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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
    mouse all
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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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    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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