:0914”(association)	0.640

BioGRID (264): CLUAP1 (Two-hybrid), CLUAP1 (Two-hybrid), CLUAP1 (Affinity Capture-RNA), CLUAP1 (Affinity Capture-RNA), CRACR2A (Affinity Capture-MS), CLUAP1 (Affinity Capture-MS), CINP (Two-hybrid), CLUAP1 (Two-hybrid), CLUAP1 (Affinity Capture-Western), CLUAP1 (Affinity Capture-MS), UBXN10 (Reconstituted Complex), CLUAP1 (Reconstituted Complex), CLUAP1 (Reconstituted Complex), CLUAP1 (Affinity Capture-MS), CLUAP1 (Affinity Capture-MS)

ESM2 similar proteins: A7RX34, A7SK48, M1V4Y8, O35594, P34609, P47822, P83829, Q08C53, Q0VIA1, Q12874, Q16G71, Q16RX1, Q24740, Q3ZCF2, Q4R6W4, Q4R6Y7, Q567U6, Q5BJT7, Q5I033, Q5R6P5, Q5ZKI4, Q61BU1, Q640U7, Q68RJ5, Q6AYJ5, Q6C5U8, Q6CT76, Q6DJ25, Q6DRJ7, Q6GP65, Q6GQI5, Q6I6D4, Q76I89, Q7TQK5, Q7ZVC2, Q8IRJ8, Q8LDS5, Q8WYA0, Q93833, Q95SK3

Diamond homologs: Q4R6Y7, Q6AYJ5, Q6I6D4, Q7ZVC2, Q8R3P7, Q96AJ1, A8BGV3

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 34 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
Intraflagellar transport	12	100.2×	6e-21
Cilium Assembly	5	22.7×	3e-05
Organelle biogenesis and maintenance	5	13.8×	2e-04

GO biological processes:

GO term	Partners	Fold	FDR
intraciliary anterograde transport	12	343.3×	2e-27
intraciliary transport	10	181.2×	2e-19
non-motile cilium assembly	7	65.6×	5e-10
smoothened signaling pathway	9	52.6×	4e-12
cilium assembly	16	38.0×	2e-20
protein transport	5	7.1×	7e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	2
Uncertain significance	291
Likely benign	153
Benign	19

Top pathogenic / likely-pathogenic (3)

Variant ID	HGVS	Classification
224333	NM_015041.3(CLUAP1):c.817C>T (p.Leu273Phe)	Pathogenic
149298	GRCh38/hg38 16p13.3(chr16:3303551-3965374)x3	Likely pathogenic
254179	NM_015041.3(IFT38):c.338T>G (p.Met113Arg)	Likely pathogenic

SpliceAI

2148 predictions. Top by Δscore:

Variant	Effect	Δscore
16:3501090:G:GG	donor_gain	1.0000
16:3506327:ATAG:A	acceptor_loss	1.0000
16:3506328:TA:T	acceptor_loss	1.0000
16:3506329:A:T	acceptor_loss	1.0000
16:3506330:G:A	acceptor_loss	1.0000
16:3512378:TCCA:T	acceptor_loss	1.0000
16:3512379:CCAG:C	acceptor_loss	1.0000
16:3512380:CA:C	acceptor_loss	1.0000
16:3512381:A:AG	acceptor_gain	1.0000
16:3512381:A:G	acceptor_loss	1.0000
16:3512382:G:A	acceptor_loss	1.0000
16:3512382:G:GG	acceptor_gain	1.0000
16:3512464:G:GT	donor_gain	1.0000
16:3512475:GAGG:G	donor_gain	1.0000
16:3512477:GG:G	donor_gain	1.0000
16:3512478:GG:G	donor_gain	1.0000
16:3512479:G:GA	donor_loss	1.0000
16:3512479:G:GG	donor_gain	1.0000
16:3512480:TAAG:T	donor_loss	1.0000
16:3515502:TCCTA:T	acceptor_loss	1.0000
16:3515503:CCTAG:C	acceptor_loss	1.0000
16:3515504:CTAG:C	acceptor_loss	1.0000
16:3515505:TAGG:T	acceptor_loss	1.0000
16:3515506:AGGA:A	acceptor_loss	1.0000
16:3515507:G:GC	acceptor_loss	1.0000
16:3515589:TTGG:T	donor_loss	1.0000
16:3515592:G:GC	donor_loss	1.0000
16:3515592:G:GG	donor_gain	1.0000
16:3515593:T:C	donor_loss	1.0000
16:3523143:A:AG	acceptor_gain	1.0000

AlphaMissense

2779 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
16:3504818:T:A	W41R	0.999
16:3504818:T:C	W41R	0.999
16:3504822:T:C	L42P	0.999
16:3508326:T:C	L86P	0.999
16:3508334:G:C	A89P	0.999
16:3506381:G:C	R62P	0.998
16:3508326:T:A	L86H	0.998
16:3508359:T:C	L97P	0.998
16:3512434:G:A	G151R	0.998
16:3512434:G:C	G151R	0.998
16:3504744:T:C	L16P	0.997
16:3504813:T:C	L39P	0.997
16:3506398:G:C	A68P	0.997
16:3508326:T:G	L86R	0.997
16:3508328:T:G	Y87D	0.997
16:3508335:C:A	A89E	0.997
16:3508346:G:C	A93P	0.997
16:3508347:C:A	A93E	0.997
16:3512444:T:C	L154P	0.997
16:3506384:T:A	V63D	0.996
16:3506404:G:C	A70P	0.996
16:3506405:C:A	A70D	0.996
16:3508311:T:A	L81H	0.996
16:3508355:G:A	E96K	0.996
16:3508362:T:C	L98P	0.996
16:3512414:C:A	A144E	0.996
16:3512435:G:A	G151E	0.996
16:3519994:T:C	L224P	0.996
16:3501074:T:C	F3L	0.995
16:3501076:C:A	F3L	0.995

dbSNP variants (sampled 300 via entrez): RS1000007245 (16:3536665 T>C), RS1000047338 (16:3506971 C>T), RS1000070201 (16:3507565 A>G), RS1000095902 (16:3538246 C>G,T), RS1000261715 (16:3533117 C>G,T), RS1000269277 (16:3499182 C>A), RS1000301057 (16:3533339 A>C), RS1000401995 (16:3503597 TTTTTTG>T,TTTTTTGTTTTTG), RS1000420994 (16:3494006 A>G), RS1000438000 (16:3508534 G>C), RS1000449870 (16:3500159 A>G), RS1000452259 (16:3493770 C>T), RS1000573817 (16:3523804 A>G), RS1000635211 (16:3534184 C>T), RS1000783182 (16:3528870 C>T)

Disease associations

OMIM: gene MIM:616787 | disease phenotypes: MIM:600268, MIM:204000, MIM:213300

GenCC curated gene-disease

Disease	Classification	Inheritance
Leber congenital amaurosis	Limited	Autosomal recessive

Mondo (4): Toriello-Lacassie-Droste syndrome (MONDO:0010854), Leber congenital amaurosis (MONDO:0018998), Joubert syndrome (MONDO:0018772), inherited retinal dystrophy (MONDO:0019118)

Orphanet (4): Oculoectodermal syndrome (Orphanet:3339), Leber congenital amaurosis (Orphanet:65), Isolated Joubert syndrome (Orphanet:475), OBSOLETE: Inherited retinal disorder (Orphanet:71862)

HPO phenotypes

1 total (1 of 1 shown, HPO-id order):

HPO	Term
HP:0000556	Retinal dystrophy

GWAS associations

4 associations (top):

Study	Trait	p-value
GCST006279_2	Cerebrospinal fluid α-synuclein levels	1.000000e-08
GCST007429_130	Lung function (FVC)	9.000000e-28
GCST007432_57	FEV1	6.000000e-17
GCST009379_162	Type 2 diabetes	1.000000e-08

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0009323	alpha synuclein measurement
EFO:0004312	vital capacity
EFO:0004314	forced expiratory volume

MeSH disease descriptors (3)

Descriptor	Name	Tree numbers
D057130	Leber Congenital Amaurosis	C11.270.516; C11.768.364
D058499	Retinal Dystrophies	C11.768.585.658
C563969	Aplasia Cutis Congenita with Epibulbar Dermoids (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	decreases expression, increases abundance, increases expression	3
bisphenol A	decreases expression, increases expression	2
Arsenic	increases expression, affects methylation, increases abundance	2
Tobacco Smoke Pollution	decreases expression	2
Cadmium Chloride	decreases expression, increases expression	2
aristolochic acid I	decreases expression	1
FR900359	increases phosphorylation	1
testosterone enanthate	affects expression	1
triphenyl phosphate	affects expression	1
di-n-butylphosphoric acid	affects expression	1
CGP 52608	affects binding, increases reaction	1
chloropicrin	decreases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
Air Pollutants	increases abundance, increases expression	1
Atrazine	decreases expression	1
Benzo(a)pyrene	affects methylation	1
Carbamazepine	affects expression	1
Doxorubicin	decreases expression	1
Ethyl Methanesulfonate	increases expression	1
Methyl Methanesulfonate	increases expression	1
Silicon Dioxide	decreases expression	1
Smoke	increases abundance, increases expression	1
Tretinoin	decreases expression	1
Urethane	decreases expression	1
Valproic Acid	affects expression	1
Asbestos, Crocidolite	decreases expression	1
Antirheumatic Agents	increases expression	1
Okadaic Acid	decreases expression	1
Lactic Acid	decreases expression	1

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT00999609	PHASE3	ACTIVE_NOT_RECRUITING	Safety and Efficacy Study in Subjects With Leber Congenital Amaurosis
NCT06891443	PHASE3	RECRUITING	Study to Evaluate Sepofarsen in Subjects With Leber Congenital Amaurosis (LCA) Type 10 (HYPERION)
NCT04224207	PHASE3	COMPLETED	Management of Retinitis Pigmentosa by Mesenchymal Stem Cells by Wharton’s Jelly Derived Mesenchymal Stem Cells
NCT07082855	PHASE3	NOT_YET_RECRUITING	A Multicenter, Randomized, Double-Blind, Controlled Clinical Study of Minocycline for the Treatment of Retinitis Pigmentosa
NCT03763227	PHASE2	COMPLETED	Intravitreal Ranibizumab (Lucentis®) in the Treatment of Non-leaking Macular Cysts in Retinal Dystrophy
NCT04068207	PHASE2	COMPLETED	Minocycline Treatment in Retinitis Pigmentosa
NCT04945772	PHASE2	COMPLETED	Efficacy and Safety of MCO-010 Optogenetic Therapy in Adults With Retinitis Pigmentosa [RESTORE]
NCT00516477	PHASE1	COMPLETED	Safety Study in Subjects With Leber Congenital Amaurosis
NCT00821340	PHASE1	COMPLETED	Clinical Trial of Gene Therapy for Leber Congenital Amaurosis Caused by RPE65 Mutations
NCT05902962	PHASE1	COMPLETED	SAD of IVT VP-001 in PRPF31 Mutation-Associated Retinal Dystrophy Subjects
NCT06319872	PHASE1	RECRUITING	The Effects of Disulfiram (Antabuse®) on Visual Acuity in Patients With Retinal Degeneration
NCT06455826	PHASE1	COMPLETED	MAD of IVT VP-001 in PRPF31 Mutation-Associated Retinal Dystrophy Subjects (Wallaby)
NCT03913143	PHASE2/PHASE3	ACTIVE_NOT_RECRUITING	A Study to Evaluate Efficacy, Safety, Tolerability and Exposure After a Repeat-dose of Sepofarsen (QR-110) in LCA10 (ILLUMINATE)
NCT04855045	PHASE2/PHASE3	UNKNOWN	An Open-label, Dose Escalation and Double-masked, Randomized, Controlled Trial Evaluating Safety and Tolerability of Sepofarsen in Children (<8 Years of Age) With LCA10 Caused by Mutations in the CEP290 Gene.
NCT00749957	PHASE1/PHASE2	COMPLETED	Phase 1/2 Safety and Efficacy Study of AAV-RPE65 Vector to Treat Leber Congenital Amaurosis
NCT01208389	PHASE1/PHASE2	ACTIVE_NOT_RECRUITING	Phase 1 Follow-on Study of AAV2-hRPE65v2 Vector in Subjects With Leber Congenital Amaurosis (LCA) 2
NCT01496040	PHASE1/PHASE2	COMPLETED	Clinical Gene Therapy Protocol for the Treatment of Retinal Dystrophy Caused by Defects in RPE65
NCT02781480	PHASE1/PHASE2	COMPLETED	Clinical Trial of Gene Therapy for the Treatment of Leber Congenital Amaurosis (LCA)
NCT03913130	PHASE1/PHASE2	TERMINATED	Extension Study to Study PQ-110-001 (NCT03140969)
NCT03920007	PHASE1/PHASE2	ACTIVE_NOT_RECRUITING	Study of Subretinally Injected ATSN-101 Administered in Patients With Leber Congenital Amaurosis Caused by Biallelic Mutations in GUCY2D
NCT05203939	PHASE1/PHASE2	ACTIVE_NOT_RECRUITING	Study to Assess the Safety and Efficacy of OCU400 for Retinitis Pigmentosa and Leber Congenital Amaurosis
NCT05906953	PHASE1/PHASE2	RECRUITING	Safety and Efficacy Trial of HG004 for Leber Congenital Amaurosis Related to Rpe65 Gene Mutations (STAR)
NCT06088992	EARLY_PHASE1	ACTIVE_NOT_RECRUITING	Leber Congenital Amaurosis Inherited Blindness of Gene Therapy Trial(LIGHT)
NCT01793168	Not specified	RECRUITING	Rare Disease Patient Registry & Natural History Study - Coordination of Rare Diseases at Sanford
NCT02435940	Not specified	RECRUITING	Inherited Retinal Degenerative Disease Registry
NCT02575430	Not specified	COMPLETED	Natural History Study in Inherited Retinal Disease Subjects Caused by Mutations in RPE65 or LRAT
NCT02714816	Not specified	COMPLETED	Natural History Study of Patients With Leber Congenital Amaurosis Associated With Mutations in RPE65
NCT02946879	Not specified	COMPLETED	Long-Term Follow-Up Gene Therapy Study for Leber Congenital Amaurosis OPTIRPE65 (Retinal Dystrophy Associated With Defects in RPE65)
NCT02970266	Not specified	COMPLETED	Genetic Decryption of Leber Congenital Amaurosis (LCA) in a Large Cohort of Independent Families.
NCT07026565	Not specified	NOT_YET_RECRUITING	Psychotherapy Group for Parents of Children With LCA
NCT00873678	Not specified	COMPLETED	Assessment of the Prevalence of Genes AHI1, NPHP1 and CEP290 in Joubert Syndrome
NCT01401998	Not specified	RECRUITING	ARPKD Database Study
NCT04874909	Not specified	COMPLETED	Classification, Functional Stratification and Biomarkers in Ciliopathy (CILLICORIRCM)
NCT03872479	PHASE1/PHASE2	UNKNOWN	Single Ascending Dose Study in Participants With LCA10
NCT04123626	PHASE1/PHASE2	ACTIVE_NOT_RECRUITING	A Study to Evaluate the Safety and Tolerability of QR-1123 in Subjects With Autosomal Dominant Retinitis Pigmentosa Due to the P23H Mutation in the RHO Gene
NCT04545736	PHASE1/PHASE2	RECRUITING	Oral Metformin for Treatment of ABCA4 Retinopathy
NCT06212297	PHASE1/PHASE2	ACTIVE_NOT_RECRUITING	Fellow-eye Study (FE) of LX101 in Subjects With Inherited Retinal Dystrophy
NCT06852963	PHASE1/PHASE2	ACTIVE_NOT_RECRUITING	A Repeat-Dose, Open-Label, Two Arm Safety and Efficacy Study of Two Doses of VP-001 Administered Intravitreally in Participants With Confirmed PRPF31 Mutation-Associated Retinal Dystrophy, Including Participants Previously Treated With VP001
NCT07177196	PHASE1/PHASE2	ACTIVE_NOT_RECRUITING	Personalized Antisense Oligonucleotide Therapy for a Single Participant With PRPH2 Mutation Associated With Retinal Dystrophy
NCT07063030	EARLY_PHASE1	RECRUITING	A Study of LX107 Gene Therapy in AIPL1-IRD Patients