Seroatlas · Human Serome Atlas

RPGR

X-linked retinitis pigmentosa GTPase regulator

Also known as: COD1, CORDX1, CRD, RP15, RP3, RPGR_HUMAN

Cross-references: UniProt · Ensembl · Human Protein Atlas · GeneCards · NCBI Gene

Protein identityUniProt · HPA

UniProt accession: Q92834
Gene: RPGR
Ensembl: ENSG00000156313
Chromosome: X
Canonical length: 1020 aa
Protein class: Cancer-related genes, Disease related genes, Human disease related genes, Predicted intracellular proteins, Predicted membrane proteins
Subcellular location: Golgi apparatus,Primary cilium,Mitochondria,Cytosol,Mid piece,Principal piece,End piece

OverviewNCBI Gene

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. [provided by RefSeq, Dec 2008]

Canonical amino-acid sequenceUniProt

1020 residues, UniProt reviewed canonical sequence.

>Q92834|RPGR
     1  MREPEELMPD SGAVFTFGKS KFAENNPGKF WFKNDVPVHL SCGDEHSAVV TGNNKLYMFG
    61  SNNWGQLGLG SKSAISKPTC VKALKPEKVK LAACGRNHTL VSTEGGNVYA TGGNNEGQLG
   121  LGDTEERNTF HVISFFTSEH KIKQLSAGSN TSAALTEDGR LFMWGDNSEG QIGLKNVSNV
   181  CVPQQVTIGK PVSWISCGYY HSAFVTTDGE LYVFGEPENG KLGLPNQLLG NHRTPQLVSE
   241  IPEKVIQVAC GGEHTVVLTE NAVYTFGLGQ FGQLGLGTFL FETSEPKVIE NIRDQTISYI
   301  SCGENHTALI TDIGLMYTFG DGRHGKLGLG LENFTNHFIP TLCSNFLRFI VKLVACGGCH
   361  MVVFAAPHRG VAKEIEFDEI NDTCLSVATF LPYSSLTSGN VLQRTLSARM RRRERERSPD
   421  SFSMRRTLPP IEGTLGLSAC FLPNSVFPRC SERNLQESVL SEQDLMQPEE PDYLLDEMTK
   481  EAEIDNSSTV ESLGETTDIL NMTHIMSLNS NEKSLKLSPV QKQKKQQTIG ELTQDTALTE
   541  NDDSDEYEEM SEMKEGKACK QHVSQGIFMT QPATTIEAFS DEEVGNDTGQ VGPQADTDGE
   601  GLQKEVYRHE NNNGVDQLDA KEIEKESDGG HSQKESEAEE IDSEKETKLA EIAGMKDLRE
   661  REKSTKKMSP FFGNLPDRGM NTESEENKDF VKKRESCKQD VIFDSERESV EKPDSYMEGA
   721  SESQQGIADG FQQPEAIEFS SGEKEDDEVE TDQNIRYGRK LIEQGNEKET KPIISKSMAK
   781  YDFKCDRLSE IPEEKEGAED SKGNGIEEQE VEANEENVKV HGGRKEKTEI LSDDLTDKAE
   841  DHEFSKTEEL KLEDVDEEIN AENVESKKKT VGDDESVPTG YHSKTEGAER TNDDSSAETI
   901  EKKEKANLEE RAICEYNENP KGYMLDDADS SSLEILENSE TTPSKDMKKT KKIFLFKRVP
   961  SINQKIVKNN NEPLPEIKSI GDQIILKSDN KDADQNHMSQ NHQNIPPTNT ERRSKSCTIL

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against RPGR can act on the native protein depends on physical access: surface and secreted proteins are reachable by circulating antibodies, intracellular proteins usually are not.

Antibody reachability: Intracellular
Secreted: No
Transmembrane segments: 0
Mean surface accessibility (rSASA): 0.52
Highest tissue expression: 17 nTPM

Expression across tissuesHPA

Tissue

pituitary gland: 17 nTPM
choroid plexus: 15 nTPM
adipose tissue: 14 nTPM
breast: 13 nTPM
fallopian tube: 12 nTPM
bone marrow: 12 nTPM

Single-cell type

endometrial ciliated cells: 393 nCPM
somatotrophs: 361 nCPM
ependymal cells: 346 nCPM
epididymal efferent duct ciliated cells: 295 nCPM
choroid plexus epithelial cells: 294 nCPM
neutrophils: 273 nCPM

Immune cell

neutrophil: 15 nTPM
eosinophil: 5.9 nTPM
MAIT T-cell: 2.9 nTPM
classical monocyte: 2.6 nTPM
myeloid DC: 2.6 nTPM
intermediate monocyte: 2.4 nTPM

Brain region

choroid plexus: 28 nTPM
medulla oblongata: 13 nTPM
midbrain: 11 nTPM
spinal cord: 10 nTPM
hypothalamus: 9.6 nTPM
pons: 8.3 nTPM

DiseaseUniProt · ClinVar · IEDB · PubMed

Four sources answering four different questions about RPGR.

Disease | AllUniProt

Conditions RPGR is implicated in, by any mechanism.

Retinitis pigmentosa 3 (RP3) MIM:300029
Retinitis pigmentosa, X-linked, and sinorespiratory infections with or without deafness (RPSRDF) MIM:300455
Cone-rod dystrophy, X-linked 1 (CORDX1) MIM:304020
Macular degeneration, atrophic, X-linked (MDXLA) MIM:300834

Disease | GeneticClinVar

791 pathogenic / likely-pathogenic of 2,039 ClinVar records.

Conditions with pathogenic or likely-pathogenic variants.

Genetic constraint and essentialitygnomAD · DepMap

Does the body need this protein intact? Low LOEUF or a strong DepMap dependency means loss or blockade of the protein is likely to be felt.

gnomAD LOEUF (loss-of-function intolerance): 0.21
gnomAD pLI: 1
gnomAD missense Z: 1.25
DepMap mean gene effect: 0.01
DepMap dependency class: none

Cancer expressionTCGA

Across TCGA tumor cohorts, this protein is over-expressed in roughly 4% of surveyed tumor types (aggregate summary; per-cohort expression, alteration, and survival load in the interactive view).

OntologyGO

Biological processes

Molecular functions

Cellular components

Protein domainsUniProt · Pfam · InterPro

KeywordsUniProt

InteractionsUniProt · HPA

Protein binding partners of RPGR in the human serome: UniProt-annotated complex subunits plus reported interactors. Each links to its own Seroatlas record.

Antibody and autoantibody relevanceSeroatlas analysis

Seroatlas reads RPGR as an antibody target. Whether an autoantibody or antibody against RPGR could matter depends on whether native RPGR is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

RPGR is annotated as predominantly intracellular. Intracellular proteins are common autoantibody markers, becoming visible to the immune system after cell injury or altered processing, but are usually markers of disease rather than direct drivers.

Annotation status

The present source text does not explicitly label RPGR as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

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