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    RBSN rabenosyn, RAB effector [ Homo sapiens (human) ]

    Gene ID: 64145, updated on 14-Nov-2024

    Summary

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    Official Symbol
    RBSNprovided by HGNC
    Official Full Name
    rabenosyn, RAB effectorprovided by HGNC
    Primary source
    HGNC:HGNC:20759
    See related
    Ensembl:ENSG00000131381 MIM:609511; AllianceGenome:HGNC:20759
    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
    KAREVS; MFANDO; ZFYVE20; Rabenosyn-5
    Summary
    This gene encodes a protein that belongs to the FYVE zinc finger family of proteins. The encoded protein interacts with Ras-related proteins that regulate membrane trafficking. A missense mutation in this gene is associated with a defect in the early endocytic pathway. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2014]
    Expression
    Ubiquitous expression in brain (RPKM 10.8), thyroid (RPKM 6.4) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See RBSN in Genome Data Viewer
    Location:
    3p25.1
    Exon count:
    15
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (15070073..15099148, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (15072487..15101645, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (15111580..15140655, complement)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:14988241-14988930 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14097 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:14989619-14990306 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:14990307-14990994 Neighboring gene FGD5 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19523 Neighboring gene nuclear receptor subfamily 2 group C member 2 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:15066535-15067034 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19524 Neighboring gene mitochondrial ribosomal protein S25 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19525 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14100 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:15139860-15140724 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:15149813-15150312 Neighboring gene ribosomal protein S24 pseudogene 10 Neighboring gene RPS3A pseudogene 53

    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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    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. RABENOSYN separation-of-function mutations uncouple endosomal recycling from lysosomal degradation, causing a distinct Mendelian disorder.
      Title: RABENOSYN separation-of-function mutations uncouple endosomal recycling from lysosomal degradation, causing a distinct Mendelian disorder.
    2. The Rab-binding module of FERARI (factors for endosome recycling and Rab interactions) consists of Rab11FIP5 and rabenosyn-5, while the SNARE-interacting module comprises VPS45 and VIPAS39.
      Title: FERARI is required for Rab11-dependent endocytic recycling.
    3. 3 consanguineous siblings with syndromic congenital myelofibrosis had a variant (NM_022340.3:c.289G>C; NP_001289307.1:p.Gly97Arg) in RBSN. All 3 were homozygous; the parents and a cousin were heterozygous. RBSN loss of function causes a severe syndromic form of congenital myelofibrosis, confirming that rabenosyn-5 plays a vital role in human development and hematopoiesis.
      Title: Syndromic congenital myelofibrosis associated with a loss-of-function variant in RBSN.
    4. A functional defect in the endocytic pathway resulting from a point mutation in Rabenosyn-5 leads to severe multi-organ disorder.
      Title: Single point mutation in Rabenosyn-5 in a female with intractable seizures and evidence of defective endocytotic trafficking.
    5. transferrin receptors are delivered selectively from clathrin-coated pits on the plasma membrane into a specific subpopulation of endosomes enriched in the multivalent Rab GTPase and phosphoinositide-binding protein Rabenosyn-5.
      Title: Rabenosyn-5 defines the fate of the transferrin receptor following clathrin-mediated endocytosis.
    6. Data implicate hVps45 and Rabenosyn-5 in post early endosome transport, and suggest that their interaction serves as a nexus to promote bidirectional transport along the endosome-to-recycling compartment and endosome-to-Golgi axes.
      Title: Common and distinct roles for the binding partners Rabenosyn-5 and Vps45 in the regulation of endocytic trafficking in mammalian cells.
    7. results demonstrate that even the structurally similar effector domains in rabenosyn-5 can achieve highly selective recognition of distinct subsets of Rab GTPases exclusively through interactions with the switch and interswitch regions
      Title: Structural basis of family-wide Rab GTPase recognition by rabenosyn-5.
    Submit: New GeneRIF Correction

    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

    • FLJ34993, MGC126210

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables phosphatidylinositol-3-phosphate binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables small GTPase binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables zinc ion binding NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in Golgi to lysosome transport IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in early endosome to Golgi transport IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in endosomal transport NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in protein transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of Golgi organization IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in cytosol IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in early endosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in early endosome membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in endosome NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    located_in endosome membrane TAS
    Traceable Author Statement
    more info
    		  
    located_in extracellular exosome HDA PubMed 
    located_in intracellular membrane-bounded organelle IDA
    Inferred from Direct Assay
    more info
    		  
    located_in plasma membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    rabenosyn-5
    Names
    110 kDa protein
    FYVE finger-containing Rab5 effector protein rabenosyn-5
    RAB effector RBSN
    zinc finger, FYVE domain containing 20

    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_041773.1 RefSeqGene

      Range
      5010..34085
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001302378.2 → NP_001289307.1  rabenosyn-5

      See identical proteins and their annotated locations for NP_001289307.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1 and 2 encode the same protein.
      Source sequence(s)
      AC090954, AK291288, BX111409
      Consensus CDS
      CCDS2623.1
      UniProtKB/Swiss-Prot
      B4DWY8, C9J4P5, Q3KP30, Q59EY8, Q8NAQ1, Q9H1K0
      UniProtKB/TrEMBL
      A8K5H3
      Related
      ENSP00000422551.1, ENST00000476527.7
      Conserved Domains (3) summary
      cd15716
      Location:151 → 262
      FYVE_RBNS5; FYVE domain found in FYVE finger-containing Rab5 effector protein rabenosyn-5 (Rbsn-5) and similar proteins
      pfam11464
      Location:461 → 499
      Rbsn; Rabenosyn Rab binding domain
      pfam16601
      Location:548 → 727
      NPF; Rabosyn-5 repeating NPF sequence-motif

    2. NM_022340.4 → NP_071735.2  rabenosyn-5

      See identical proteins and their annotated locations for NP_071735.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript. Variants 1 and 2 encode the same protein.
      Source sequence(s)
      AB209673, AC090954, AY009133, BF513881, BX111409, DA320360
      Consensus CDS
      CCDS2623.1
      UniProtKB/Swiss-Prot
      B4DWY8, C9J4P5, Q3KP30, Q59EY8, Q8NAQ1, Q9H1K0
      UniProtKB/TrEMBL
      A8K5H3
      Related
      ENSP00000253699.3, ENST00000253699.7
      Conserved Domains (3) summary
      cd15716
      Location:151 → 262
      FYVE_RBNS5; FYVE domain found in FYVE finger-containing Rab5 effector protein rabenosyn-5 (Rbsn-5) and similar proteins
      pfam11464
      Location:461 → 499
      Rbsn; Rabenosyn Rab binding domain
      pfam16601
      Location:548 → 727
      NPF; Rabosyn-5 repeating NPF sequence-motif

    RNA

    1. NR_126155.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks several exons and its 3' terminal exon extends past a splice site that is used in variant 1. This variant is represented as non-coding because it lacks a large portion of the coding region found in variant 1 and the predicted protein does not meet RefSeq quality criteria.
      Source sequence(s)
      BC032628, DA320360
      Related
      ENST00000449050.5

    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_000003.12 Reference GRCh38.p14 Primary Assembly

      Range
      15070073..15099148 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005265385.5 → XP_005265442.1  rabenosyn-5 isoform X1

      See identical proteins and their annotated locations for XP_005265442.1

      UniProtKB/Swiss-Prot
      B4DWY8, C9J4P5, Q3KP30, Q59EY8, Q8NAQ1, Q9H1K0
      UniProtKB/TrEMBL
      A8K5H3
      Conserved Domains (3) summary
      cd15716
      Location:151 → 262
      FYVE_RBNS5; FYVE domain found in FYVE finger-containing Rab5 effector protein rabenosyn-5 (Rbsn-5) and similar proteins
      pfam11464
      Location:461 → 499
      Rbsn; Rabenosyn Rab binding domain
      pfam16601
      Location:548 → 727
      NPF; Rabosyn-5 repeating NPF sequence-motif

    2. XM_005265384.5 → XP_005265441.1  rabenosyn-5 isoform X1

      See identical proteins and their annotated locations for XP_005265441.1

      UniProtKB/Swiss-Prot
      B4DWY8, C9J4P5, Q3KP30, Q59EY8, Q8NAQ1, Q9H1K0
      UniProtKB/TrEMBL
      A8K5H3
      Conserved Domains (3) summary
      cd15716
      Location:151 → 262
      FYVE_RBNS5; FYVE domain found in FYVE finger-containing Rab5 effector protein rabenosyn-5 (Rbsn-5) and similar proteins
      pfam11464
      Location:461 → 499
      Rbsn; Rabenosyn Rab binding domain
      pfam16601
      Location:548 → 727
      NPF; Rabosyn-5 repeating NPF sequence-motif

    3. XM_017007023.2 → XP_016862512.1  rabenosyn-5 isoform X1

      UniProtKB/Swiss-Prot
      B4DWY8, C9J4P5, Q3KP30, Q59EY8, Q8NAQ1, Q9H1K0
      UniProtKB/TrEMBL
      A8K5H3
      Conserved Domains (3) summary
      cd15716
      Location:151 → 262
      FYVE_RBNS5; FYVE domain found in FYVE finger-containing Rab5 effector protein rabenosyn-5 (Rbsn-5) and similar proteins
      pfam11464
      Location:461 → 499
      Rbsn; Rabenosyn Rab binding domain
      pfam16601
      Location:548 → 727
      NPF; Rabosyn-5 repeating NPF sequence-motif

    4. XM_047448707.1 → XP_047304663.1  rabenosyn-5 isoform X1

      UniProtKB/Swiss-Prot
      B4DWY8, C9J4P5, Q3KP30, Q59EY8, Q8NAQ1, Q9H1K0

    5. XM_047448706.1 → XP_047304662.1  rabenosyn-5 isoform X1

      UniProtKB/Swiss-Prot
      B4DWY8, C9J4P5, Q3KP30, Q59EY8, Q8NAQ1, Q9H1K0

    6. XM_011534001.3 → XP_011532303.1  rabenosyn-5 isoform X2

      UniProtKB/TrEMBL
      A8K5H3
      Conserved Domains (3) summary
      cd15716
      Location:63 → 174
      FYVE_RBNS5; FYVE domain found in FYVE finger-containing Rab5 effector protein rabenosyn-5 (Rbsn-5) and similar proteins
      pfam11464
      Location:370 → 409
      Rbsn; Rabenosyn Rab binding domain
      pfam16601
      Location:460 → 639
      NPF; Rabosyn-5 repeating NPF sequence-motif

    7. XM_047448708.1 → XP_047304664.1  rabenosyn-5 isoform X4

    8. XM_017007026.2 → XP_016862515.1  rabenosyn-5 isoform X3

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      15072487..15101645 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054347521.1 → XP_054203496.1  rabenosyn-5 isoform X1

      UniProtKB/Swiss-Prot
      B4DWY8, C9J4P5, Q3KP30, Q59EY8, Q8NAQ1, Q9H1K0

    2. XM_054347518.1 → XP_054203493.1  rabenosyn-5 isoform X1

      UniProtKB/Swiss-Prot
      B4DWY8, C9J4P5, Q3KP30, Q59EY8, Q8NAQ1, Q9H1K0

    3. XM_054347517.1 → XP_054203492.1  rabenosyn-5 isoform X1

      UniProtKB/Swiss-Prot
      B4DWY8, C9J4P5, Q3KP30, Q59EY8, Q8NAQ1, Q9H1K0

    4. XM_054347520.1 → XP_054203495.1  rabenosyn-5 isoform X1

      UniProtKB/Swiss-Prot
      B4DWY8, C9J4P5, Q3KP30, Q59EY8, Q8NAQ1, Q9H1K0

    5. XM_054347519.1 → XP_054203494.1  rabenosyn-5 isoform X1

      UniProtKB/Swiss-Prot
      B4DWY8, C9J4P5, Q3KP30, Q59EY8, Q8NAQ1, Q9H1K0

    6. XM_054347522.1 → XP_054203497.1  rabenosyn-5 isoform X2

    7. XM_054347524.1 → XP_054203499.1  rabenosyn-5 isoform X4

    8. XM_054347523.1 → XP_054203498.1  rabenosyn-5 isoform X3

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9H1K0.2 GenPept UniProtKB/Swiss-Prot:Q9H1K0

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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