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    RPGRIP1 RPGR interacting protein 1 [ Homo sapiens (human) ]

    Gene ID: 57096, updated on 14-Nov-2024

    Summary

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    Official Symbol
    RPGRIP1provided by HGNC
    Official Full Name
    RPGR interacting protein 1provided by HGNC
    Primary source
    HGNC:HGNC:13436
    See related
    Ensembl:ENSG00000092200 MIM:605446; AllianceGenome:HGNC:13436
    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
    LCA6; RGI1; RGRIP; CORD13; RPGRIP; RPGRIP1d
    Summary
    This gene encodes a photoreceptor protein that interacts with retinitis pigmentosa GTPase regulator protein and is a key component of cone and rod photoreceptor cells. Mutations in this gene lead to autosomal recessive congenital blindness. [provided by RefSeq, Oct 2008]
    Expression
    Restricted expression toward testis (RPKM 14.5) See more
    Orthologs
    mouse all
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    Genomic context

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    See RPGRIP1 in Genome Data Viewer
    Location:
    14q11.2
    Exon count:
    26
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (21280083..21351301)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (15477514..15548760)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (21748242..21819460)

    Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 641 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:21686859-21687402 Neighboring gene heterogeneous nuclear ribonucleoprotein C Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:21722469-21723406 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:21734420-21735000 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:21735001-21735580 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:21737080-21737704 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:21737705-21738330 Neighboring gene mitochondrial ribosomal protein S17 pseudogene 6 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr14:21777043-21777570 Neighboring gene ReSE screen-validated silencer GRCh37_chr14:21817331-21817510 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr14:21820143-21821342 Neighboring gene SPT16 homolog, facilitates chromatin remodeling subunit Neighboring gene uncharacterized LOC107984643 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr14:21859227-21860426 Neighboring gene chromodomain helicase DNA binding protein 8

    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. Thumb duplication: molecular analysis of different clinical types. Kyriazis Z, et al. Eur J Orthop Surg Traumatol, 2019 Feb. PMID 30498907
    2. Limited proteolysis differentially modulates the stability and subcellular localization of domains of RPGRIP1 that are distinctly affected by mutations in Leber's congenital amaurosis. Lu X, et al. Hum Mol Genet, 2005 May 15. PMID 15800011, Free PMC Article
    3. A Novel Recessive RPGRIP1 Mutation Causing Leber Congenital Amaurosis. Abouzeid H, et al. Klin Monbl Augenheilkd, 2016 Apr. PMID 27116508
    4. Complete exon-intron structure of the RPGR-interacting protein (RPGRIP1) gene allows the identification of mutations underlying Leber congenital amaurosis. Gerber S, et al. Eur J Hum Genet, 2001 Aug. PMID 11528500
    5. Targeted next generation sequencing identified novel mutations in RPGRIP1 associated with both retinitis pigmentosa and Leber's congenital amaurosis in unrelated Chinese patients. Huang H, et al. Oncotarget, 2017 May 23. PMID 28456785, Free PMC Article

    See all (56) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. RPGRIP1-related retinal disease presenting as isolated cone dysfunction.
      Title: RPGRIP1-related retinal disease presenting as isolated cone dysfunction.
    2. Molecular genetics with clinical characteristics of Leber congenital amaurosis in the Han population of western China.
      Title: Molecular genetics with clinical characteristics of Leber congenital amaurosis in the Han population of western China.
    3. Noncoding mutation in RPGRIP1 contributes to inherited retinal degenerations.
      Title: Noncoding mutation in RPGRIP1 contributes to inherited retinal degenerations.
    4. Whole Locus Sequencing Identifies a Prevalent Founder Deep Intronic RPGRIP1 Pathologic Variant in the French Leber Congenital Amaurosis Cohort.
      Title: Whole Locus Sequencing Identifies a Prevalent Founder Deep Intronic RPGRIP1 Pathologic Variant in the French Leber Congenital Amaurosis Cohort.
    5. Clinical and molecular findings in a cohort of 152 Brazilian severe early onset inherited retinal dystrophy patients.
      Title: Clinical and molecular findings in a cohort of 152 Brazilian severe early onset inherited retinal dystrophy patients.
    6. Data indicate that the c. 2889delT (p.P963 fs) mutation in the retinitis pigmentosa GTPase regulator interacting protein 1 (RPGRIP1) gene works as a pathogenic mutation that contributes to the progression of Leber congenital amaurosis (LCA).
      Title: Identification of a novel RPGRIP1 mutation in an Iranian family with leber congenital amaurosis by exome sequencing.
    7. Although the patients had 2 mutated genes in common (RPGRIP1 and TMEM216), they only shared one common mutation in RPGRIP1 gene. Thus, it seems that this common RPGRIP1 mutation is associated with radial polydactyly but probably does not play a significant role in the Wassel type differentiation.
      Title: Thumb duplication: molecular analysis of different clinical types.
    8. Loss of Rpgrip1 expression is associated with Ciliopathy.
      Title: Cell type-specific regulation of ciliary transition zone assembly in vertebrates.
    9. Gene capture sequencing results found three probands carrying mutations of RPGRIP1, which was known to be associated with pathogenesis of LCA (Leber's congenital amaurosis). By further clinical analysis, two probands were confirmed to be retinitis pigmentosa (RP) patients and one was confirmed to be LCA patient. These novel mutations were co-segregated with the disease phenotype in their families.
      Title: Targeted next generation sequencing identified novel mutations in RPGRIP1 associated with both retinitis pigmentosa and Leber's congenital amaurosis in unrelated Chinese patients.
    10. Neurodevelopmental delay and brain atrophy in the CT scan were reported. Genomic sequencing identified a novel homozygous deletion, c.[420delG], in RPGRIP1. This mutation was not detected in 80 ethnically matched controls and has not been reported elsewhere. CONCLUSIONS: Identifying new mutations in Leber congenital amaurosis-related genes and their clinical manifestations can improve our understanding of the disease and.
      Title: A Novel Recessive RPGRIP1 Mutation Causing Leber Congenital Amaurosis.
    Submit: New GeneRIF Correction See all GeneRIFs (27)

    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

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    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

    Clone Names

    • DKFZp686P0897

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in neural precursor cell proliferation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in non-motile cilium assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in retinal rod cell development IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in visual perception IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in axoneme IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in ciliary rootlet IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in photoreceptor connecting cilium IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in photoreceptor connecting cilium ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in photoreceptor distal connecting cilium IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    X-linked retinitis pigmentosa GTPase regulator-interacting protein 1
    Names
    retinitis pigmentosa GTPase regulator interacting protein 1

    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_008933.2 RefSeqGene

      Range
      5002..76220
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001377523.1 → NP_001364452.1  X-linked retinitis pigmentosa GTPase regulator-interacting protein 1 isoform 2

      Status: REVIEWED

      Source sequence(s)
      AL135744, BC039089
      Consensus CDS
      CCDS91848.1
      UniProtKB/TrEMBL
      B4DX25
      Related
      ENSP00000372391.4, ENST00000382933.8

    2. NM_001377948.1 → NP_001364877.1  X-linked retinitis pigmentosa GTPase regulator-interacting protein 1 isoform 3

      Status: REVIEWED

      Source sequence(s)
      AF260257, AL135744
      UniProtKB/TrEMBL
      G3V3I7
      Conserved Domains (4) summary
      cd00030
      Location:443 → 550
      C2; C2 domain
      COG1196
      Location:60 → 218
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
      pfam11618
      Location:261 → 398
      C2-C2_1; First C2 domain of RPGR-interacting protein 1
      pfam18111
      Location:756 → 921
      RPGR1_C; Retinitis pigmentosa G-protein regulator interacting C-terminal

    3. NM_001377949.1 → NP_001364878.1  X-linked retinitis pigmentosa GTPase regulator-interacting protein 1 isoform 4

      Status: REVIEWED

      Source sequence(s)
      AL135744
      UniProtKB/TrEMBL
      B4DX25
      Conserved Domains (1) summary
      pfam18111
      Location:476 → 641
      RPGR1_C; Retinitis pigmentosa G-protein regulator interacting C-terminal

    4. NM_001377950.1 → NP_001364879.1  X-linked retinitis pigmentosa GTPase regulator-interacting protein 1 isoform 5

      Status: REVIEWED

      Source sequence(s)
      AL135744
      UniProtKB/TrEMBL
      B4DX25
      Conserved Domains (1) summary
      pfam18111
      Location:440 → 605
      RPGR1_C; Retinitis pigmentosa G-protein regulator interacting C-terminal

    5. NM_001377951.1 → NP_001364880.1  X-linked retinitis pigmentosa GTPase regulator-interacting protein 1 isoform 6

      Status: REVIEWED

      Source sequence(s)
      AL135744
      Conserved Domains (1) summary
      pfam18111
      Location:275 → 440
      RPGR1_C; Retinitis pigmentosa G-protein regulator interacting C-terminal

    6. NM_020366.4 → NP_065099.3  X-linked retinitis pigmentosa GTPase regulator-interacting protein 1 isoform 1

      See identical proteins and their annotated locations for NP_065099.3

      Status: REVIEWED

      Source sequence(s)
      AL135744
      Consensus CDS
      CCDS45080.1
      UniProtKB/Swiss-Prot
      Q7Z2W6, Q8IXV5, Q96KN7, Q96QA8, Q9HB94, Q9HB95, Q9HBK6, Q9NR40
      UniProtKB/TrEMBL
      G3V3F7
      Related
      ENSP00000382895.2, ENST00000400017.7
      Conserved Domains (3) summary
      cd00030
      Location:801 → 908
      C2; C2 domain
      pfam11618
      Location:619 → 756
      C2-C2_1; First C2 domain of RPGR-interacting protein 1
      cl12057
      Location:321 → 382
      Seryl_tRNA_N; Seryl-tRNA synthetase N-terminal domain

    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_000014.9 Reference GRCh38.p14 Primary Assembly

      Range
      21280083..21351301
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005267879.2 → XP_005267936.1  X-linked retinitis pigmentosa GTPase regulator-interacting protein 1 isoform X1

      UniProtKB/TrEMBL
      G3V3I7
      Conserved Domains (2) summary
      cd00030
      Location:443 → 550
      C2; C2 domain
      pfam11618
      Location:261 → 398
      C2-C2_1; First C2 domain of RPGR-interacting protein 1

    2. XM_011536978.1 → XP_011535280.1  X-linked retinitis pigmentosa GTPase regulator-interacting protein 1 isoform X2

      UniProtKB/TrEMBL
      G3V3I7
      Conserved Domains (2) summary
      cd00030
      Location:443 → 550
      C2; C2 domain
      pfam11618
      Location:261 → 398
      C2-C2_1; First C2 domain of RPGR-interacting protein 1

    3. XM_024449663.1 → XP_024305431.1  X-linked retinitis pigmentosa GTPase regulator-interacting protein 1 isoform X3

      UniProtKB/TrEMBL
      G3V3I7
      Conserved Domains (3) summary
      cd00030
      Location:443 → 550
      C2; C2 domain
      pfam11618
      Location:261 → 398
      C2-C2_1; First C2 domain of RPGR-interacting protein 1
      cl25732
      Location:60 → 218
      SMC_N; RecF/RecN/SMC N terminal domain

    4. XM_011536981.1 → XP_011535283.1  X-linked retinitis pigmentosa GTPase regulator-interacting protein 1 isoform X6

      UniProtKB/TrEMBL
      B4DX25
      Conserved Domains (1) summary
      pfam11618
      Location:261 → 381
      C2-C2_1; First C2 domain of RPGR-interacting protein 1

    5. XM_017021473.2 → XP_016876962.1  X-linked retinitis pigmentosa GTPase regulator-interacting protein 1 isoform X7

      UniProtKB/TrEMBL
      B4DX25

    6. XM_024449664.1 → XP_024305432.1  X-linked retinitis pigmentosa GTPase regulator-interacting protein 1 isoform X8

      UniProtKB/TrEMBL
      B4DX25
      Conserved Domains (1) summary
      pfam11618
      Location:261 → 381
      C2-C2_1; First C2 domain of RPGR-interacting protein 1

    7. XM_011536979.1 → XP_011535281.1  X-linked retinitis pigmentosa GTPase regulator-interacting protein 1 isoform X5

      UniProtKB/TrEMBL
      G3V3I7
      Conserved Domains (2) summary
      cd00030
      Location:371 → 478
      C2; C2 domain
      cl14603
      Location:257 → 326
      C2; C2 domain

    8. XM_011536982.1 → XP_011535284.1  X-linked retinitis pigmentosa GTPase regulator-interacting protein 1 isoform X10

      UniProtKB/TrEMBL
      B4DX25

    9. XM_024449666.1 → XP_024305434.1  X-linked retinitis pigmentosa GTPase regulator-interacting protein 1 isoform X11

      UniProtKB/TrEMBL
      B4DX25

    10. XM_047431609.1 → XP_047287565.1  X-linked retinitis pigmentosa GTPase regulator-interacting protein 1 isoform X12

    11. XM_005267880.2 → XP_005267937.1  X-linked retinitis pigmentosa GTPase regulator-interacting protein 1 isoform X4

      UniProtKB/TrEMBL
      G3V3I7
      Conserved Domains (2) summary
      cd00030
      Location:432 → 539
      C2; C2 domain
      pfam11618
      Location:250 → 387
      C2-C2_1; First C2 domain of RPGR-interacting protein 1

    12. XM_005267881.3 → XP_005267938.1  X-linked retinitis pigmentosa GTPase regulator-interacting protein 1 isoform X9

      UniProtKB/TrEMBL
      G3V3I7
      Related
      ENSP00000451262.1, ENST00000555587.5
      Conserved Domains (2) summary
      cd00030
      Location:259 → 366
      C2; C2 domain
      pfam11618
      Location:77 → 214
      C2-C2_1; First C2 domain of RPGR-interacting protein 1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060938.1 Alternate T2T-CHM13v2.0

      Range
      15477514..15548760
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054376422.1 → XP_054232397.1  X-linked retinitis pigmentosa GTPase regulator-interacting protein 1 isoform X1

    2. XM_054376423.1 → XP_054232398.1  X-linked retinitis pigmentosa GTPase regulator-interacting protein 1 isoform X2

    3. XM_054376424.1 → XP_054232399.1  X-linked retinitis pigmentosa GTPase regulator-interacting protein 1 isoform X3

    4. XM_054376427.1 → XP_054232402.1  X-linked retinitis pigmentosa GTPase regulator-interacting protein 1 isoform X6

    5. XM_054376428.1 → XP_054232403.1  X-linked retinitis pigmentosa GTPase regulator-interacting protein 1 isoform X7

    6. XM_054376429.1 → XP_054232404.1  X-linked retinitis pigmentosa GTPase regulator-interacting protein 1 isoform X8

    7. XM_054376426.1 → XP_054232401.1  X-linked retinitis pigmentosa GTPase regulator-interacting protein 1 isoform X5

    8. XM_054376431.1 → XP_054232406.1  X-linked retinitis pigmentosa GTPase regulator-interacting protein 1 isoform X10

    9. XM_054376432.1 → XP_054232407.1  X-linked retinitis pigmentosa GTPase regulator-interacting protein 1 isoform X11

    10. XM_054376433.1 → XP_054232408.1  X-linked retinitis pigmentosa GTPase regulator-interacting protein 1 isoform X12

    11. XM_054376425.1 → XP_054232400.1  X-linked retinitis pigmentosa GTPase regulator-interacting protein 1 isoform X4

    12. XM_054376430.1 → XP_054232405.1  X-linked retinitis pigmentosa GTPase regulator-interacting protein 1 isoform X9

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q96KN7.2 GenPept UniProtKB/Swiss-Prot:Q96KN7

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