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RPGR retinitis pigmentosa GTPase regulator [ Homo sapiens (human) ]

Gene ID: 6103, updated on 2-Nov-2024

Summary

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Official Symbol
RPGRprovided by HGNC
Official Full Name
retinitis pigmentosa GTPase regulatorprovided by HGNC
Primary source
HGNC:HGNC:10295
See related
Ensembl:ENSG00000156313 MIM:312610; AllianceGenome:HGNC:10295
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
CRD; RP3; COD1; PCDX; RP15; XLRP3; orf15; CORDX1
Summary
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]
Expression
Ubiquitous expression in testis (RPKM 2.6), lung (RPKM 2.3) and 25 other tissues See more
Orthologs
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Genomic context

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See RPGR in Genome Data Viewer
Location:
Xp11.4
Exon count:
25
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (38269163..38327509, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (37672761..37731102, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (38128416..38186762, complement)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene sushi repeat containing protein X-linked Neighboring gene uncharacterized LOC124905176 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20735 Neighboring gene ReSE screen-validated silencer GRCh37_chrX:38191193-38191385 Neighboring gene HNF4 motif-containing MPRA enhancer 122 Neighboring gene ornithine transcarbamylase Neighboring gene CRIPTO pseudogene 1 Neighboring gene BAG1 pseudogene 1

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. [Novel RPGR gene mutation in a Chinese family with X-linked recessive retinitis pigmentosa]. Li ZL, et al. Zhonghua Yan Ke Za Zhi, 2011 Jun. PMID 21914266
  2. Identification of a novel RPGR exon ORF15 mutation in a family with X-linked retinitis pigmentosa. Jin ZB, et al. Arch Ophthalmol, 2007 Oct. PMID 17923551
  3. Retinal phenotype of an X-linked pseudo-Usher syndrome in association with the G173R mutation in the RPGR gene. Iannaccone A, et al. Adv Exp Med Biol, 2008. PMID 18188948
  4. Discordant phenotypes in fraternal twins having an identical mutation in exon ORF15 of the RPGR gene. Walia S, et al. Arch Ophthalmol, 2008 Mar. PMID 18332319
  5. Phenotypic progression in X-linked retinitis pigmentosa secondary to a novel mutation in the RPGR gene. Al-Maskari A, et al. Eye (Lond), 2009 Mar. PMID 19218993

See all (179) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Clinical sequencing of the retinitis pigmentosa gene RPGR in over 1,000 cases of vision loss.
    Title: Clinical sequencing of the retinitis pigmentosa gene RPGR in over 1,000 cases of vision loss.
  2. Primary Ciliary Dyskinesia and Retinitis Pigmentosa: Novel RPGR Variant and Possible Modifier Gene.
    Title: Primary Ciliary Dyskinesia and Retinitis Pigmentosa: Novel RPGR Variant and Possible Modifier Gene.
  3. Towards a Long-Read Sequencing Approach for the Molecular Diagnosis of RPGR[ORF15] Genetic Variants.
    Title: Towards a Long-Read Sequencing Approach for the Molecular Diagnosis of RPGR(ORF15) Genetic Variants.
  4. Identification of the RPGR Gene Pathogenic Variants in a Cohort of Polish Male Patients with Retinitis Pigmentosa Phenotype.
    Title: Identification of the RPGR Gene Pathogenic Variants in a Cohort of Polish Male Patients with Retinitis Pigmentosa Phenotype.
  5. RPGR: Deep Phenotyping and Genetic Characterization With Findings Specific to the 3'-end of ORF15.
    Title: RPGR: Deep Phenotyping and Genetic Characterization With Findings Specific to the 3'-end of ORF15.
  6. Skewed X-inactivation is associated with retinal dystrophy in female carriers of RPGR mutations.
    Title: Skewed X-inactivation is associated with retinal dystrophy in female carriers of RPGR mutations.
  7. Long-Read Nanopore Sequencing of RPGR ORF15 is Enhanced Following DNase I Treatment of MinION Flow Cells.
    Title: Long-Read Nanopore Sequencing of RPGR ORF15 is Enhanced Following DNase I Treatment of MinION Flow Cells.
  8. Clinical characteristics of high myopia in female carriers of pathogenic RPGR mutations: a case series and review of the literature.
    Title: Clinical characteristics of high myopia in female carriers of pathogenic RPGR mutations: a case series and review of the literature.
  9. Genotypic and phenotypic characterisation of RP2- and RPGR-associated X-linked inherited retinal dystrophy, including female manifestations.
    Title: Genotypic and phenotypic characterisation of RP2- and RPGR-associated X-linked inherited retinal dystrophy, including female manifestations.
  10. Genetic spectrum, retinal phenotype, and peripapillary RNFL thickness in RPGR heterozygotes.
    Title: Genetic spectrum, retinal phenotype, and peripapillary RNFL thickness in RPGR heterozygotes.
Submit: New GeneRIF Correction See all GeneRIFs (124)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Macular degeneration, X-linked atrophic
MedGen: C3151784 OMIM: 300834 GeneReviews: Not available
not available
Retinitis pigmentosa 3
MedGen: C1845667 OMIM: 300029 GeneReviews: Nonsyndromic Retinitis Pigmentosa Overview
not available
Retinitis pigmentosa, X-linked, and sinorespiratory infections, with or without deafness
MedGen: C2749137 OMIM: 300455 GeneReviews: Not available
not available
X-linked cone-rod dystrophy 1
MedGen: C1844776 OMIM: 304020 GeneReviews: Not available
not available

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

HIV-1 interactions

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Replication interactions

Interaction Pubs
Knockdown of retinitis pigmentosa GTPase regulator (RPGR) by shRNA library screening inhibits HIV-1 replication in cultured Jurkat T-cells PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables RNA binding HDA PubMed 
enables guanyl-nucleotide exchange factor activity IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables ubiquitin protein ligase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
Process Evidence Code Pubs
involved_in cilium assembly IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in intracellular protein transport TAS
Traceable Author Statement
more info
 PubMed 
involved_in intraciliary transport IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in intraciliary transport ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in protein ubiquitination IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in ubiquitin-dependent protein catabolic process IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in visual perception IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in visual perception IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
is_active_in Golgi apparatus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in Golgi apparatus IDA
Inferred from Direct Assay
more info
  
located_in Golgi apparatus ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in centrosome IDA
Inferred from Direct Assay
more info
 PubMed 
located_in ciliary basal body ISS
Inferred from Sequence or Structural Similarity
more info
  
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
  
is_active_in photoreceptor outer segment IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in photoreceptor outer segment IDA
Inferred from Direct Assay
more info
 PubMed 
located_in sperm flagellum ISS
Inferred from Sequence or Structural Similarity
more info
  

General protein information

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Preferred Names
X-linked retinitis pigmentosa GTPase regulator
Names
retinitis pigmentosa 15
retinitis pigmentosa 3 GTPase regulator

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_009553.1 RefSeqGene

    Range
    5027..48128
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_000328.3 → NP_000319.1  X-linked retinitis pigmentosa GTPase regulator isoform A

    See identical proteins and their annotated locations for NP_000319.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (A) uses an alternate splice site and contains multiple alternative exons in the 3' coding region, compared to variant C. The resulting isoform (A, also referred to as isoform 1) is shorter and has a distinct C-terminus, compared to isoform C.
    Source sequence(s)
    AL606748, BX644678, CA313540, U57629
    Consensus CDS
    CCDS14246.1
    UniProtKB/TrEMBL
    A8K717
    Related
    ENSP00000493468.2, ENST00000642395.2
    Conserved Domains (2) summary
    pfam00415
    Location:158 → 205
    RCC1; Regulator of chromosome condensation (RCC1) repeat
    pfam13540
    Location:142 → 171
    RCC1_2; Regulator of chromosome condensation (RCC1) repeat

  2. NM_001034853.2 → NP_001030025.1  X-linked retinitis pigmentosa GTPase regulator isoform C

    See identical proteins and their annotated locations for NP_001030025.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (C) encodes the longest isoform (C).
    Source sequence(s)
    AL606748, BK005711, BP233620
    Consensus CDS
    CCDS35229.1
    UniProtKB/Swiss-Prot
    Q92834
    Related
    ENSP00000495537.1, ENST00000645032.1
    Conserved Domains (2) summary
    pfam00415
    Location:314 → 360
    RCC1; Regulator of chromosome condensation (RCC1) repeat
    cl27697
    Location:38 → 312
    RCC1; Regulator of chromosome condensation (RCC1) repeat

  3. NM_001367245.1 → NP_001354174.1  X-linked retinitis pigmentosa GTPase regulator isoform D

    Status: REVIEWED

    Source sequence(s)
    AL606748
    UniProtKB/TrEMBL
    A8K717
    Conserved Domains (2) summary
    pfam00415
    Location:313 → 359
    RCC1; Regulator of chromosome condensation (RCC1) repeat
    cl27697
    Location:38 → 311
    RCC1; Regulator of chromosome condensation (RCC1) repeat

  4. NM_001367246.1 → NP_001354175.1  X-linked retinitis pigmentosa GTPase regulator isoform E

    Status: REVIEWED

    Source sequence(s)
    AL606748
    Consensus CDS
    CCDS94589.1
    UniProtKB/TrEMBL
    A8K717
    Related
    ENSP00000494557.1, ENST00000644337.1
    Conserved Domains (2) summary
    pfam00415
    Location:314 → 342
    RCC1; Regulator of chromosome condensation (RCC1) repeat
    cl27697
    Location:38 → 312
    RCC1; Regulator of chromosome condensation (RCC1) repeat

  5. NM_001367247.1 → NP_001354176.1  X-linked retinitis pigmentosa GTPase regulator isoform F

    Status: REVIEWED

    Source sequence(s)
    AL606748
    UniProtKB/TrEMBL
    A8K717
    Conserved Domains (3) summary
    pfam00415
    Location:314 → 360
    RCC1; Regulator of chromosome condensation (RCC1) repeat
    cl26511
    Location:456 → 688
    Neuromodulin_N; Gap junction protein N-terminal region
    cl27697
    Location:38 → 312
    RCC1; Regulator of chromosome condensation (RCC1) repeat

  6. NM_001367248.1 → NP_001354177.1  X-linked retinitis pigmentosa GTPase regulator isoform G

    Status: REVIEWED

    Source sequence(s)
    AL606748
    UniProtKB/TrEMBL
    A8K717
    Conserved Domains (2) summary
    pfam00415
    Location:324 → 370
    RCC1; Regulator of chromosome condensation (RCC1) repeat
    cl27697
    Location:48 → 322
    RCC1; Regulator of chromosome condensation (RCC1) repeat

  7. NM_001367249.1 → NP_001354178.1  X-linked retinitis pigmentosa GTPase regulator isoform H

    Status: REVIEWED

    Source sequence(s)
    AL606748
    UniProtKB/TrEMBL
    A8K717
    Conserved Domains (2) summary
    pfam00415
    Location:313 → 359
    RCC1; Regulator of chromosome condensation (RCC1) repeat
    cl27697
    Location:38 → 311
    RCC1; Regulator of chromosome condensation (RCC1) repeat

  8. NM_001367250.1 → NP_001354179.1  X-linked retinitis pigmentosa GTPase regulator isoform I

    Status: REVIEWED

    Source sequence(s)
    AL606748
    UniProtKB/TrEMBL
    A8K717
    Conserved Domains (3) summary
    pfam00415
    Location:313 → 359
    RCC1; Regulator of chromosome condensation (RCC1) repeat
    cl26511
    Location:455 → 687
    Neuromodulin_N; Gap junction protein N-terminal region
    cl27697
    Location:38 → 311
    RCC1; Regulator of chromosome condensation (RCC1) repeat

  9. NM_001367251.1 → NP_001354180.1  X-linked retinitis pigmentosa GTPase regulator isoform J

    Status: REVIEWED

    Source sequence(s)
    AL606748
    Consensus CDS
    CCDS94588.1
    UniProtKB/TrEMBL
    A0A2R8Y414, A0A2R8YFT6
    Related
    ENSP00000496728.1, ENST00000644238.1
    Conserved Domains (2) summary
    pfam00415
    Location:314 → 342
    RCC1; Regulator of chromosome condensation (RCC1) repeat
    cl27697
    Location:38 → 312
    RCC1; Regulator of chromosome condensation (RCC1) repeat

RNA

  1. NR_159803.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AL606748
    Related
    ENST00000646020.1

  2. NR_159804.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AL606748

  3. NR_159805.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AL606748
    Related
    ENST00000642739.1

  4. NR_159806.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AL606748
    Related
    ENST00000645124.1

  5. NR_159807.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AL606748, BC031624
    Related
    ENST00000474584.5

  6. NR_159808.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AL606748
    Related
    ENST00000642170.1

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000023.11 Reference GRCh38.p14 Primary Assembly

    Range
    38269163..38327509 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047442330.1 → XP_047298286.1  X-linked retinitis pigmentosa GTPase regulator isoform X2

  2. XM_047442329.1 → XP_047298285.1  X-linked retinitis pigmentosa GTPase regulator isoform X1

    UniProtKB/Swiss-Prot
    B1ARN3, E9PE28, O00702, O00737, Q3KN84, Q8N5T6, Q92834, Q93039, Q9HD29, Q9UMR1
    Related
    ENSP00000343671.3, ENST00000339363.7

  3. XM_047442331.1 → XP_047298287.1  X-linked retinitis pigmentosa GTPase regulator isoform X3

RNA

  1. XR_007068198.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    37672761..37731102 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054327520.1 → XP_054183495.1  X-linked retinitis pigmentosa GTPase regulator isoform X2

  2. XM_054327519.1 → XP_054183494.1  X-linked retinitis pigmentosa GTPase regulator isoform X1

    UniProtKB/Swiss-Prot
    B1ARN3, E9PE28, O00702, O00737, Q3KN84, Q8N5T6, Q92834, Q93039, Q9HD29, Q9UMR1

  3. XM_054327521.1 → XP_054183496.1  X-linked retinitis pigmentosa GTPase regulator isoform X3

RNA

  1. XR_008485504.1 RNA Sequence

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_001023582.1: Suppressed sequence

    Description
    NM_001023582.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q92834.2 GenPept UniProtKB/Swiss-Prot:Q92834

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