RAB29 RAB29, member RAS oncogene family [Homo sapiens (human)] - Gene

Summary

Official Symbol: RAB29provided by HGNC
Official Full Name: RAB29, member RAS oncogene familyprovided by HGNC
Primary source: HGNC:HGNC:9789
See related: Ensembl:ENSG00000117280 MIM:603949; AllianceGenome:HGNC:9789
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: RAB7L; RAB7L1
Summary: Enables several functions, including dynein complex binding activity; guanyl ribonucleotide binding activity; and kinesin binding activity. Involved in several processes, including positive regulation of T cell receptor signaling pathway; positive regulation of receptor recycling; and toxin transport. Located in several cellular components, including Golgi apparatus; endosome; and vacuole. [provided by Alliance of Genome Resources, Apr 2022]
Expression: Broad expression in kidney (RPKM 27.5), thyroid (RPKM 17.1) and 24 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 1q32.1

Exon count:: 6

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	1	NC_000001.11 (205767986..205775482, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	1	NC_060925.1 (205032659..205040160, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	1	NC_000001.10 (205737114..205744610, complement)

Chromosome 1 - NC_000001.11 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?

The atypical Rab GTPase associated with Parkinson's disease, Rab29, is localized to membranes.
Title: The atypical Rab GTPase associated with Parkinson's disease, Rab29, is localized to membranes.
Expression of RAB7L1 in Patients with Pituitary Adenomas.
Title: Expression of RAB7L1 in Patients with Pituitary Adenomas.
Distinct Roles for RAB10 and RAB29 in Pathogenic LRRK2-Mediated Endolysosomal Trafficking Alterations.
Title: Distinct Roles for RAB10 and RAB29 in Pathogenic LRRK2-Mediated Endolysosomal Trafficking Alterations.
Association of RIT2 and RAB7L1 with Parkinson's disease: a case-control study in a Taiwanese cohort and a meta-analysis in Asian populations.
Title: Association of RIT2 and RAB7L1 with Parkinson's disease: a case-control study in a Taiwanese cohort and a meta-analysis in Asian populations.
LRRK2 associates with and dissociates from distinct membrane compartments to phosphorylate Rab substrates including Rab29
Title: Membrane association but not identity is required for LRRK2 activation and phosphorylation of Rab GTPases.
This study highlights a novel role of Rab7l1 in the phagosomal maturation process and hints at unique strategies of mycobacteria used to interfere with Rab7l1 function to favor its survival inside human macrophages.
Title: Mycobacterial PknG Targets the Rab7l1 Signaling Pathway To Inhibit Phagosome-Lysosome Fusion.
Results suggest reciprocal regulation between LRRK2 and Rab protein substrates, where Rab7L1-mediated upregulation of LRRK2 kinase activity results in the stabilization of membrane and GTP-bound Rab proteins that may be unable to interact with Rab effector proteins.
Title: LRRK2 phosphorylates membrane-bound Rabs and is activated by GTP-bound Rab7L1 to promote recruitment to the trans-Golgi network.
RAB7L1gene rs1572913 polymorphism (T allele, TC and TT genotype) was associated with decreased risk of PD.
Title: Association between PARK16 and Parkinson's disease: A meta-analysis.
Mutations in leucine-rich repeat kinase 2 (LRRK2) are the major genetic cause of autosomal-dominantly inherited Parkinson's disease. LRRK2 is implicated in the regulation of intracellular trafficking, neurite outgrowth and PD risk in connection with Rab7L1, a putative interactor of LRRK2. The modulation of Ser72 phosphorylation in Rab7L1 resulted in an alteration of the trans-Golgi network.
Title: Parkinson's disease-associated mutant LRRK2 phosphorylates Rab7L1 and modifies trans-Golgi morphology.
Genetic ablation of RAB7L1 in SH-SY5Y cells recapitulated the findings in amyotrophic lateral sclerosis and frontotemporal dementia fibroblasts and induced pluripotent stem cell neurons
Title: C9orf72 and RAB7L1 regulate vesicle trafficking in amyotrophic lateral sclerosis and frontotemporal dementia.

Submit: New GeneRIF Correction See all GeneRIFs (22)

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

SHGC-76255 (e-PCR)
- UniSTS:55587

D8S2279 (e-PCR)
- UniSTS:473907

D11S3114 (e-PCR)
- UniSTS:152207

RAB7L1__6957 (e-PCR)
- UniSTS:468632

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables GDP binding	IDA Inferred from Direct Assay more info	PubMed
enables GTP binding	IDA Inferred from Direct Assay more info	PubMed
enables GTPase activity	IBA Inferred from Biological aspect of Ancestor more info
enables dynein complex binding	IDA Inferred from Direct Assay more info	PubMed
enables kinesin binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables small GTPase binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in Golgi organization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in T cell activation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cell differentiation	IEA Inferred from Electronic Annotation more info
involved_in cellular detoxification	IMP Inferred from Mutant Phenotype more info	PubMed
NOT involved_in endoplasmic reticulum to Golgi vesicle-mediated transport	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in intracellular protein transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in melanosome organization	IBA Inferred from Biological aspect of Ancestor more info
involved_in mitochondrion organization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in modulation by host of viral process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of neuron projection development	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of T cell receptor signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of intracellular protein transport	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of receptor recycling	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protein localization to ciliary membrane	ISS Inferred from Sequence or Structural Similarity more info
involved_in protein localization to membrane	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of retrograde transport, endosome to Golgi	IEA Inferred from Electronic Annotation more info
involved_in response to bacterium	IDA Inferred from Direct Assay more info	PubMed
involved_in retrograde transport, endosome to Golgi	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in synapse assembly	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in Golgi apparatus	IDA Inferred from Direct Assay more info	PubMed
located_in cis-Golgi network	IDA Inferred from Direct Assay more info	PubMed
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in cytoskeleton	IEA Inferred from Electronic Annotation more info
located_in cytosol	IDA Inferred from Direct Assay more info
located_in early endosome	IDA Inferred from Direct Assay more info	PubMed
is_active_in endomembrane system	IBA Inferred from Biological aspect of Ancestor 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 intracellular vesicle	IDA Inferred from Direct Assay more info	PubMed
is_active_in melanosome	IBA Inferred from Biological aspect of Ancestor more info
located_in mitochondrion	IDA Inferred from Direct Assay more info	PubMed
located_in perinuclear region of cytoplasm	IEA Inferred from Electronic Annotation more info
located_in plasma membrane	IEA Inferred from Electronic Annotation more info
located_in recycling endosome	IDA Inferred from Direct Assay more info	PubMed
is_active_in trans-Golgi network	IBA Inferred from Biological aspect of Ancestor more info
located_in trans-Golgi network	IDA Inferred from Direct Assay more info	PubMed
located_in vacuole	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: ras-related protein Rab-7L1

Names: RAB7, member RAS oncogene family-like 1; rab-7-like protein 1; ras-related protein Rab-29

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_001135662.2 → NP_001129134.1 ras-related protein Rab-7L1 isoform 1

See identical proteins and their annotated locations for NP_001129134.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) lacks a segment in the 5' UTR, as compared to variant 1. Variants 1 and 2 encode the same isoform (1).

Source sequence(s)

AC119673, AK313000, CF528995, DA284582

Consensus CDS

CCDS1459.1

UniProtKB/Swiss-Prot

B4E1K3, C9JE77, O14966

UniProtKB/TrEMBL

A0A024R999, B2R7I9, Q53EX5, Q6FGU7

Related

ENSP00000235932.4, ENST00000235932.8

Conserved Domains (1) summary

cd04107
Location:8 → 203

Rab32_Rab38; Rab GTPase families 18 (Rab18) and 32 (Rab32)
NM_001135663.2 → NP_001129135.1 ras-related protein Rab-7L1 isoform 2

See identical proteins and their annotated locations for NP_001129135.1

Status: VALIDATED

Description

Transcript Variant: This variant (3) has an additional segment in the 5' UTR and lacks an in-frame coding exon, as compared to variant 1. The resulting isoform (2) lacks an internal segment, as compared to isoform 2.

Source sequence(s)

AC119673, AK303879, CF528995, DA284582, DC314882

Consensus CDS

CCDS44301.1

UniProtKB/TrEMBL

B2R7I9, Q53EX5

Related

ENSP00000389899.2, ENST00000446390.6

Conserved Domains (1) summary

cd04107
Location:8 → 179

Rab32_Rab38; Rab GTPase families 18 (Rab18) and 32 (Rab32)
NM_001135664.2 → NP_001129136.1 ras-related protein Rab-7L1 isoform 3

See identical proteins and their annotated locations for NP_001129136.1

Status: VALIDATED

Description

Transcript Variant: This variant (4) lacks an internal exon, which results in a downstream AUG start codon, as compared to variant 1. The resulting isoform (4) has a shorter N-terminus, as compared to isoform 1.

Source sequence(s)

AC119673, CF528995, DA284582, DA377295

Consensus CDS

CCDS44302.1

UniProtKB/Swiss-Prot

O14966

Related

ENSP00000416613.2, ENST00000437324.6

Conserved Domains (1) summary

cl38936
Location:1 → 131

P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases
NM_003929.3 → NP_003920.1 ras-related protein Rab-7L1 isoform 1

See identical proteins and their annotated locations for NP_003920.1

Status: VALIDATED

Description

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

Source sequence(s)

AC119673, BX647960, CF528995, DA284582, DC365059

Consensus CDS

CCDS1459.1

UniProtKB/Swiss-Prot

B4E1K3, C9JE77, O14966

UniProtKB/TrEMBL

A0A024R999, B2R7I9, Q53EX5, Q6FGU7

Related

ENSP00000356107.3, ENST00000367139.8

Conserved Domains (1) summary

cd04107
Location:8 → 203

Rab32_Rab38; Rab GTPase families 18 (Rab18) and 32 (Rab32)

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_000001.11 Reference GRCh38.p14 Primary Assembly

Range

205767986..205775482 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006711606.4 → XP_006711669.1 ras-related protein Rab-7L1 isoform X3

See identical proteins and their annotated locations for XP_006711669.1

UniProtKB/Swiss-Prot

O14966

Conserved Domains (1) summary

cl38936
Location:1 → 131

P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases
XM_047433508.1 → XP_047289464.1 ras-related protein Rab-7L1 isoform X2
XM_005245571.2 → XP_005245628.1 ras-related protein Rab-7L1 isoform X1

See identical proteins and their annotated locations for XP_005245628.1

UniProtKB/Swiss-Prot

B4E1K3, C9JE77, O14966

UniProtKB/TrEMBL

A0A024R999, B2R7I9, Q53EX5, Q6FGU7

Conserved Domains (1) summary

cd04107
Location:8 → 203

Rab32_Rab38; Rab GTPase families 18 (Rab18) and 32 (Rab32)
XM_047433509.1 → XP_047289465.1 ras-related protein Rab-7L1 isoform X2
XM_047433505.1 → XP_047289461.1 ras-related protein Rab-7L1 isoform X1

UniProtKB/Swiss-Prot

B4E1K3, C9JE77, O14966

UniProtKB/TrEMBL

A0A024R999, Q6FGU7
XM_006711605.4 → XP_006711668.1 ras-related protein Rab-7L1 isoform X3

See identical proteins and their annotated locations for XP_006711668.1

UniProtKB/Swiss-Prot

O14966

Conserved Domains (1) summary

cl38936
Location:1 → 131

P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases
XM_017002750.2 → XP_016858239.1 ras-related protein Rab-7L1 isoform X2

UniProtKB/TrEMBL

B2R7I9, Q53EX5

Conserved Domains (1) summary

cd04107
Location:8 → 179

Rab32_Rab38; Rab GTPase families 18 (Rab18) and 32 (Rab32)
XM_047433507.1 → XP_047289463.1 ras-related protein Rab-7L1 isoform X2
XM_005245569.2 → XP_005245626.1 ras-related protein Rab-7L1 isoform X1

See identical proteins and their annotated locations for XP_005245626.1

UniProtKB/Swiss-Prot

B4E1K3, C9JE77, O14966

UniProtKB/TrEMBL

A0A024R999, B2R7I9, Q53EX5, Q6FGU7

Conserved Domains (1) summary

cd04107
Location:8 → 203

Rab32_Rab38; Rab GTPase families 18 (Rab18) and 32 (Rab32)
XM_017002748.2 → XP_016858237.1 ras-related protein Rab-7L1 isoform X2

UniProtKB/TrEMBL

B2R7I9, Q53EX5

Conserved Domains (1) summary

cd04107
Location:8 → 179

Rab32_Rab38; Rab GTPase families 18 (Rab18) and 32 (Rab32)
XM_017002749.2 → XP_016858238.1 ras-related protein Rab-7L1 isoform X2

UniProtKB/TrEMBL

B2R7I9, Q53EX5

Conserved Domains (1) summary

cd04107
Location:8 → 179

Rab32_Rab38; Rab GTPase families 18 (Rab18) and 32 (Rab32)
XM_005245570.2 → XP_005245627.1 ras-related protein Rab-7L1 isoform X1

See identical proteins and their annotated locations for XP_005245627.1

UniProtKB/Swiss-Prot

B4E1K3, C9JE77, O14966

UniProtKB/TrEMBL

A0A024R999, B2R7I9, Q53EX5, Q6FGU7

Related

ENSP00000402910.1, ENST00000414729.1

Conserved Domains (1) summary

cd04107
Location:8 → 203

Rab32_Rab38; Rab GTPase families 18 (Rab18) and 32 (Rab32)

Alternate T2T-CHM13v2.0

Genomic

NC_060925.1 Alternate T2T-CHM13v2.0

Range

205032659..205040160 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054339477.1 → XP_054195452.1 ras-related protein Rab-7L1 isoform X2
XM_054339471.1 → XP_054195446.1 ras-related protein Rab-7L1 isoform X1

UniProtKB/Swiss-Prot

B4E1K3, C9JE77, O14966

UniProtKB/TrEMBL

A0A024R999, Q6FGU7
XM_054339472.1 → XP_054195447.1 ras-related protein Rab-7L1 isoform X1

UniProtKB/Swiss-Prot

B4E1K3, C9JE77, O14966

UniProtKB/TrEMBL

A0A024R999, Q6FGU7
XM_054339480.1 → XP_054195455.1 ras-related protein Rab-7L1 isoform X3
XM_054339475.1 → XP_054195450.1 ras-related protein Rab-7L1 isoform X2
XM_054339476.1 → XP_054195451.1 ras-related protein Rab-7L1 isoform X2
XM_054339469.1 → XP_054195444.1 ras-related protein Rab-7L1 isoform X1

UniProtKB/Swiss-Prot

B4E1K3, C9JE77, O14966

UniProtKB/TrEMBL

A0A024R999, Q6FGU7
XM_054339473.1 → XP_054195448.1 ras-related protein Rab-7L1 isoform X2
XM_054339474.1 → XP_054195449.1 ras-related protein Rab-7L1 isoform X2
XM_054339470.1 → XP_054195445.1 ras-related protein Rab-7L1 isoform X1

UniProtKB/Swiss-Prot

B4E1K3, C9JE77, O14966

UniProtKB/TrEMBL

A0A024R999, Q6FGU7
XM_054339478.1 → XP_054195453.1 ras-related protein Rab-7L1 isoform X2
XM_054339479.1 → XP_054195454.1 ras-related protein Rab-7L1 isoform X3