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

Gene ID: 64145, updated on 3-Apr-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
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
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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_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (15070073..15099148, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (15072487..15101645, complement)
105.20220307 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
  • 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. RABENOSYN separation-of-function mutations uncouple endosomal recycling from lysosomal degradation, causing a distinct Mendelian disorder. Paul F, et al. Hum Mol Genet, 2022 Oct 28. PMID 35652444
  2. Syndromic congenital myelofibrosis associated with a loss-of-function variant in RBSN. Magoulas PL, et al. Blood, 2018 Aug 9. PMID 29784638, Free PMC Article
  3. Single point mutation in Rabenosyn-5 in a female with intractable seizures and evidence of defective endocytotic trafficking. Stockler S, et al. Orphanet J Rare Dis, 2014 Sep 20. PMID 25233840, Free PMC Article
  4. VipD of Legionella pneumophila targets activated Rab5 and Rab22 to interfere with endosomal trafficking in macrophages. Ku B, et al. PLoS Pathog, 2012. PMID 23271971, Free PMC Article
  5. Rabenosyn-5 defines the fate of the transferrin receptor following clathrin-mediated endocytosis. Navaroli DM, et al. Proc Natl Acad Sci U S A, 2012 Feb 21. PMID 22308388, Free PMC Article

See all (57) citations in PubMed

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)

Genotypes

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 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 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, ENST00000476527.6
    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_2023_10

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

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