VPS41 VPS41 subunit of HOPS complex [Homo sapiens (human)] - Gene

Summary

Official Symbol: VPS41provided by HGNC
Official Full Name: VPS41 subunit of HOPS complexprovided by HGNC
Primary source: HGNC:HGNC:12713
See related: Ensembl:ENSG00000006715 MIM:605485; AllianceGenome:HGNC:12713
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: HVPS41; HVSP41; SCAR29; hVps41p
Summary: Vesicle mediated protein sorting plays an important role in segregation of intracellular molecules into distinct organelles. Genetic studies in yeast have identified more than 40 vacuolar protein sorting (VPS) genes involved in vesicle transport to vacuoles. This gene encodes the human ortholog of yeast Vps41 protein which is also conserved in Drosophila, tomato, and Arabidopsis. Expression studies in yeast and human indicate that this protein may be involved in the formation and fusion of transport vesicles from the Golgi. Several transcript variants encoding different isoforms have been described for this gene, however, the full-length nature of not all is known. [provided by RefSeq, Jul 2008]
Expression: Ubiquitous expression in brain (RPKM 18.7), gall bladder (RPKM 13.0) and 25 other tissues See more
Orthologs: mouse all
NEW: Try the new Gene table
Try the new Transcript table

Genomic context

Location:: 7p14.1

Exon count:: 31

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	7	NC_000007.14 (38722974..38909191, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	7	NC_060931.1 (38880029..39066224, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	7	NC_000007.13 (38762574..38948791, complement)

Chromosome 7 - NC_000007.14 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help

See details

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

Go to the top of the page Help

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Neurodegenerative VPS41 variants inhibit HOPS function and mTORC1-dependent TFEB/TFE3 regulation.
Title: Neurodegenerative VPS41 variants inhibit HOPS function and mTORC1-dependent TFEB/TFE3 regulation.
Bi-allelic variants in HOPS complex subunit VPS41 cause cerebellar ataxia and abnormal membrane trafficking.
Title: Bi-allelic variants in HOPS complex subunit VPS41 cause cerebellar ataxia and abnormal membrane trafficking.
Loss-of-Function Variants in HOPS Complex Genes VPS16 and VPS41 Cause Early Onset Dystonia Associated with Lysosomal Abnormalities.
Title: Loss-of-Function Variants in HOPS Complex Genes VPS16 and VPS41 Cause Early Onset Dystonia Associated with Lysosomal Abnormalities.
Here, the authors show that Vps8 overexpression inhibits homotypic fusion and vacuole protein sorting (HOPS)-dependent trafficking routes including late endosome maturation, autophagosome-lysosome fusion, crinophagy and lysosome-related organelle formation. Mechanistically, Vps8 overexpression abolishes the late endosomal localization of HOPS-specific Vps41/Lt and prevents HOPS assembly.
Title: Vps8 overexpression inhibits HOPS-dependent trafficking routes by outcompeting Vps41/Lt.
Our results indicate that an ARF-like GTPase gene product, ARL-8, mitigates endocytic Ab neurodegeneration in a VPS-41-dependent manner, rather than through RAB-7 and AP3 as with alpha-synuclein..we demonstrate that the LC3 orthologue, LGG-2, plays a critical role in Ab toxicity with ARL-8.
Title: Distinct functional roles of Vps41-mediated neuroprotection in Alzheimer's and Parkinson's disease models of neurodegeneration.
VPS18 recruits VPS41 to the human HOPS complex via a RING-RING interaction
Title: VPS18 recruits VPS41 to the human HOPS complex via a RING-RING interaction.
VPS41 subunit of HOPS complex was defined to be the major partner for interacting with RILP.
Title: RILP interacts with HOPS complex via VPS41 subunit to regulate endocytic trafficking.
hVps41 and VAMP7 are specifically involved in the fusion of trans-Golgi network-derived lysosome-associated membrane protein carriers with late endosomes.
Title: hVps41 and VAMP7 function in direct TGN to late endosome transport of lysosomal membrane proteins.
Vps41 knockdown impairs late endosome fusion and fusion between late endosomes and lysosomes.
Title: The HOPS proteins hVps41 and hVps39 are required for homotypic and heterotypic late endosome fusion.
Both a functional heterotetrameric adaptor protein complex and a homotypic fusion and vacuole protein sorting-tethering complex are required for VPS41 to elicit neuroprotection in a transgenic model of Parkinson's disease.
Title: Functional analysis of VPS41-mediated neuroprotection in Caenorhabditis elegans and mammalian models of Parkinson's disease.

Submit: New GeneRIF Correction See all GeneRIFs (12)

Phenotypes

Go to the top of the page Help

Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Spinocerebellar ataxia, autosomal recessive 29 MedGen: C5543595 OMIM: 619389 GeneReviews: Not available	not available

EBI GWAS Catalog

Description
A genome-wide study of common SNPs and CNVs in cognitive performance in the CANTAB. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

Go to the top of the page Help

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

Go to the top of the page Help

Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

Go to the top of the page Help

Markers

GDB:1317280 (e-PCR)
- UniSTS:74759

D7S2507 (e-PCR), detects polymorphism
- UniSTS:68390

RH122058 (e-PCR)
- UniSTS:134694

NoName (e-PCR)
- UniSTS:236594

SHGC-107203 (e-PCR)
- UniSTS:170298

GDB:1318016 (e-PCR)
- UniSTS:6483

SHGC-56039 (e-PCR)
- UniSTS:8537

D7S2507 (e-PCR), detects polymorphism
- UniSTS:35484

GDB:314167 (e-PCR)
- UniSTS:10426

SHGC-78828 (e-PCR)
- UniSTS:95699

SHGC-24379 (e-PCR)
- UniSTS:81121

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables identical protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables microtubule binding	IEA Inferred from Electronic Annotation more info
enables molecular_function	ND No biological Data available more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in Golgi vesicle transport	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in biological_process	ND No biological Data available more info
involved_in cellular response to starvation	IBA Inferred from Biological aspect of Ancestor more info
involved_in endosomal vesicle fusion	IBA Inferred from Biological aspect of Ancestor more info
involved_in endosomal vesicle fusion	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in endosomal vesicle fusion	NAS Non-traceable Author Statement more info	PubMed
involved_in endosome to lysosome transport	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in late endosome to lysosome transport	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in macroautophagy	IBA Inferred from Biological aspect of Ancestor more info
involved_in protein targeting to vacuole	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of SNARE complex assembly	NAS Non-traceable Author Statement more info	PubMed
involved_in vesicle-mediated transport	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
part_of AP-3 adaptor complex	IDA Inferred from Direct Assay more info	PubMed
located_in Golgi apparatus	IEA Inferred from Electronic Annotation more info
located_in Golgi-associated vesicle	IMP Inferred from Mutant Phenotype more info	PubMed
part_of HOPS complex	IBA Inferred from Biological aspect of Ancestor more info
part_of HOPS complex	IDA Inferred from Direct Assay more info	PubMed
part_of HOPS complex	IMP Inferred from Mutant Phenotype more info	PubMed
part_of HOPS complex	NAS Non-traceable Author Statement more info	PubMed
part_of clathrin complex	IDA Inferred from Direct Assay more info	PubMed
located_in clathrin-coated vesicle	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	IDA Inferred from Direct Assay more info	PubMed
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 membrane	IDA Inferred from Direct Assay more info	PubMed
located_in endosome membrane	TAS Traceable Author Statement more info
is_active_in late endosome	IBA Inferred from Biological aspect of Ancestor more info
located_in late endosome	IDA Inferred from Direct Assay more info	PubMed
located_in late endosome membrane	IDA Inferred from Direct Assay more info	PubMed
part_of lysosomal HOPS complex	IDA Inferred from Direct Assay more info	PubMed
located_in lysosomal membrane	HDA more info	PubMed
located_in lysosomal membrane	IDA Inferred from Direct Assay more info	PubMed
located_in lysosome	IDA Inferred from Direct Assay more info	PubMed
located_in membrane	IDA Inferred from Direct Assay more info	PubMed
located_in microtubule cytoskeleton	IEA Inferred from Electronic Annotation more info

General protein information

Go to the top of the page Help

Preferred Names: vacuolar protein sorting-associated protein 41 homolog

Names: S53; VPS41, HOPS complex subunit; vacuolar assembly protein 41; vacuolar protein sorting 41 homolog

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

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_014396.4 → NP_055211.2 vacuolar protein sorting-associated protein 41 homolog isoform 1

See identical proteins and their annotated locations for NP_055211.2

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes the full-length isoform (1).

Source sequence(s)

AC004850, BC044851, U87309

Consensus CDS

CCDS5457.1

UniProtKB/Swiss-Prot

E9PF36, P49754, Q86TP8, Q99851, Q99852

UniProtKB/TrEMBL

B2RB94

Related

ENSP00000309457.4, ENST00000310301.9

Conserved Domains (3) summary

smart00299
Location:571 → 708

CLH; Clathrin heavy chain repeat homology

sd00039
Location:138 → 169

7WD40; WD40 repeat [structural motif]

cd16690
Location:787 → 841

RING-H2_Vps41; RING finger, H2 subclass, found in vacuolar protein sorting-associated protein 41 (Vps41) and similar proteins
NM_080631.4 → NP_542198.2 vacuolar protein sorting-associated protein 41 homolog isoform 2

Status: REVIEWED

Description

Transcript Variant: This variant (2) is missing a sequence segment in the coding region compared to transcript variant 1. However, it maintains the same reading frame and encodes an isoform (2) which is 25 aa shorter than isoform 1.

Source sequence(s)

AC004850, BC044851

Consensus CDS

CCDS5458.2

UniProtKB/TrEMBL

B2RB94

Related

ENSP00000379297.2, ENST00000395969.6

Conserved Domains (2) summary

smart00299
Location:546 → 683

CLH; Clathrin heavy chain repeat homology

cd16690
Location:762 → 816

RING-H2_Vps41; RING finger, H2 subclass, found in vacuolar protein sorting-associated protein 41 (Vps41) and similar proteins