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

Summary

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

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_000003.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Tissue-specific circular RNA induction during human fetal development
Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
BioProject: PRJNA270632
Publication: PMID 26076956
Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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 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.
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.
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.
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.
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.

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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)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D11S2921 (e-PCR)
- UniSTS:152074

GDB:434012 (e-PCR)
- UniSTS:157204

D8S2278 (e-PCR)
- UniSTS:473906

D8S2279 (e-PCR)
- UniSTS:473907

D3S4025 (e-PCR)
- UniSTS:42315

L18426 (e-PCR)
- UniSTS:34648

ZFYVE20__4951 (e-PCR)
- UniSTS:462958

STS-N59228 (e-PCR)
- UniSTS:27000

D3S4113 (e-PCR)
- UniSTS:51579

L29953 (e-PCR)
- UniSTS:52164

SGC34220 (e-PCR)
- UniSTS:9164

SHGC-82427 (e-PCR)
- UniSTS:104409

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 more info	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

NG_041773.1 RefSeqGene

Range

5010..34085

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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

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

NC_000003.12 Reference GRCh38.p14 Primary Assembly

Range

15070073..15099148 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/Swiss-Prot

B4DWY8, C9J4P5, Q3KP30, Q59EY8, Q8NAQ1, Q9H1K0

UniProtKB/TrEMBL

A8K5H3
XM_047448706.1 → XP_047304662.1 rabenosyn-5 isoform X1

UniProtKB/Swiss-Prot

B4DWY8, C9J4P5, Q3KP30, Q59EY8, Q8NAQ1, Q9H1K0

UniProtKB/TrEMBL

A8K5H3
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
XM_047448708.1 → XP_047304664.1 rabenosyn-5 isoform X4
XM_017007026.2 → XP_016862515.1 rabenosyn-5 isoform X3