RABEP1 rabaptin, RAB GTPase binding effector protein 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: RABEP1provided by HGNC
Official Full Name: rabaptin, RAB GTPase binding effector protein 1provided by HGNC
Primary source: HGNC:HGNC:17677
See related: Ensembl:ENSG00000029725 MIM:603616; AllianceGenome:HGNC:17677
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: RAB5EP; RABPT5
Summary: Enables protein domain specific binding activity and protein homodimerization activity. Involved in vesicle-mediated transport. Located in endocytic vesicle and endosome. Part of protein-containing complex. [provided by Alliance of Genome Resources, Apr 2022]
Expression: Ubiquitous expression in brain (RPKM 23.0), prostate (RPKM 14.6) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 17p13.2

Exon count:: 21

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	17	NC_000017.11 (5282284..5386340)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	17	NC_060941.1 (5176049..5280075)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	17	NC_000017.10 (5185579..5289660)

Chromosome 17 - NC_000017.11 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: 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?

SH2B1 and RABEP1 genetic variants are associated with worsening of LDL and glucose parameters in patients treated with psychotropic drugs
Title: Association of variants in SH2B1 and RABEP1 with worsening of low-density lipoprotein and glucose parameters in patients treated with psychotropic drugs.
The results contradict the model of feedback activation of Rab5 and instead indicate that Rbpt5 is recruited by both Rabex5 recognizing ubiquitylated cargo and by Rab4 to activate Rab5 in a feed-forward manner.
Title: Rabaptin5 is recruited to endosomes by Rab4 and Rabex5 to regulate endosome maturation.
ITSN2L interacts with RABEP1 and stimulates its degradation in regulation of endocytosis.
Title: ITSN2L Interacts with and Negatively Regulates RABEP1.
The pleckstrin homology domain (PH) of PLD1 itself promotes degradation of HIF-1alpha, then accelerates EGFR endocytosis via upregulation of rabaptin-5 and suppresses tumor progression.
Title: The pleckstrin homology domain of phospholipase D1 accelerates EGFR endocytosis by increasing the expression of the Rab5 effector, rabaptin-5.
analysis of Rabex-5 GEF activation by Rabaptin-5
Title: Molecular mechanism for Rabex-5 GEF activation by Rabaptin-5.
The disruption of Rabaptin-5 Ser407 phosphorylation reduces persistent cell migration in 2D and alphavbeta3-dependent invasion.
Title: PKD controls αvβ3 integrin recycling and tumor cell invasive migration through its substrate Rabaptin-5.
Silencing of Rabaptin-5 induces down-regulation of recycling of K(V)10.1 channel in transfected cells and reduction of K(V)10.1 current density in cells natively expressing K(V)10.1, indicating a role of Rabaptin-5 in channel trafficking.
Title: Physical and functional interaction of KV10.1 with Rabaptin-5 impacts ion channel trafficking.
Breast cancer cell line studies showed that microRNA, miR-373, was capable of promoting breast cancer invasion and metastasis via translational inhibition of TXNIP and RABEP1 that were the direct target genes of miR-373.
Title: Global identification of miR-373-regulated genes in breast cancer by quantitative proteomics.
The authors determined that increased listeriolysin O-independent dissolution of vacuoles during RABEP1 knockdown required the Listeria monocytogenes broad-range phospholipase C (PC-PLC).
Title: Perturbation of vacuolar maturation promotes listeriolysin O-independent vacuolar escape during Listeria monocytogenes infection of human cells.
GGAs, a family of Arf-dependent clathrin adaptors involved in selection of TGN cargo, interact with the Rabaptin-5-Rabex-5 complex, a Rab4/Rab5 effector regulating endosome fusion
Title: Divalent interaction of the GGAs with the Rabaptin-5-Rabex-5 complex.

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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

EBI GWAS Catalog

Description
Genetics of rheumatoid arthritis contributes to biology and drug discovery. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
Nef	nef	Genome-wide shRNA screening identifies RABEP1, which is required for HIV-1 Nef-induced downregulation of CD4 in HeLa CD4+ cells	PubMed

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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

RH67786 (e-PCR)
- UniSTS:75782

RH25190 (e-PCR)
- UniSTS:89870

RH15968 (e-PCR)
- UniSTS:21266

STS-AA019366 (e-PCR)
- UniSTS:78616

SGC34223 (e-PCR)
- UniSTS:1334

D17S1367E (e-PCR)
- UniSTS:55108

G42908 (e-PCR)
- UniSTS:94817

STS-R01262 (e-PCR)
- UniSTS:10595

WI-12505 (e-PCR)
- UniSTS:6506

G59307 (e-PCR)
- UniSTS:136622

D17S1401E (e-PCR)
- UniSTS:150449

D17S1421E (e-PCR)
- UniSTS:150463

D15S629E (e-PCR)
- UniSTS:149968

SHGC-35667 (e-PCR)
- UniSTS:32978

WI-18700 (e-PCR)
- UniSTS:52698

D17S1662 (e-PCR)
- UniSTS:42222

STS-H59437 (e-PCR)
- UniSTS:51195

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables GTPase activator activity	IEA Inferred from Electronic Annotation more info
enables growth factor activity	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein domain specific binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein homodimerization activity	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in Golgi to plasma membrane transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in Golgi to plasma membrane transport	ISS Inferred from Sequence or Structural Similarity more info
involved_in apoptotic process	IEA Inferred from Electronic Annotation more info
involved_in endocytosis	IEA Inferred from Electronic Annotation more info
involved_in membrane fusion	TAS Traceable Author Statement more info	PubMed
involved_in protein localization to ciliary membrane	ISS Inferred from Sequence or Structural Similarity more info
involved_in protein transport	IEA Inferred from Electronic Annotation more info
involved_in signal transduction	IEA Inferred from Electronic Annotation more info
involved_in vesicle-mediated transport	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in early endosome	TAS Traceable Author Statement more info	PubMed
located_in early endosome membrane	TAS Traceable Author Statement more info
is_active_in endocytic vesicle	IBA Inferred from Biological aspect of Ancestor more info
located_in endocytic vesicle	IDA Inferred from Direct Assay more info	PubMed
is_active_in endosome	IBA Inferred from Biological aspect of Ancestor more info
located_in endosome	IDA Inferred from Direct Assay more info	PubMed
located_in intracellular membrane-bounded organelle	IDA Inferred from Direct Assay more info
part_of protein-containing complex	IMP Inferred from Mutant Phenotype more info	PubMed
located_in recycling endosome	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: rab GTPase-binding effector protein 1

Names: neurocrescin; rabaptin-4; rabaptin-5; rabaptin-5alpha; renal carcinoma antigen NY-REN-17

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.

mRNA and Protein(s)

NM_001083585.3 → NP_001077054.1 rab GTPase-binding effector protein 1 isoform 2

See identical proteins and their annotated locations for NP_001077054.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 3' coding region, compared to variant 1, resulting in an isoform (2) that is shorter than isoform 1.

Source sequence(s)

AF098638, AL157499, BC041700, BM678290, DB124187, DB169027, EB387308

Consensus CDS

CCDS42243.1

UniProtKB/TrEMBL

B4DMM4

Related

ENSP00000339569.6, ENST00000341923.10

Conserved Domains (2) summary

pfam03528
Location:9 → 495

Rabaptin; Rabaptin

pfam09311
Location:533 → 806

Rab5-bind; Rabaptin-like protein
NM_001291581.2 → NP_001278510.1 rab GTPase-binding effector protein 1 isoform 3

Status: VALIDATED

Description

Transcript Variant: This variant (3) lacks an alternate in-frame exon in the 5' coding region, compared to variant 1, resulting in an isoform (3) that is shorter than isoform 1.

Source sequence(s)

AF098638, AK297535, AK314183, AL157499, BC041700, BM678290, DB124187, DB169027, EB387308

UniProtKB/TrEMBL

B4DMM4

Conserved Domains (3) summary

pfam03528
Location:11 → 452

Rabaptin; Rabaptin

pfam09311
Location:490 → 796

Rab5-bind; Rabaptin-like protein

cl23887
Location:630 → 775

DUF4349; Domain of unknown function (DUF4349)
NM_001291582.2 → NP_001278511.1 rab GTPase-binding effector protein 1 isoform 4

Status: VALIDATED

Description

Transcript Variant: This variant (4) lacks several 3' exons but contains an alternate 3' terminal exon, and it thus differs in its 3' coding region and 3' UTR, compared to variant 1. The encoded isoform (4) has a distinct C-terminus and is significantly shorter than isoform 1.

Source sequence(s)

BC018742, DB169027

Conserved Domains (1) summary

pfam03528
Location:9 → 190

Rabaptin
NM_004703.6 → NP_004694.2 rab GTPase-binding effector protein 1 isoform 1

See identical proteins and their annotated locations for NP_004694.2

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).

Source sequence(s)

AF098638, AK314183, AL157499, BC041700, BM678290, DB124187, DB169027, EB387308

Consensus CDS

CCDS45592.1

UniProtKB/Swiss-Prot

B2RAG7, O95369, Q15276, Q8IVX3

UniProtKB/TrEMBL

B4DMM4

Related

ENSP00000445408.2, ENST00000537505.6

Conserved Domains (2) summary

pfam03528
Location:9 → 495

Rabaptin; Rabaptin

pfam09311
Location:533 → 839

Rab5-bind; Rabaptin-like protein

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

NC_000017.11 Reference GRCh38.p14 Primary Assembly

Range

5282284..5386340

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047437039.1 → XP_047292995.1 rab GTPase-binding effector protein 1 isoform X2
XM_047437038.1 → XP_047292994.1 rab GTPase-binding effector protein 1 isoform X2
XM_011524060.3 → XP_011522362.1 rab GTPase-binding effector protein 1 isoform X1

UniProtKB/TrEMBL

B4DMM4

Conserved Domains (2) summary

pfam03528
Location:9 → 517

Rabaptin; Rabaptin

pfam09311
Location:555 → 861

Rab5-bind; Rabaptin-like protein
XM_047437040.1 → XP_047292996.1 rab GTPase-binding effector protein 1 isoform X3
XM_047437041.1 → XP_047292997.1 rab GTPase-binding effector protein 1 isoform X4

Alternate T2T-CHM13v2.0

Genomic

NC_060941.1 Alternate T2T-CHM13v2.0

Range

5176049..5280075

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054317759.1 → XP_054173734.1 rab GTPase-binding effector protein 1 isoform X2
XM_054317758.1 → XP_054173733.1 rab GTPase-binding effector protein 1 isoform X2
XM_054317757.1 → XP_054173732.1 rab GTPase-binding effector protein 1 isoform X1
XM_054317760.1 → XP_054173735.1 rab GTPase-binding effector protein 1 isoform X3
XM_054317761.1 → XP_054173736.1 rab GTPase-binding effector protein 1 isoform X4