RPGR

gene
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Also known as CORDX1

Summary

RPGR (retinitis pigmentosa GTPase regulator, HGNC:10295) is a protein-coding gene on chromosome Xp11.4, encoding X-linked retinitis pigmentosa GTPase regulator (Q92834). Acts as a guanine-nucleotide releasing factor (GEF) for RAB8A and RAB37 by promoting the conversion of inactive RAB-GDP to the active form RAB-GTP.

This gene encodes a protein with a series of six RCC1-like domains (RLDs), characteristic of the highly conserved guanine nucleotide exchange factors. The encoded protein is found in the Golgi body and interacts with RPGRIP1. This protein localizes to the outer segment of rod photoreceptors and is essential for their viability. Mutations in this gene have been associated with X-linked retinitis pigmentosa (XLRP). Multiple alternatively spliced transcript variants that encode different isoforms of this gene have been reported, but the full-length natures of only some have been determined.

Source: NCBI Gene 6103 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): RPGR-related retinopathy (Definitive, ClinGen) — +6 more curated relationships
  • Clinical variants (ClinVar): 2,050 total — 495 pathogenic, 236 likely-pathogenic
  • Phenotypes (HPO): 111
  • MANE Select transcript: NM_001034853

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:10295
Approved symbolRPGR
Nameretinitis pigmentosa GTPase regulator
LocationXp11.4
Locus typegene with protein product
StatusApproved
AliasesCORDX1
Ensembl geneENSG00000156313
Ensembl biotypeprotein_coding
OMIM312610
Entrez6103

Gene structure

Transcript identifiers

Ensembl transcripts: 19 — 9 protein_coding, 6 nonsense_mediated_decay, 3 retained_intron, 1 protein_coding_CDS_not_defined

ENST00000339363, ENST00000464437, ENST00000470183, ENST00000474584, ENST00000476559, ENST00000482855, ENST00000494707, ENST00000494841, ENST00000642170, ENST00000642373, ENST00000642395, ENST00000642558, ENST00000642739, ENST00000644238, ENST00000644337, ENST00000645032, ENST00000645124, ENST00000646020, ENST00000647261

RefSeq mRNA: 9 — MANE Select: NM_001034853 NM_000328, NM_001034853, NM_001367245, NM_001367246, NM_001367247, NM_001367248, NM_001367249, NM_001367250, NM_001367251

CCDS: CCDS14246, CCDS35229, CCDS94588, CCDS94589

Canonical transcript exons

ENST00000645032 — 15 exons

ExonStartEnd
ENSE000010257113829728438297452
ENSE000010257123832285338322945
ENSE000010257153831731638317465
ENSE000010257163831061538310773
ENSE000010257173832102738321089
ENSE000010257223831882938318987
ENSE000010257233829139338291484
ENSE000010257283832339938323524
ENSE000010257343830463538304790
ENSE000014777613828440838287245
ENSE000034748323829095938291024
ENSE000034999353828786138288041
ENSE000035181463829895638299141
ENSE000035913933830124738301371
ENSE000039027953832734038327509

Expression profiles

Bgee: expression breadth ubiquitous, 281 present calls, max score 95.61.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 8.2875 / max 192.8364, expressed in 1647 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter IDTPM avgSamples expressed
1989023.98421408
1989032.13161126
1989011.7743435
1989040.2714102
1989000.126134

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
spermCL:000001995.61gold quality
bronchial epithelial cellCL:000232894.94gold quality
right uterine tubeUBERON:000130294.54gold quality
right lungUBERON:000216793.88gold quality
epithelium of bronchusUBERON:000203193.79gold quality
male germ cellCL:000001593.04gold quality
bronchusUBERON:000218592.79gold quality
adenohypophysisUBERON:000219692.57gold quality
mucosa of paranasal sinusUBERON:000503092.24gold quality
pituitary glandUBERON:000000791.34gold quality
tibial nerveUBERON:000132390.18gold quality
subcutaneous adipose tissueUBERON:000219089.85gold quality
choroid plexus epitheliumUBERON:000391189.83gold quality
omental fat padUBERON:001041489.68gold quality
peritoneumUBERON:000235889.61gold quality
upper lobe of left lungUBERON:000895289.51gold quality
left uterine tubeUBERON:000130389.06gold quality
upper lobe of lungUBERON:000894888.92gold quality
adipose tissue of abdominal regionUBERON:000780888.61gold quality
sural nerveUBERON:001548888.58gold quality
mucosa of stomachUBERON:000119988.54gold quality
secondary oocyteCL:000065588.30gold quality
olfactory segment of nasal mucosaUBERON:000538687.77gold quality
body of uterusUBERON:000985387.09gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047386.61gold quality
endocervixUBERON:000045886.28gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099186.18gold quality
ectocervixUBERON:001224986.06gold quality
epithelium of nasopharynxUBERON:000195185.75gold quality
calcaneal tendonUBERON:000370185.68gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes10.22

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

44 targeting RPGR, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-340-5P100.0072.504437
HSA-MIR-3163100.0077.238605
HSA-MIR-5692A100.0074.406850
HSA-MIR-4789-3P99.9970.752484
HSA-MIR-428299.9975.366408
HSA-MIR-3692-3P99.9870.272139
HSA-MIR-570-3P99.9672.414910
HSA-MIR-548AJ-3P99.9673.385345
HSA-MIR-548X-3P99.9673.385345
HSA-MIR-548J-3P99.9472.614881
HSA-MIR-548AE-3P99.9372.664867
HSA-MIR-548AH-3P99.9372.544872
HSA-MIR-548AM-3P99.9372.544872
HSA-MIR-548AQ-3P99.9372.664867
HSA-MIR-335-3P99.9373.364958
HSA-MIR-3682-5P99.9367.971163
HSA-MIR-129799.9173.413162
HSA-MIR-548AZ-3P99.8270.563549
HSA-MIR-323A-3P99.7970.301739
HSA-MIR-26A-5P99.7873.522303
HSA-MIR-26B-5P99.7873.512305
HSA-MIR-446599.7172.562096
HSA-MIR-1212499.6869.172700
HSA-MIR-7161-5P99.6868.921592
HSA-MIR-46699.6770.852863
HSA-MIR-548U99.6567.781463
HSA-MIR-432899.5771.064094
HSA-MIR-4753-5P99.5468.511356
HSA-MIR-203A-3P99.4970.562806
HSA-MIR-548G-3P99.4868.672159

Literature-anchored findings (GeneRIF, showing 40)

  • Insertional/deletional mutations observed in the three families with X-linked retinitis pigmentosa are all different and new, and are predicted to lead to a frameshift, resulting in a truncated protein. (PMID:11754050)
  • X-linked cone-rod dystrophy (locus COD1): identification of mutations in RPGR exon ORF15 (PMID:11857109)
  • A mutation in this gene causes X-linked cone dystrophy. This type of hereditary retinal degeneration is distinct from retinitis pigmentosa. (PMID:11875055)
  • A comprehensive mutation analysis of RP2 and RPGR in a North American cohort of families with X-linked retinitis pigmentosa. (PMID:11992260)
  • RPGR and RPGRIP isoforms are distributed and co-localized at restricted foci throughout the outer segments of human and bovine, but not mice rod photoreceptors. (PMID:12140192)
  • Identification of an RPGR mutation in atrophic macular degeneration expands the phenotypic range from retinitis pigmentosa. (PMID:12160730)
  • RPGR mutations in most families with definite X linkage and clustering of mutations in a short sequence stretch of exon ORF15. (PMID:12657579)
  • Different RPGR mutations lead to distinct RP (retinitis pigmentosa) phenotypes, with a highly variable inter- and intrafamilial phenotypic spectrum of disease (PMID:14516808)
  • Among patients with RPGR mutations, those with ORF15 mutations had, on average, a significantly larger visual field area and a borderline larger ERG amplitude than did patients with RPGR mutations in exons 1-14 (PMID:14564670)
  • Mutations in the RPGR gene is associated with X-linked retinitis pigmentosa (PMID:14566651)
  • Sequencing revealed skipping of exon 2 in the mutated transcript, leading to in-frame deletion of 42 amino acids affecting the critical RCC1-like domain. (PMID:15364249)
  • RPGR ORF15 isoform co-localizes with RPGRIP1 at centrioles and basal bodies and interacts with nucleophosmin. (PMID:15772089)
  • Two families were identified with nonsense mutations, and clinical evaluation revealed them both to have a similar phenotype. (PMID:15914600)
  • RPGR-ORF15, which is mutated in retinitis pigmentosa, associates with SMC1, SMC3, and microtubule transport proteins. (PMID:16043481)
  • This 30 kb deletion contains the exons coding for the RCC1-like domain of RPGR. It is the first report of a macrodeletion that spans the entire RCC1-like domain of RPGR in X-linked retinitis pigmentosa patients (PMID:16052169)
  • Finding expands the spectrum of RPGR mutations causing X-linked dominant retinitis pigmentosa in Chinese family and is useful for further genetic consultation and genetic diagnosis. (PMID:16086276)
  • the mutational risk in the RPGR gene appears not to be altered by the haplotype background (PMID:16273303)
  • This report expands the clinical heterogeneity spectrum caused by RPGR mutations and our knowledge concerning the molecular pathologic condition that pertains to Coats’-like RP. (PMID:16387007)
  • We describe a novel PRPF31 mutation and present the first case of a homozygous mutation in the RPGR gene in a female individual. (PMID:16917484)
  • A defect in trafficking of opsins to outer segments exists in a carrier with the RPGR Gly436Asp mutation. (PMID:16935610)
  • In this cohort of XLRP families, as has happened in previous studies, RP3 also seems to be the most prevalent form of XLRP, and, based on the results, the authors propose a four-step protocol for molecular diagnosis of XLRP families. (PMID:16936086)
  • 26 new mutations in RP2 and RPGR patients with X-linked Retinitis Pigmentosa. (PMID:16969763)
  • Three ORF15 mutations and one RP2 mutation in five Japanese retinitis pigmentosa families. (PMID:17093403)
  • All disease-causing mutations occur in one or more RPGR isoforms containing the carboxyl-terminal exon open reading frame 15 (ORF15), which are widely expressed but show their highest expression in the connecting cilia of rod and cone photoreceptors. (PMID:17195164)
  • the ORF15 and RCC1-like domain of RPGR play a crucial role in the human retina (PMID:17249551)
  • Patients with X-linked retinitis pigmentosa due to RPGR mutations lose visual acuity and visual field more rapidly than do patients with dominant retinitis pigmentosa due to RHO mutations. (PMID:17325176)
  • The nucleotide substitution affects regulated alternative splicing of the novel RPGR isoform and suggests a tight adjustment of splicing as a prerequisite for proper function of photoreceptors. (PMID:17405150)
  • These results indicate that an additional gene (or genes), linked to RPGR, modulate disease expression in severely affected carriers. (PMID:17480003)
  • The proportion of RP2-mediated XLRP in the Danish population is higher and the proportion of RPGR-ORF15 is lower than reported in other studies. (PMID:17724181)
  • Associated with retinitis pigmentosa in all hemizygous males and four of five heterozygous female carriers in Chinese family. These results revealed broader xlRP genotypic and phenotypic spectrum of RPGR mutations. (PMID:17893654)
  • Inner retinal laminar abnormalities in RPGR-XLRP are likely to reflect a neuronal-glial retinal remodeling response to photoreceptor loss and are detectable relatively early in the disease course. (PMID:17898302)
  • We identified a novel mutation in the 3’ end of a highly repetitive region of exon open reading frame 15 (ORF15) and documented the detailed phenotypes of the patients with XLRP with the mutation. (PMID:17923551)
  • Retinal phenotype of an X-linked pseudo-Usher syndrome in association with the G173R mutation in the RPGR gene is reported. (PMID:18188948)
  • An identical mutation in RPGR-ORF15 manifested distinct clinical phenotypes in individuals of the same family. (PMID:18332319)
  • This novel mutation in RPGRcauses X-Linked RP with complete penetrance in males and females and affected females are highly myopic but retain better visual function than affected males. (PMID:19218993)
  • Four different RPGR ORF15 mutations were found in four probands and all mutations in the ORF15 exon resulted in premature truncation of the RPGR protein. (PMID:19429592)
  • RPGR is involved in cilia-dependent cascades during development in zebrafish. (PMID:19815619)
  • These findings show that splicing of RPGR is precisely regulated in a tissue-dependent fashion and suggest that mutations in RPGR frequently interfere with the expression of alternative transcript isoforms. (PMID:19834030)
  • Our results expand the frequency and spectrum of mutations at RPGR and RP2 as well as their associated clinical phenotypes in Chinese patients. (PMID:20021257)
  • The pedigree we have investigated here represents the first Czech family with an identified molecular genetic cause of retinitis pigmentosa (PMID:20064120)

Cross-species orthologs

7 orthologs

OrganismSymbolGene ID
danio_reriorpgraENSDARG00000056617
danio_reriorpgrbENSDARG00000057074
mus_musculusRpgrENSMUSG00000031174
rattus_norvegicusRpgrENSRNOG00000003013
drosophila_melanogasterRcc1FBGN0002638
drosophila_melanogasterCG7420FBGN0031344
caenorhabditis_elegansWBGENE00004304

Paralogs (9): ALS2 (ENSG00000003393), HERC1 (ENSG00000103657), SERGEF (ENSG00000129158), RCBTB1 (ENSG00000136144), RCBTB2 (ENSG00000136161), RCCD1 (ENSG00000166965), RCC2 (ENSG00000179051), RCC1 (ENSG00000180198), RCC1L (ENSG00000274523)

Protein

Protein identifiers

X-linked retinitis pigmentosa GTPase regulatorQ92834 (reviewed: Q92834)

All UniProt accessions (11): Q92834, A0A0S2Z4Y6, A0A2R8Y414, A0A2R8Y4C9, A0A2R8Y838, A0A2R8YDN2, A0A2R8YF02, A0A2R8YFT6, A0A2R8YGY6, H7C4H4, H7C4L1

UniProt curated annotations — full annotation on UniProt →

Function. Acts as a guanine-nucleotide releasing factor (GEF) for RAB8A and RAB37 by promoting the conversion of inactive RAB-GDP to the active form RAB-GTP. GEF activity towards RAB8A may facilitate ciliary trafficking by modulating ciliary intracellular localization of RAB8A. GEF activity towards RAB37 maintains autophagic homeostasis and retinal function. Involved in photoreceptor integrity. May control cilia formation by regulating actin stress filaments and cell contractility. May be involved in microtubule organization and regulation of transport in primary cilia. May play a critical role in spermatogenesis and in intraflagellar transport processes.

Subunit / interactions. Interacts with SPATA7. Interacts with CEP290. Interacts with WHRN. Interacts with PDE6D. Interacts with RPGRIP1. Interacts with RPGRIP1L. PDE6D, RPGRIP1 and RPGRIP1L may compete for the same binding sites. Interacts with RAB37 and RAB8A (in GDP-bound forms); functions as GEF for RAB37 and RAB8A. Isoform 6 interacts with NPM1 (via C-terminus). Isoform 6 interacts with SMC1A and SMC3.

Subcellular location. Cytoplasm. Cytoskeleton. Flagellum axoneme. Golgi apparatus. Cell projection. Cilium Cytoplasm. Microtubule organizing center. Centrosome. Cilium basal body. Cilium axoneme.

Tissue specificity. Heart, brain, placenta, lung, liver, muscle, kidney, retina, pancreas and fetal retinal pigment epithelium. Isoform 3 is found only in the retina. Colocalizes with RPGRIP1 in the outer segment of rod photoreceptors and cone outer segments.

Post-translational modifications. Prenylated.

Disease relevance. Retinitis pigmentosa 3 (RP3) [MIM:300029] An X-linked 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. In RP3, affected males have a severe phenotype, and carrier females show a wide spectrum of clinical features ranging from completely asymptomatic to severe retinitis pigmentosa. Heterozygous women can manifest a form of choroidoretinal degeneration which is distinguished from other types by the absence of visual defects in the presence of a brilliant, scintillating, golden-hued, patchy appearance most striking around the macula, called a tapetal-like retinal reflex. The disease is caused by variants affecting the gene represented in this entry. Retinitis pigmentosa, X-linked, and sinorespiratory infections with or without deafness (RPSRDF) [MIM:300455] A disease characterized by the association of retinitis pigmentosa with recurrent upper and lower airway infections. Some patients also develop progressive hearing loss. The disease is caused by variants affecting the gene represented in this entry. Cone-rod dystrophy, X-linked 1 (CORDX1) [MIM:304020] An inherited retinal dystrophy characterized by retinal pigment deposits visible on fundus examination, predominantly in the macular region, and initial loss of cone photoreceptors followed by rod degeneration. This leads to decreased visual acuity and sensitivity in the central visual field, followed by loss of peripheral vision. Severe loss of vision occurs earlier than in retinitis pigmentosa. In cone-rod dystrophy X-linked type 1 the degree of rod-photoreceptor involvement can be variable, with degeneration increasing as the disease progresses. Affected individuals (essentially all of whom are males) present with decreased visual acuity, myopia, photophobia, abnormal color vision, full peripheral visual fields, decreased photopic electroretinographic responses, and granularity of the macular retinal pigment epithelium. Although penetrance appears to be nearly 100%, there is variable expressivity with respect to age at onset and severity of symptoms. The disease is caused by variants affecting the gene represented in this entry. Macular degeneration, atrophic, X-linked (MDXLA) [MIM:300834] An ocular disorder characterized by macular atrophy causing progressive loss of visual acuity with minimal peripheral visual impairment. Some patients manifest extensive macular degeneration plus peripheral loss of retinal pigment epithelium and choriocapillaries. Full-field electroretinograms (ERGs) show normal cone and rod responses in some affected males despite advanced macular degeneration. The disease is caused by variants affecting the gene represented in this entry.

Domain organisation. The RCC1 repeat region mediates interactions with RPGRIP1.

Isoforms (6)

UniProt IDNamesCanonical?
Q92834-11yes
Q92834-22
Q92834-33
Q92834-44
Q92834-55
Q92834-66, ORF15

RefSeq proteins (9): NP_000319, NP_001030025, NP_001354174, NP_001354175, NP_001354176, NP_001354177, NP_001354178, NP_001354179, NP_001354180 (=MANE)

Domains & families (InterPro)

IDNameType
IPR000408Reg_chr_condensRepeat
IPR009091RCC1/BLIP-IIHomologous_superfamily
IPR051625Signaling_Regulatory_DomainFamily
IPR058923RCC1-like_domDomain

Pfam: PF25390

UniProt features (109 total): sequence variant 36, strand 30, compositionally biased region 9, splice variant 7, repeat 6, helix 5, region of interest 3, sequence conflict 3, modified residue 3, mutagenesis site 2, turn 2, chain 1, propeptide 1, lipid moiety-binding region 1

Structure

Experimental structures (PDB)

3 structures.

PDBMethodResolution (Å)
4JHNX-RAY DIFFRACTION1.7
4QAMX-RAY DIFFRACTION1.83
4JHPX-RAY DIFFRACTION1.9

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q92834-F156.590.34

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): 418, 518, 1017, 1017

Mutagenesis-validated functional residues (2):

PositionPhenotype
36does not reduce interaction with pde6d.
323abolishes interaction with rpgrip1.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 393 (showing top): GOBP_REGULATION_OF_AUTOPHAGY, GOBP_INTRACELLULAR_PROTEIN_TRANSPORT, GOBP_PROTEIN_LOCALIZATION_TO_CILIUM, GOLDRATH_IMMUNE_MEMORY, GAUSSMANN_MLL_AF4_FUSION_TARGETS_A_UP, GOBP_MACROMOLECULE_CATABOLIC_PROCESS, GOBP_NEUROGENESIS, GOCC_MICROTUBULE_ORGANIZING_CENTER, GOBP_ANIMAL_ORGAN_MORPHOGENESIS, GOBP_EYE_PHOTORECEPTOR_CELL_DIFFERENTIATION, ONKEN_UVEAL_MELANOMA_UP, GOBP_REGULATION_OF_CATABOLIC_PROCESS, GOBP_POSITIVE_REGULATION_OF_CATABOLIC_PROCESS, GOBP_SENSORY_PERCEPTION_OF_LIGHT_STIMULUS, GOBP_CILIUM_ORGANIZATION

GO Biological Process (11): ubiquitin-dependent protein catabolic process (GO:0006511), intracellular protein transport (GO:0006886), visual perception (GO:0007601), positive regulation of autophagy (GO:0010508), protein ubiquitination (GO:0016567), intraciliary transport (GO:0042073), eye photoreceptor cell development (GO:0042462), cilium assembly (GO:0060271), protein localization to non-motile cilium (GO:0097499), cell projection organization (GO:0030030), cilium organization (GO:0044782)

GO Molecular Function (4): RNA binding (GO:0003723), guanyl-nucleotide exchange factor activity (GO:0005085), ubiquitin protein ligase activity (GO:0061630), protein binding (GO:0005515)

GO Cellular Component (14): photoreceptor outer segment (GO:0001750), cytoplasm (GO:0005737), Golgi apparatus (GO:0005794), centrosome (GO:0005813), axoneme (GO:0005930), photoreceptor connecting cilium (GO:0032391), ciliary basal body (GO:0036064), sperm flagellum (GO:0036126), microtubule organizing center (GO:0005815), cytoskeleton (GO:0005856), cilium (GO:0005929), motile cilium (GO:0031514), cell projection (GO:0042995), photoreceptor cell cilium (GO:0097733)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure5
cilium3
cilium organization2
protein localization to cilium2
photoreceptor cell cilium2
microtubule organizing center2
protein ubiquitination1
modification-dependent protein catabolic process1
intracellular protein localization1
protein transport1
intracellular transport1
sensory perception of light stimulus1
autophagy1
positive regulation of catabolic process1
regulation of autophagy1
protein modification by small protein conjugation1
transport along microtubule1
eye photoreceptor cell differentiation1
photoreceptor cell development1
axoneme assembly1
intraciliary transport involved in cilium assembly1
organelle assembly1
trans-Golgi to periciliary membrane compartment transport1
plasma membrane bounded cell projection assembly1
ciliary transition zone assembly1
cellular component organization1
organelle organization1
plasma membrane bounded cell projection organization1
nucleic acid binding1
GTP binding1
GDP binding1
GTPase regulator activity1
ubiquitin-protein transferase activity1
ubiquitin-like protein ligase activity1
binding1
intracellular anatomical structure1
cytoplasm1
endomembrane system1
intracellular membrane-bounded organelle1
centriole1

Protein interactions and networks

STRING

2084 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
RPGRRPGRIP1Q96KN7999
RPGRIQCB1Q15051985
RPGRCEP290O15078971
RPGRRPGRIP1LQ68CZ1943
RPGRNPHP4O75161909
RPGRIFT88Q13099899
RPGRABCA4P78363899
RPGRRHOP08100858
RPGRRPE65Q16518843
RPGRCACNA1FO60840843
RPGRNPHP1O15259840
RPGREYSQ5T1H1832
RPGRPRPF31Q8WWY3824
RPGRPRPH2P23942816
RPGRDNAI1Q9UI46798

IntAct

60 interactions, top by confidence:

ABTypeScore
PDE6DARL3psi-mi:“MI:0914”(association)0.920
RPGRPDE6Dpsi-mi:“MI:0407”(direct interaction)0.860
PDE6DRPGRpsi-mi:“MI:0407”(direct interaction)0.860
PDE6DRPGRpsi-mi:“MI:0915”(physical association)0.860
RPGRIP1RPGRpsi-mi:“MI:0915”(physical association)0.840
RPGRRPGRIP1psi-mi:“MI:0915”(physical association)0.840
RPGRNPHP4psi-mi:“MI:2364”(proximity)0.730
RPGRNPHP4psi-mi:“MI:0915”(physical association)0.730
Arl2PDE6Dpsi-mi:“MI:0915”(physical association)0.710
PDE6DRHEBpsi-mi:“MI:0915”(physical association)0.650
RPGRIP1NEK4psi-mi:“MI:0914”(association)0.620
Arl3PDE6Dpsi-mi:“MI:0915”(physical association)0.600
RPGRNPHP1psi-mi:“MI:0915”(physical association)0.560
RPGRRPGRIP1psi-mi:“MI:0915”(physical association)0.560
RPGRHOMEZpsi-mi:“MI:0915”(physical association)0.560
RPGRpsi-mi:“MI:0915”(physical association)0.560

BioGRID (87): RPGRIP1 (Two-hybrid), RPGR (Affinity Capture-MS), RPGR (Proximity Label-MS), BIRC6 (Proximity Label-MS), NPHP4 (Proximity Label-MS), NUDC (Proximity Label-MS), NUDCD2 (Proximity Label-MS), NUDCD3 (Proximity Label-MS), RPGRIP1L (Proximity Label-MS), UNC45A (Proximity Label-MS), DNAJA1 (Proximity Label-MS), DNAJC7 (Proximity Label-MS), DNM2 (Proximity Label-MS), FKBP4 (Proximity Label-MS), RHOA (Proximity Label-MS)

ESM2 similar proteins: A1Z1Q3, A6H8Y1, A7MBJ2, B2RX14, B8QB46, D3ZF42, F6QRE9, O02751, O70551, O94972, P17029, P23497, Q08995, Q08AY6, Q0V9E9, Q13342, Q3UVR3, Q3UZ39, Q498E6, Q587J6, Q588U8, Q5BLK4, Q5DTT8, Q5RD27, Q5RE50, Q5RHP9, Q5T7B8, Q5T7N2, Q5TAX3, Q5VYS8, Q61687, Q63HK3, Q6IQ55, Q6PCX9, Q7Z5L2, Q8BJM3, Q8BUH8, Q8IW19, Q8L7S0, Q92834

Diamond homologs: A6NED2, D3ZGQ5, F1RD40, O75592, O95199, O95714, P0C5Y8, P18754, P23800, P25171, P25183, P58544, Q15034, Q15751, Q4R828, Q4U2R1, Q52KW8, Q5BIW4, Q5DX34, Q5GLZ8, Q5PQN1, Q5RCZ7, Q6NRS1, Q6NXM2, Q6NYE2, Q6PAV2, Q6ZPR6, Q7TPH6, Q7ZZC8, Q86SG6, Q8BK67, Q8BTU7, Q8IVU3, Q8K1R7, Q8K2J9, Q8NDN9, Q8SSY6, Q8TD19, Q8VE37, Q90XC2

SIGNOR signaling

2 interactions.

AEffectBMechanism
RPGR“up-regulates activity”RAB8A“guanine nucleotide exchange factor”
RPGRIP1“down-regulates activity”RPGRbinding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 29 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:

PathwayPartnersFoldFDR
Anchoring of the basal body to the plasma membrane528.3×1e-04
Cell Cycle59.0×7e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

2050 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic495
Likely pathogenic236
Uncertain significance548
Likely benign332
Benign109

Top pathogenic / likely-pathogenic (30)

Variant IDHGVSClassification
1065689NM_001034853.2(RPGR):c.1754-3C>GPathogenic
1172694NM_001034853.2(RPGR):c.736_745dup (p.Ala249fs)Pathogenic
1172696NM_001034853.2(RPGR):c.2455_2468dup (p.Lys823_Gly824insTer)Pathogenic
1184953NM_001034853.2(RPGR):c.1932_1933insC (p.Gly645fs)Pathogenic
1208230NM_001034853.2(RPGR):c.2330del (p.Lys777fs)Pathogenic
1213920NM_001034853.2(RPGR):c.779-2A>GPathogenic
1213921NM_001034853.2(RPGR):c.2078_2148dup (p.Gln717delinsArgArgAsnTer)Pathogenic
1213922NM_001034853.2(RPGR):c.1541C>G (p.Ser514Ter)Pathogenic
1213924NM_001034853.2(RPGR):c.934+2T>CPathogenic
1213925NM_001034853.2(RPGR):c.897T>A (p.Tyr299Ter)Pathogenic
1213926NM_001034853.2(RPGR):c.665T>G (p.Leu222Ter)Pathogenic
1275779NM_001034853.2(RPGR):c.2218G>T (p.Glu740Ter)Pathogenic
1275798NM_001034853.2(RPGR):c.3070G>T (p.Glu1024Ter)Pathogenic
1284333NM_001034853.2(RPGR):c.3150_3151del (p.Glu1051fs)Pathogenic
1284488NM_001034853.2(RPGR):c.3212_3218del (p.Glu1071fs)Pathogenic
1297114NM_001034853.2(RPGR):c.1582_1585del (p.Thr528fs)Pathogenic
1297120NM_001034853.2(RPGR):c.2420_2435del (p.Glu807fs)Pathogenic
1297121NM_001034853.2(RPGR):c.2491G>T (p.Glu831Ter)Pathogenic
1297740NM_001034853.2(RPGR):c.1796dup (p.Asn599fs)Pathogenic
1333218NM_001034853.2(RPGR):c.1379del (p.Leu460fs)Pathogenic
1455429NM_001034853.2(RPGR):c.2679_2680del (p.Glu894fs)Pathogenic
1456564NM_001034853.2(RPGR):c.1220C>A (p.Ser407Ter)Pathogenic
1460223NM_001034853.2(RPGR):c.2293G>T (p.Glu765Ter)Pathogenic
1686131NM_001034853.2(RPGR):c.2522_2525dup (p.Glu843fs)Pathogenic
1686132NM_001034853.2(RPGR):c.2470G>T (p.Gly824Ter)Pathogenic
1691867NM_001034853.2(RPGR):c.544_545del (p.Val182fs)Pathogenic
1701595NM_001034853.2(RPGR):c.2480_2520dup (p.Glu841fs)Pathogenic
1701807NM_001034853.2(RPGR):c.2512del (p.Glu838fs)Pathogenic
1707409NM_001034853.2(RPGR):c.1302dup (p.Leu435fs)Pathogenic
1708067NM_001034853.2(RPGR):c.2149C>T (p.Gln717Ter)Pathogenic

SpliceAI

3861 predictions. Top by Δscore:

VariantEffectΔscore
X:38269833:C:CCacceptor_gain1.0000
X:38276581:TCATA:Tdonor_loss1.0000
X:38276582:CATA:Cdonor_loss1.0000
X:38276583:ATAC:Adonor_loss1.0000
X:38276584:TACC:Tdonor_loss1.0000
X:38276585:ACCTT:Adonor_loss1.0000
X:38276586:C:Gdonor_loss1.0000
X:38276770:ATCC:Aacceptor_loss1.0000
X:38276771:TC:Tacceptor_gain1.0000
X:38276772:CC:Cacceptor_gain1.0000
X:38276772:CCTGT:Cacceptor_loss1.0000
X:38276773:C:Aacceptor_loss1.0000
X:38276774:T:Gacceptor_loss1.0000
X:38276792:C:CTacceptor_gain1.0000
X:38290855:G:GGdonor_gain1.0000
X:38291022:TGT:Tacceptor_gain1.0000
X:38291022:TGTCT:Tacceptor_loss1.0000
X:38291024:TCTG:Tacceptor_loss1.0000
X:38291025:C:CCacceptor_gain1.0000
X:38291025:C:CGacceptor_loss1.0000
X:38291026:T:Gacceptor_loss1.0000
X:38298362:T:TAdonor_gain1.0000
X:38298928:TATTA:Tdonor_gain1.0000
X:38299004:T:Adonor_gain1.0000
X:38310613:AC:Adonor_gain1.0000
X:38310614:CC:Cdonor_gain1.0000
X:38310771:CTG:Cacceptor_gain1.0000
X:38310774:C:CCacceptor_gain1.0000
X:38310777:T:TCacceptor_gain1.0000
X:38317462:TCCT:Tacceptor_gain1.0000

AlphaMissense

7576 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
X:38317445:A:GW164R0.999
X:38317445:A:TW164R0.999
X:38301347:C:AG320V0.998
X:38301347:C:TG320E0.998
X:38304769:C:TG267E0.998
X:38304754:C:TG272D0.997
X:38304770:C:AG267W0.997
X:38304748:A:GL274P0.996
X:38310749:C:TG215E0.996
X:38318841:C:GA153P0.996
X:38318963:C:TG112D0.996
X:38301348:C:GG320R0.995
X:38301348:C:TG320R0.995
X:38304647:C:GA308P0.995
X:38304754:C:AG272V0.995
X:38317441:C:TG165D0.995
X:38317442:C:GG165R0.995
X:38317443:C:AW164C0.995
X:38317443:C:GW164C0.995
X:38318840:G:TA153D0.995
X:38318939:C:TG120E0.995
X:38322897:C:TG68E0.995
X:38304646:G:TA308D0.994
X:38317387:G:TP183H0.994
X:38317441:C:AG165V0.994
X:38318844:A:GS152P0.994
X:38318940:C:GG120R0.994
X:38318940:C:TG120R0.994
X:38318956:A:CN114K0.994
X:38318956:A:TN114K0.994

dbSNP variants (sampled 300 via entrez): RS1000109075 (X:38310574 C>T), RS1000201411 (X:38323766 G>A), RS1000221282 (X:38328959 T>C), RS1000340897 (X:38311006 T>C), RS1000397233 (X:38311298 C>G), RS1000542679 (X:38310105 G>A), RS1000555420 (X:38305767 A>G), RS1000721728 (X:38275765 TAA>T), RS1000760342 (X:38290001 T>C), RS1000894314 (X:38300877 TGA>T), RS1000926397 (X:38300299 T>C), RS1000944858 (X:38287127 C>A,T), RS1000980546 (X:38296144 T>C), RS1001154289 (X:38313273 T>C), RS1001192841 (X:38289482 T>C)

Disease associations

OMIM: gene MIM:312610 | disease phenotypes: MIM:244400, MIM:300029, MIM:300834, MIM:304020, MIM:268000, MIM:120970, MIM:204000, MIM:310500, MIM:617238, MIM:312612

GenCC curated gene-disease

DiseaseClassificationInheritance
retinitis pigmentosa 3DefinitiveX-linked
primary ciliary dyskinesia-retinitis pigmentosa syndromeStrongX-linked
cone-rod dystrophySupportiveAutosomal dominant
primary ciliary dyskinesiaSupportiveAutosomal dominant
retinitis pigmentosaSupportiveAutosomal dominant
macular degeneration, X-linked atrophicLimitedX-linked

ClinGen Gene-Disease Validity (1)

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

DiseaseClassificationInheritance
RPGR-related retinopathyDefinitiveXL

Mondo (20): primary ciliary dyskinesia (MONDO:0016575), retinitis pigmentosa 3 (MONDO:0010227), macular degeneration, X-linked atrophic (MONDO:0010443), X-linked cone-rod dystrophy 1 (MONDO:0010566), RPGR-related retinopathy (MONDO:0100437), inherited retinal dystrophy (MONDO:0019118), retinitis pigmentosa (MONDO:0019200), X-linked cone-rod dystrophy (MONDO:0021155), cone-rod dystrophy (MONDO:0015993), optic atrophy (MONDO:0003608), Leber congenital amaurosis (MONDO:0018998), congenital stationary night blindness (MONDO:0016293), retinal disorder (MONDO:0005283), esophageal atresia (MONDO:0001044), pyloric stenosis (MONDO:0001561)

Orphanet (8): Primary ciliary dyskinesia (Orphanet:244), Cone rod dystrophy (Orphanet:1872), Primary ciliary dyskinesia-retinitis pigmentosa syndrome (Orphanet:247522), Retinitis pigmentosa (Orphanet:791), OBSOLETE: Inherited retinal disorder (Orphanet:71862), Leber congenital amaurosis (Orphanet:65), Congenital stationary night blindness (Orphanet:215), Progressive cone dystrophy (Orphanet:1871)

HPO phenotypes

111 total (30 of 111 shown, HPO-id order):

HPOTerm
HP:0000119Abnormality of the genitourinary system
HP:0000238Hydrocephalus
HP:0000365Hearing impairment
HP:0000388Otitis media
HP:0000389Chronic otitis media
HP:0000403Recurrent otitis media
HP:0000405Conductive hearing impairment
HP:0000407Sensorineural hearing impairment
HP:0000501Glaucoma
HP:0000505Visual impairment
HP:0000510Rod-cone dystrophy
HP:0000512Abnormal electroretinogram
HP:0000529Progressive visual loss
HP:0000539Abnormality of refraction
HP:0000540Hypermetropia
HP:0000543Optic disc pallor
HP:0000545Myopia
HP:0000546Retinal degeneration
HP:0000551Color vision defect
HP:0000563Keratoconus
HP:0000602Ophthalmoplegia
HP:0000603Central scotoma
HP:0000608Macular degeneration
HP:0000613Photophobia
HP:0000618Blindness
HP:0000639Nystagmus
HP:0000648Optic atrophy
HP:0000662Nyctalopia
HP:0000750Delayed speech and language development
HP:0000842Hyperinsulinemia

GWAS associations

0 associations (top):

MeSH disease descriptors (17)

DescriptorNameTree numbers
D002925Ciliary Motility DisordersC08.200; C09.150; C16.131.077.245.500; C16.320.184.500
D000077765Cone DystrophyC11.270.151; C11.768.216
D000071700Cone-Rod DystrophiesC11.270.152; C11.768.585.658.250; C16.320.290.152
D004933Esophageal AtresiaC06.198.330; C06.405.117.260; C16.131.314.330
D017219Gastric Outlet ObstructionC06.405.748.340
D007619Kartagener SyndromeC08.127.384.500; C08.200.531; C08.695.501; C09.150.531; C14.240.400.280.500; C14.280.400.280.500; C16.131.077.245.500.531; C16.131.240.400.280.500; C16.131.740.501; C16.131.810.250.500; C16.320.184.500.531; C16.320.480
D057130Leber Congenital AmaurosisC11.270.516; C11.768.364
D009896Optic AtrophyC10.292.700.225; C11.640.451
D011707Pyloric StenosisC06.405.748.340.690
D012164Retinal DiseasesC11.768
D058499Retinal DystrophiesC11.768.585.658
D012174Retinitis PigmentosaC11.270.684; C11.768.585.658.500; C16.320.290.684
C564438Cone-Rod Dystrophy, X-Linked, Type 1 (supp.)
C536122Night blindness, congenital stationary (supp.)
C564520Retinitis Pigmentosa 3 (supp.)
C564065Retinitis Pigmentosa 6 (supp.)
C567595Retinitis Pigmentosa, X-Linked, And Sinorespiratory Infections, With Or Without Deafness (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
sodium arsenitedecreases expression, increases expression2
Air Pollutantsaffects expression, increases abundance, increases expression2
Cyclosporineincreases expression2
aristolochic acid Idecreases expression1
FR900359decreases phosphorylation1
dicrotophosdecreases expression1
triphenyl phosphateaffects expression1
tris(1,3-dichloro-2-propyl)phosphateincreases expression1
cobaltous chloridedecreases expression1
butyraldehydedecreases expression1
cupric chlorideincreases expression1
coumarindecreases phosphorylation1
pentanaldecreases expression1
2-amino-1-methyl-6-phenylimidazo(4,5-b)pyridinedecreases expression1
di-n-butylphosphoric acidaffects expression1
perfluorooctane sulfonic acidincreases expression1
(+)-JQ1 compoundincreases expression1
Resveratrolaffects cotreatment, increases expression1
Sunitinibincreases expression1
Arsenic Trioxidedecreases expression1
Benzo(a)pyreneaffects methylation, increases methylation1
Caffeineincreases phosphorylation1
Estradiolaffects expression1
Hydrogen Peroxideaffects expression1
Mercuric Chlorideaffects response to substance1
Ozoneaffects expression, increases abundance1
Plant Extractsaffects cotreatment, increases expression1
Smokeincreases abundance, increases expression1
Tobacco Smoke Pollutiondecreases expression1
Valproic Acidincreases expression1

Clinical trials (associated diseases)

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

TrialPhaseStatusTitle
NCT00717080PHASE4COMPLETEDThe Role of Capsular Tension Ring (CTR) in Anterior Capsular Contraction
NCT00000114PHASE3COMPLETEDRandomized Trial of Vitamin A and Vitamin E Supplementation for Retinitis Pigmentosa
NCT00000116PHASE3COMPLETEDRandomized Trial of DHA for Retinitis Pigmentosa Patients Receiving Vitamin A
NCT00346333PHASE3COMPLETEDClinical Trial of Lutein for Patients With Retinitis Pigmentosa Receiving Vitamin A
NCT01786395PHASE3TERMINATEDPhase III Efficacy and Safety Clinical Study of UF-021 for Treatment of Retinitis Pigmentosa
NCT04224207PHASE3COMPLETEDManagement of Retinitis Pigmentosa by Mesenchymal Stem Cells by Wharton’s Jelly Derived Mesenchymal Stem Cells
NCT04636853PHASE3COMPLETEDCB-PRP in Retinitis Pigmentosa and Dry Age-related Macular Degeneration
NCT05537220PHASE3ACTIVE_NOT_RECRUITINGOral N-acetylcysteine for Retinitis Pigmentosa
NCT05800301PHASE3COMPLETEDManagement of Retinitis Pigmentosa Via Combination of Wharton’s Jelly-derived Mesenchymal Stem Cells and Magnovision
NCT05926583PHASE3ACTIVE_NOT_RECRUITINGA Study of AAV5-hRKp.RPGR for the Treatment of Japanese Participants With X-linked Retinitis Pigmentosa
NCT06388200PHASE3ACTIVE_NOT_RECRUITINGA Phase 3 Study Of OCU400 Gene Therapy for the Treatment Of Retinitis Pigmentosa
NCT07082855PHASE3NOT_YET_RECRUITINGA Multicenter, Randomized, Double-Blind, Controlled Clinical Study of Minocycline for the Treatment of Retinitis Pigmentosa
NCT07290530PHASE3NOT_YET_RECRUITING24-Month Trial of NPI-001 for the Preservation of Photoreceptors in Retinitis Pigmentosa Associated With Usher Syndrome
NCT01773278PHASE2RECRUITINGCholesterol and Antioxidant Treatment in Patients With Smith-Lemli-Opitz Syndrome (SLOS)
NCT02871778PHASE2COMPLETEDClearing Lungs With ENaC Inhibition in Primary Ciliary Dyskinesia
NCT07318974PHASE2ACTIVE_NOT_RECRUITINGMelatonin Therapy for Improving ICSI Outcomes in Women With Diminished Ovarian Reserve
NCT00100230PHASE2COMPLETEDDHA and X-Linked Retinitis Pigmentosa
NCT00447980PHASE2COMPLETEDA Study of Encapsulated Cell Technology (ECT) Implant for Participants With Early Stage Retinitis Pigmentosa
NCT00447993PHASE2COMPLETEDA Study of Encapsulated Cell Technology (ECT) Implant for Patients With Late Stage Retinitis Pigmentosa
NCT01233609PHASE2COMPLETEDTrial of Oral Valproic Acid for Retinitis Pigmentosa
NCT01399515PHASE2COMPLETEDEfficacy and Safety of Oral Valproic Acid for Retinitis Pigmentosa
NCT01530659PHASE2COMPLETEDRetinal Imaging in CNTF -Releasing Encapsulated Cell Implant Treated Patients for Early-stage Retinitis Pigmentosa
NCT01560715PHASE2COMPLETEDAutologous Bone Marrow-Derived Stem Cells Transplantation For Retinitis Pigmentosa
NCT02609165PHASE2COMPLETEDNerve Growth Factor Eye Drops Treatment in Patients With Retinitis Pigmentosa and Cystoid Macular Edema
NCT02661711PHASE2COMPLETEDAflibercept for Macular Oedema With Underlying Retinitis Pigmentosa (AMOUR) Study
NCT02804360PHASE2UNKNOWNIntravitreal Dexamethasone Implant in Retinitis Pigmentosa-related Macular Edema- a Retrospective Study
NCT02837640PHASE2UNKNOWNStudying a Potential Protective Effect of L-Dopa on Retinitis Pigmentosa
NCT03073733PHASE2COMPLETEDSafety and Efficacy of Intravitreal Injection of Human Retinal Progenitor Cells in Adults With Retinitis Pigmentosa
NCT04068207PHASE2COMPLETEDMinocycline Treatment in Retinitis Pigmentosa
NCT04356716PHASE2COMPLETEDSildenafil for Treatment of Choroidal Ischemia
NCT04604899PHASE2COMPLETEDSafety of Repeat Intravitreal Injection of Human Retinal Progenitor Cells (jCell) in Adult Subjects With Retinitis Pigmentosa
NCT04763369PHASE2UNKNOWNInvestigation of Therapeutic Efficacy and Safety of UMSCs for the Management of Retinitis Pigmentosa (RP)
NCT04864496PHASE2UNKNOWNEffects of Treatment With N- Acetylcysteine on Visual Outcomes in Patients With Retinitis Pigmentosa
NCT04945772PHASE2COMPLETEDEfficacy and Safety of MCO-010 Optogenetic Therapy in Adults With Retinitis Pigmentosa [RESTORE]
NCT05085964PHASE2TERMINATEDAn Open-Label Extension Study to Evaluate Safety & Tolerability of QR-421a in Subjects With Retinitis Pigmentosa
NCT05392179PHASE2COMPLETEDA Study in Subjects With Retinitis Pigmentosa
NCT06627179PHASE2RECRUITINGStudy to Evaluate Ultevursen in Subjects With Retinitis Pigmentosa (RP) Due to Mutations in Exon 13 of the USH2A Gene
NCT06628947PHASE2RECRUITINGA Phase II Study of Intravitreal KIO-301 in Patients With Late-stage Retinitis Pigmentosa
NCT06912633PHASE2RECRUITINGSafety of a Single, Intravitreal Injection of 6.0M jCell (Famzeretcel) in Retinitis Pigmentosa (RP)
NCT03763227PHASE2COMPLETEDIntravitreal Ranibizumab (Lucentis®) in the Treatment of Non-leaking Macular Cysts in Retinal Dystrophy