ZNF408

Summary

ZNF408 (zinc finger protein 408, HGNC:20041) is a protein-coding gene on chromosome 11p11.2, encoding Zinc finger protein 408 (Q9H9D4). May be involved in transcriptional regulation.

The protein encoded by this gene contains ten tandem zinc fingers and an N-terminal SET domain, so it is likely a DNA binding protein that interacts with other proteins. In adults, the encoded protein is expressed most highly in retina. Consequently, defects in this gene have been associated with familial exudative vitreoretinopathy (FEVR) and retinitis pigmentosa (RP).

Source: NCBI Gene 79797 — RefSeq curated summary.

At a glance

• Gene–disease (curated): exudative vitreoretinopathy 6 (Strong, GenCC) — +3 more curated relationships
• GWAS associations: 5
• Clinical variants (ClinVar): 639 total — 5 pathogenic, 6 likely-pathogenic
• Phenotypes (HPO): 80
• MANE Select transcript: NM_024741

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:20041
Approved symbol	ZNF408
Name	zinc finger protein 408
Location	11p11.2
Locus type	gene with protein product
Status	Approved
Aliases	FLJ12827, PRDM17
Ensembl gene	ENSG00000175213
Ensembl biotype	protein_coding
OMIM	616454
Entrez	79797

Gene structure

Transcript identifiers

Ensembl transcripts: 6 — 4 retained_intron, 2 protein_coding

ENST00000311764, ENST00000526410, ENST00000527008, ENST00000531866, ENST00000534481, ENST00000877975

RefSeq mRNA: 2 — MANE Select: NM_024741 NM_001184751, NM_024741

CCDS: CCDS7923

Canonical transcript exons

ENST00000311764 — 5 exons

Exon	Start	End
ENSE00001181414	46702984	46703243
ENSE00001181417	46702704	46702765
ENSE00001181426	46701031	46701099
ENSE00001228139	46704353	46705912
ENSE00003535642	46701399	46701676

Expression profiles

Bgee: expression breadth ubiquitous, 224 present calls, max score 89.00.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 5.2887 / max 75.2944, expressed in 1742 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
114154	5.2887	1742

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
endothelial cell	CL:0000115	89.00	silver quality
tendon of biceps brachii	UBERON:0008188	88.81	silver quality
cervix squamous epithelium	UBERON:0006922	88.11	gold quality
diaphragm	UBERON:0001103	86.44	gold quality
vena cava	UBERON:0004087	86.01	gold quality
type B pancreatic cell	CL:0000169	85.75	gold quality
olfactory bulb	UBERON:0002264	85.55	gold quality
granulocyte	CL:0000094	85.10	gold quality
amniotic fluid	UBERON:0000173	83.58	gold quality
right lobe of liver	UBERON:0001114	83.17	gold quality
mucosa of transverse colon	UBERON:0004991	83.05	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	83.04	gold quality
thymus	UBERON:0002370	82.35	silver quality
parotid gland	UBERON:0001831	82.18	silver quality
sural nerve	UBERON:0015488	81.63	gold quality
lower esophagus mucosa	UBERON:0035834	81.52	gold quality
gluteal muscle	UBERON:0002000	81.51	gold quality
buccal mucosa cell	CL:0002336	81.50	gold quality
leukocyte	CL:0000738	81.47	gold quality
mononuclear cell	CL:0000842	81.39	gold quality
monocyte	CL:0000576	81.35	gold quality
squamous epithelium	UBERON:0006914	81.30	silver quality
blood	UBERON:0000178	81.22	gold quality
gastrocnemius	UBERON:0001388	81.19	gold quality
apex of heart	UBERON:0002098	80.69	gold quality
visceral pleura	UBERON:0002401	80.60	silver quality
muscle of leg	UBERON:0001383	80.25	gold quality
muscle organ	UBERON:0001630	80.10	gold quality
bone marrow	UBERON:0002371	80.09	gold quality
skeletal muscle organ	UBERON:0014892	80.09	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	2.38

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 8)

• Data indicate ZNF408 missense variant (p.Ser126Asn) in 132 familial exudative vitreoretinopathy (FEVR) individuals in a Japanese family. (PMID:23716654)
• ZNF408, previously associated with Familial Exudative Vitreoretinopathy (FEVR), is a new gene causing autosomal recessive rtinitis pigmentosa. (PMID:25882705)
• Several novel mutations (missense, non-stop and insertion) were detected in the coding regions of FZD4, TSPAN12 and ZNF408 genes among the unrelated vitreoretinopathy probands. (PMID:27316669)
• In conclusion, we report a novel mutation in ZNF408 causing autosomal recessive retinitis pigmentosa with vitreal alterations in three members of a Tunisian family, which further accentuates the role of this new gene in the susceptibility to retinitis pigmentosa. (PMID:28095122)
• In a Pakistani family with retinal degeneration, whole-exome sequencing identified 2 homozygous missense variants: c.1304G>A; p.Arg435Gln in ZNF408 (NM_024741) and c.902G>A; p.Gly301Asp in C1QTNF4 (NM_031909). Both segregated with the retinal phenotype in this family and were absent in ethnically matched control chromosomes. (PMID:29721947)
• p.H455Y ZNF408 has reduced DNA-binding ability, as compared to the wild-type protein. The fact that the p.H455Y mutation disrupts the expression of genes important for the development of vasculature sheds further light on the molecular mechanisms underlying ZNF408-associated familial exudative vitreoretinopathy. (PMID:29982478)
• This is the first study to report a group of patients with digenic familial exudative vitreoretinopathy (FEVR). In most affected eyes, the stage was more severe than stage 3. We speculate that the phenotype of FEVR is more severe in patients with digenic rather than monogenic variants of FEVR-related genes. (PMID:30097784)
• Genetic and clinical characteristics of ZNF408-related familial exudative vitreoretinopathy. (PMID:37684015)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
danio_rerio	znf408	ENSDARG00000036043
mus_musculus	Zfp408	ENSMUSG00000075040

Paralogs (51): WIZ (ENSG00000011451), ZNF416 (ENSG00000083817), MYNN (ENSG00000085274), PRDM4 (ENSG00000110851), PRDM2 (ENSG00000116731), ZBTB17 (ENSG00000116809), ZNF644 (ENSG00000122482), GZF1 (ENSG00000125812), ZNF426 (ENSG00000130818), ZNF287 (ENSG00000141040), ZNF697 (ENSG00000143067), ZNF687 (ENSG00000143373), ZNF214 (ENSG00000149050), ZNF547 (ENSG00000152433), ZNF776 (ENSG00000152443), ZNF230 (ENSG00000159882), ZNF222 (ENSG00000159885), ZNF233 (ENSG00000159915), ZNF333 (ENSG00000160961), ZNF319 (ENSG00000166188), ZNF592 (ENSG00000166716), ZNF646 (ENSG00000167395), ZNF507 (ENSG00000168813), ZNF768 (ENSG00000169957), ZNF417 (ENSG00000173480), ZBTB41 (ENSG00000177888), ZNF223 (ENSG00000178386), ZNF852 (ENSG00000178917), ZNF784 (ENSG00000179922), ZNF572 (ENSG00000180938), ZNF707 (ENSG00000181135), ZNF746 (ENSG00000181220), ZNF467 (ENSG00000181444), ZNF530 (ENSG00000183647), ZNF17 (ENSG00000186272), ZNF527 (ENSG00000189164), ZKSCAN7 (ENSG00000196345), ZNF34 (ENSG00000196378), ZNF774 (ENSG00000196391), ZNF777 (ENSG00000196453)

Protein

Protein identifiers

Zinc finger protein 408 — Q9H9D4 (reviewed: Q9H9D4)

Alternative names: PR domain zinc finger protein 17

All UniProt accessions (1): Q9H9D4

UniProt curated annotations — full annotation on UniProt →

Function. May be involved in transcriptional regulation.

Subcellular location. Nucleus.

Tissue specificity. Highest expression is observed in adult retina; abundantly expressed in the fetal eye. In the retina, it is detected in the outer nuclear layer, especially cone and rod photoreceptor cells, ganglion cell layer and both outer and inner plexiform layers (at protein level). Expressed in retinal blood vessels (at protein level).

Disease relevance. Vitreoretinopathy, exudative 6 (EVR6) [MIM:616468] An autosomal dominant form of exudative vitreoretinopathy, a form of exudative vitreoretinopathy, a disorder of the retinal vasculature characterized by an abrupt cessation of growth of peripheral capillaries, leading to an avascular peripheral retina. This may lead to compensatory retinal neovascularization, which is thought to be induced by hypoxia from the initial avascular insult. New vessels are prone to leakage and rupture causing exudates and bleeding, followed by scarring, retinal detachment and blindness. Clinical features can be highly variable, even within the same family. Patients with mild forms of the disease are asymptomatic, and their only disease related abnormality is an arc of avascular retina in the extreme temporal periphery. The disease is caused by variants affecting the gene represented in this entry. Retinitis pigmentosa 72 (RP72) [MIM:616469] A retinal dystrophy belonging to the group of pigmentary retinopathies. Retinitis pigmentosa is characterized by retinal pigment deposits visible on fundus examination and primary loss of rod photoreceptor cells followed by secondary loss of cone photoreceptors. Patients typically have night vision blindness and loss of midperipheral visual field. As their condition progresses, they lose their far peripheral visual field and eventually central vision as well. The disease is caused by variants affecting the gene represented in this entry.

RefSeq proteins (2): NP_001171680, NP_079017* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001214	SET_dom	Domain
IPR013087	Znf_C2H2_type	Domain
IPR036236	Znf_C2H2_sf	Homologous_superfamily
IPR044412	PRDM17_PR-SET	Domain
IPR046341	SET_dom_sf	Homologous_superfamily
IPR050331	Zinc_finger_PRDM4/PRDM1/PRDM14	Family

Pfam: PF00096, PF21549

UniProt features (21 total): zinc finger region 10, sequence variant 6, compositionally biased region 2, chain 1, region of interest 1, modified residue 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9H9D4-F1	56.25	0.01

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): 322

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 209 (showing top): RNGTGGGC_UNKNOWN, ROVERSI_GLIOMA_COPY_NUMBER_UP, SRF_C, ELK1_01, P300_01, NRF2_01, MODULE_48, MODULE_95, CETS1P54_01, SCGGAAGY_ELK1_02, MGGAAGTG_GABP_B, MZF1_02, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, ELK1_02, WAKABAYASHI_ADIPOGENESIS_PPARG_BOUND_8D

GO Biological Process (1): regulation of transcription by RNA polymerase II (GO:0006357)

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), zinc ion binding (GO:0008270), identical protein binding (GO:0042802), DNA binding (GO:0003677), protein binding (GO:0005515), metal ion binding (GO:0046872)

GO Cellular Component (1): nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
RNA polymerase II transcription regulatory region sequence-specific DNA binding	2
regulation of DNA-templated transcription	1
transcription by RNA polymerase II	1
cis-regulatory region sequence-specific DNA binding	1
chromatin	1
DNA-binding transcription factor activity	1
regulation of transcription by RNA polymerase II	1
transition metal ion binding	1
protein binding	1
nucleic acid binding	1
binding	1
cation binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

1238 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF408	TSPAN12	O95859	841
ZNF408	FZD4	Q9ULV1	727
ZNF408	NDP	Q00604	724
ZNF408	LRP5	O75197	638
ZNF408	KIF11	P52732	628
ZNF408	RCBTB1	Q8NDN9	599
ZNF408	CSTPP1	Q9H6J7	566
ZNF408	SLC61A1	Q6N075	525
ZNF408	ARHGAP1	Q07960	495
ZNF408	KPRP	Q5T749	475
ZNF408	MYG1	Q9HB07	461
ZNF408	EYS	Q5T1H1	445
ZNF408	MVK	Q03426	430
ZNF408	LGR4	Q9BXB1	420
ZNF408	ABHD12	Q8N2K0	419

IntAct

243 interactions, top by confidence:

A	B	Type	Score
ZNF408	CEP70	psi-mi:“MI:0915”(physical association)	0.840
CEP70	ZNF408	psi-mi:“MI:0915”(physical association)	0.840
ZNF408	ZNF408	psi-mi:“MI:0915”(physical association)	0.820
ZNF408	ZNF408	psi-mi:“MI:0407”(direct interaction)	0.820
ZNF408	MDFI	psi-mi:“MI:0915”(physical association)	0.760
MDFI	ZNF408	psi-mi:“MI:0915”(physical association)	0.760
LZTS2	ZNF408	psi-mi:“MI:0915”(physical association)	0.740
TRIM41	ZNF408	psi-mi:“MI:0915”(physical association)	0.740
ZNF408	ZNF792	psi-mi:“MI:0915”(physical association)	0.720
ZNF792	ZNF408	psi-mi:“MI:0915”(physical association)	0.720
CALCOCO2	ZNF408	psi-mi:“MI:0915”(physical association)	0.670
KHDRBS3	ZNF408	psi-mi:“MI:0915”(physical association)	0.670
ZNF408	ZNF330	psi-mi:“MI:0915”(physical association)	0.670
ZBTB8A	ZNF408	psi-mi:“MI:0915”(physical association)	0.670
DVL3	ZNF408	psi-mi:“MI:0915”(physical association)	0.670
ZNF408	THAP1	psi-mi:“MI:0915”(physical association)	0.670
LDOC1	ZNF408	psi-mi:“MI:0915”(physical association)	0.620
PDE4DIP	ZNF408	psi-mi:“MI:0915”(physical association)	0.560
ZNF408	GPATCH2L	psi-mi:“MI:0915”(physical association)	0.560
GPATCH2L	ZNF408	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (219): ZNF408 (Two-hybrid), ZNF408 (Two-hybrid), ZNF408 (Two-hybrid), CEP70 (Two-hybrid), ZNF792 (Two-hybrid), ZNF408 (Two-hybrid), ZNF408 (Two-hybrid), ZNF408 (Two-hybrid), ZNF408 (Two-hybrid), RALYL (Two-hybrid), CEP70 (Two-hybrid), ZNF408 (Two-hybrid), KRTAP4-12 (Two-hybrid), ZNF408 (Two-hybrid), ZNF408 (Affinity Capture-MS)

ESM2 similar proteins: A0JNJ4, A2APT9, A6NEL2, A6NP61, B1ASB6, B1WBS3, B2RXF5, F6WEQ6, O15015, O43918, O88282, O88286, O95785, P98168, P98169, Q2M3G4, Q2MHN3, Q2QGD7, Q3U1J1, Q3U381, Q497V6, Q5SW24, Q5SXM2, Q6YND2, Q6ZMQ8, Q6ZMY3, Q7TN08, Q7TSX9, Q80SU3, Q80YE4, Q811H0, Q8BG26, Q8BZW2, Q8C8V1, Q8IX07, Q8IY92, Q8N143, Q8N1G0, Q8NC74, Q8TBE0

Diamond homologs: A2ANX9, B0YDH7, O15391, O57311, O57415, O60315, O60481, O62836, O73689, O95409, P03001, P08048, P0C6P6, P10925, P17010, P17012, P18719, P20662, P22227, P25490, P36197, P46684, P56270, P56670, P56671, P79797, P80944, Q00899, Q12145, Q12531, Q13105, Q13351, Q14119, Q15915, Q29419, Q2FAY8, Q3TTC2, Q3UH06, Q3Y4E1, Q52V16

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 67 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	7	10.8×	3e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	5
Likely pathogenic	6
Uncertain significance	424
Likely benign	177
Benign	12

Top pathogenic / likely-pathogenic (11)

Variant ID	HGVS	Classification
204316	NM_024741.3(ZNF408):c.363_364del (p.Ala122fs)	Pathogenic
3248951	NM_024741.3(ZNF408):c.274G>T (p.Glu92Ter)	Pathogenic
3775521	NM_024741.3(ZNF408):c.331-2A>G	Pathogenic
812466	NM_024741.3(ZNF408):c.1697T>A (p.Leu566His)	Pathogenic
978986	NM_024741.3(ZNF408):c.653-1G>T	Pathogenic
1175791	NM_024741.3(ZNF408):c.111del (p.Gln38fs)	Likely pathogenic
3028200	NM_024741.3(ZNF408):c.604C>T (p.Gln202Ter)	Likely pathogenic
3028203	NM_024741.3(ZNF408):c.1219C>T (p.Arg407Trp)	Likely pathogenic
3250277	NM_024741.3(ZNF408):c.1996del (p.Glu666fs)	Likely pathogenic
3654268	NM_024741.3(ZNF408):c.653-1G>A	Likely pathogenic
931150	NM_024741.3(ZNF408):c.943C>T (p.Gln315Ter)	Likely pathogenic

SpliceAI

622 predictions. Top by Δscore:

Variant	Effect	Δscore
11:46701653:G:GT	donor_gain	1.0000
11:46701674:G:GT	donor_gain	1.0000
11:46702979:TGCA:T	acceptor_loss	1.0000
11:46702980:GCA:G	acceptor_loss	1.0000
11:46702981:CAGCT:C	acceptor_loss	1.0000
11:46702982:A:AG	acceptor_gain	1.0000
11:46702982:A:G	acceptor_loss	1.0000
11:46702982:AGCTT:A	acceptor_gain	1.0000
11:46702983:G:GC	acceptor_gain	1.0000
11:46702983:GC:G	acceptor_gain	1.0000
11:46702983:GCT:G	acceptor_gain	1.0000
11:46702983:GCTT:G	acceptor_gain	1.0000
11:46702983:GCTTG:G	acceptor_gain	1.0000
11:46703201:G:GT	donor_gain	1.0000
11:46703243:GGT:G	donor_loss	1.0000
11:46703244:G:GG	donor_gain	1.0000
11:46703245:T:A	donor_loss	1.0000
11:46704350:CA:C	acceptor_loss	1.0000
11:46704351:A:AG	acceptor_gain	1.0000
11:46704351:AGATC:A	acceptor_loss	1.0000
11:46704352:G:GA	acceptor_gain	1.0000
11:46704352:GATC:G	acceptor_gain	1.0000
11:46701098:CGGT:C	donor_loss	0.9900
11:46701100:G:GG	donor_gain	0.9900
11:46701101:T:A	donor_loss	0.9900
11:46701397:A:AG	acceptor_gain	0.9900
11:46701398:G:GG	acceptor_gain	0.9900
11:46701398:GCCC:G	acceptor_gain	0.9900
11:46701554:G:GT	donor_gain	0.9900
11:46701653:G:T	donor_gain	0.9900

AlphaMissense

4624 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
11:46704784:T:C	F362L	0.999
11:46704786:C:A	F362L	0.999
11:46704786:C:G	F362L	0.999
11:46705036:T:C	F446L	0.998
11:46705038:T:A	F446L	0.998
11:46705038:T:G	F446L	0.998
11:46705213:T:C	F505L	0.998
11:46705215:T:A	F505L	0.998
11:46705215:T:G	F505L	0.998
11:46705357:T:C	C553R	0.998
11:46705405:C:G	H569D	0.998
11:46705491:C:A	H597Q	0.998
11:46705491:C:G	H597Q	0.998
11:46705525:T:C	C609R	0.998
11:46704931:T:C	C411R	0.997
11:46705158:T:A	H486Q	0.997
11:46705158:T:G	H486Q	0.997
11:46705214:T:C	F505S	0.997
11:46705297:T:C	F533L	0.997
11:46705299:C:A	F533L	0.997
11:46705299:C:G	F533L	0.997
11:46705367:G:A	C556Y	0.997
11:46705419:C:A	H573Q	0.997
11:46705419:C:G	H573Q	0.997
11:46705441:T:C	C581R	0.997
11:46704785:T:C	F362S	0.996
11:46705009:T:C	F437L	0.996
11:46705011:T:A	F437L	0.996
11:46705011:T:G	F437L	0.996
11:46705037:T:C	F446S	0.996

dbSNP variants (sampled 300 via entrez): RS1000785085 (11:46702674 T>A,C), RS1001450352 (11:46705719 T>G), RS1001795395 (11:46705903 T>C), RS1002962758 (11:46702375 G>A), RS1003066750 (11:46706243 C>T), RS1003247872 (11:46701033 G>T), RS1003630769 (11:46704673 C>A,G), RS1003636228 (11:46700834 G>A,C), RS1003925659 (11:46706250 A>C,G), RS1004365981 (11:46704023 G>A,C), RS1005155834 (11:46700412 T>C), RS1005346775 (11:46703549 G>A,C), RS1005513471 (11:46700628 C>T), RS1005885618 (11:46703715 G>T), RS1005937467 (11:46703345 A>C,G)

Disease associations

OMIM: gene MIM:616454 | disease phenotypes: MIM:616468, MIM:616469, MIM:133780

GenCC curated gene-disease

Disease	Classification	Inheritance
exudative vitreoretinopathy 6	Strong	Autosomal dominant
retinitis pigmentosa 72	Strong	Autosomal recessive
retinitis pigmentosa	Supportive	Autosomal dominant
exudative vitreoretinopathy	Supportive	Autosomal dominant

Mondo (7): exudative vitreoretinopathy 6 (MONDO:0014652), retinitis pigmentosa 72 (MONDO:0014653), inherited retinal dystrophy (MONDO:0019118), exudative vitreoretinopathy 1 (MONDO:0007589), optic atrophy (MONDO:0003608), exudative vitreoretinopathy (MONDO:0019516), retinitis pigmentosa (MONDO:0019200)

Orphanet (4): Retinitis pigmentosa (Orphanet:791), Familial exudative vitreoretinopathy (Orphanet:891), OBSOLETE: Inherited retinal disorder (Orphanet:71862), Retinopathy of prematurity (Orphanet:90050)

HPO phenotypes

80 total (30 of 80 shown, HPO-id order):

HPO	Term
HP:0000006	Autosomal dominant inheritance
HP:0000007	Autosomal recessive inheritance
HP:0000252	Microcephaly
HP:0000365	Hearing impairment
HP:0000405	Conductive hearing impairment
HP:0000407	Sensorineural hearing impairment
HP:0000501	Glaucoma
HP:0000505	Visual impairment
HP:0000510	Rod-cone dystrophy
HP:0000512	Abnormal electroretinogram
HP:0000518	Cataract
HP:0000529	Progressive visual loss
HP:0000533	Chorioretinal atrophy
HP:0000541	Retinal detachment
HP:0000543	Optic disc pallor
HP:0000545	Myopia
HP:0000546	Retinal degeneration
HP:0000551	Color vision defect
HP:0000563	Keratoconus
HP:0000568	Microphthalmia
HP:0000602	Ophthalmoplegia
HP:0000613	Photophobia
HP:0000618	Blindness
HP:0000639	Nystagmus
HP:0000648	Optic atrophy
HP:0000662	Nyctalopia
HP:0000666	Horizontal nystagmus
HP:0000842	Hyperinsulinemia
HP:0001004	Lymphedema
HP:0001105	Retinal atrophy

GWAS associations

5 associations (top):

Study	Trait	p-value
GCST004521_122	Autism spectrum disorder or schizophrenia	3.000000e-13
GCST004521_165	Autism spectrum disorder or schizophrenia	3.000000e-08
GCST005795_33	Femoral neck bone mineral density	5.000000e-09
GCST006803_20	Schizophrenia	3.000000e-13
GCST007825_4	Alzheimer’s disease or fasting glucose levels (pleiotropy)	3.000000e-16

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0007785	femoral neck bone mineral density

MeSH disease descriptors (4)

Descriptor	Name	Tree numbers
D009896	Optic Atrophy	C10.292.700.225; C11.640.451
D058499	Retinal Dystrophies	C11.768.585.658
D012174	Retinitis Pigmentosa	C11.270.684; C11.768.585.658.500; C16.320.290.684
C536382	Exudative vitreoretinopathy 1 (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

27 total (human), top 27 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Tobacco Smoke Pollution	increases expression	2
aristolochic acid I	increases expression	1
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamide	decreases expression	1
FR900359	increases phosphorylation	1
TAK-243	increases sumoylation	1
tris(1,3-dichloro-2-propyl)phosphate	increases expression	1
sodium arsenite	increases expression	1
potassium chromate(VI)	increases expression, affects cotreatment	1
ferrous chloride	decreases expression	1
epigallocatechin gallate	affects cotreatment, increases expression	1
di-n-butylphosphoric acid	affects expression	1
abrine	increases expression	1
PCI 5002	affects cotreatment, increases expression	1
Irinotecan	affects cotreatment, increases expression	1
Caffeine	decreases phosphorylation	1
Copper	affects binding, decreases expression	1
Dioxins	increases mutagenesis	1
Disulfiram	affects binding, decreases expression	1
Doxorubicin	decreases expression	1
Fluorouracil	affects cotreatment, increases expression	1
Methyl Methanesulfonate	increases expression	1
Silver	increases expression	1
Smoke	decreases expression	1
Thiram	increases expression	1
Zinc	increases expression, affects cotreatment	1
Copper Sulfate	increases expression	1
Acrylamide	increases expression	1

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT00717080	PHASE4	COMPLETED	The Role of Capsular Tension Ring (CTR) in Anterior Capsular Contraction
NCT06520410	PHASE4	RECRUITING	Safety and Efficacy of 18 mm Short Vitrectomy Probe for Pediatric Vitreoretinal Surgeries
NCT00000114	PHASE3	COMPLETED	Randomized Trial of Vitamin A and Vitamin E Supplementation for Retinitis Pigmentosa
NCT00000116	PHASE3	COMPLETED	Randomized Trial of DHA for Retinitis Pigmentosa Patients Receiving Vitamin A
NCT00346333	PHASE3	COMPLETED	Clinical Trial of Lutein for Patients With Retinitis Pigmentosa Receiving Vitamin A
NCT01786395	PHASE3	TERMINATED	Phase III Efficacy and Safety Clinical Study of UF-021 for Treatment of Retinitis Pigmentosa
NCT04224207	PHASE3	COMPLETED	Management of Retinitis Pigmentosa by Mesenchymal Stem Cells by Wharton’s Jelly Derived Mesenchymal Stem Cells
NCT04636853	PHASE3	COMPLETED	CB-PRP in Retinitis Pigmentosa and Dry Age-related Macular Degeneration
NCT05537220	PHASE3	ACTIVE_NOT_RECRUITING	Oral N-acetylcysteine for Retinitis Pigmentosa
NCT05800301	PHASE3	COMPLETED	Management of Retinitis Pigmentosa Via Combination of Wharton’s Jelly-derived Mesenchymal Stem Cells and Magnovision
NCT05926583	PHASE3	ACTIVE_NOT_RECRUITING	A Study of AAV5-hRKp.RPGR for the Treatment of Japanese Participants With X-linked Retinitis Pigmentosa
NCT06388200	PHASE3	ACTIVE_NOT_RECRUITING	A Phase 3 Study Of OCU400 Gene Therapy for the Treatment Of Retinitis Pigmentosa
NCT07082855	PHASE3	NOT_YET_RECRUITING	A Multicenter, Randomized, Double-Blind, Controlled Clinical Study of Minocycline for the Treatment of Retinitis Pigmentosa
NCT07290530	PHASE3	NOT_YET_RECRUITING	24-Month Trial of NPI-001 for the Preservation of Photoreceptors in Retinitis Pigmentosa Associated With Usher Syndrome
NCT00100230	PHASE2	COMPLETED	DHA and X-Linked Retinitis Pigmentosa
NCT00447980	PHASE2	COMPLETED	A Study of Encapsulated Cell Technology (ECT) Implant for Participants With Early Stage Retinitis Pigmentosa
NCT00447993	PHASE2	COMPLETED	A Study of Encapsulated Cell Technology (ECT) Implant for Patients With Late Stage Retinitis Pigmentosa
NCT01233609	PHASE2	COMPLETED	Trial of Oral Valproic Acid for Retinitis Pigmentosa
NCT01399515	PHASE2	COMPLETED	Efficacy and Safety of Oral Valproic Acid for Retinitis Pigmentosa
NCT01530659	PHASE2	COMPLETED	Retinal Imaging in CNTF -Releasing Encapsulated Cell Implant Treated Patients for Early-stage Retinitis Pigmentosa
NCT01560715	PHASE2	COMPLETED	Autologous Bone Marrow-Derived Stem Cells Transplantation For Retinitis Pigmentosa
NCT02609165	PHASE2	COMPLETED	Nerve Growth Factor Eye Drops Treatment in Patients With Retinitis Pigmentosa and Cystoid Macular Edema
NCT02661711	PHASE2	COMPLETED	Aflibercept for Macular Oedema With Underlying Retinitis Pigmentosa (AMOUR) Study
NCT02804360	PHASE2	UNKNOWN	Intravitreal Dexamethasone Implant in Retinitis Pigmentosa-related Macular Edema- a Retrospective Study
NCT02837640	PHASE2	UNKNOWN	Studying a Potential Protective Effect of L-Dopa on Retinitis Pigmentosa
NCT03073733	PHASE2	COMPLETED	Safety and Efficacy of Intravitreal Injection of Human Retinal Progenitor Cells in Adults With Retinitis Pigmentosa
NCT04068207	PHASE2	COMPLETED	Minocycline Treatment in Retinitis Pigmentosa
NCT04356716	PHASE2	COMPLETED	Sildenafil for Treatment of Choroidal Ischemia
NCT04604899	PHASE2	COMPLETED	Safety of Repeat Intravitreal Injection of Human Retinal Progenitor Cells (jCell) in Adult Subjects With Retinitis Pigmentosa
NCT04763369	PHASE2	UNKNOWN	Investigation of Therapeutic Efficacy and Safety of UMSCs for the Management of Retinitis Pigmentosa (RP)
NCT04864496	PHASE2	UNKNOWN	Effects of Treatment With N- Acetylcysteine on Visual Outcomes in Patients With Retinitis Pigmentosa
NCT04945772	PHASE2	COMPLETED	Efficacy and Safety of MCO-010 Optogenetic Therapy in Adults With Retinitis Pigmentosa [RESTORE]
NCT05085964	PHASE2	TERMINATED	An Open-Label Extension Study to Evaluate Safety & Tolerability of QR-421a in Subjects With Retinitis Pigmentosa
NCT05392179	PHASE2	COMPLETED	A Study in Subjects With Retinitis Pigmentosa
NCT06627179	PHASE2	RECRUITING	Study to Evaluate Ultevursen in Subjects With Retinitis Pigmentosa (RP) Due to Mutations in Exon 13 of the USH2A Gene
NCT06628947	PHASE2	RECRUITING	A Phase II Study of Intravitreal KIO-301 in Patients With Late-stage Retinitis Pigmentosa
NCT06912633	PHASE2	RECRUITING	Safety of a Single, Intravitreal Injection of 6.0M jCell (Famzeretcel) in Retinitis Pigmentosa (RP)
NCT05107921	PHASE2	UNKNOWN	Bromfenac Sodium Hydrate Eye Drops in Familial Exudative Vitreoretinopathy
NCT03763227	PHASE2	COMPLETED	Intravitreal Ranibizumab (Lucentis®) in the Treatment of Non-leaking Macular Cysts in Retinal Dystrophy
NCT00063765	PHASE1	COMPLETED	Evaluation of Safety of Ciliary Neurotrophic Factor Implants in the Eye