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

Gene ID: 27072, updated on 27-Nov-2024

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
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Genomic context

See VPS41 in Genome Data Viewer
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_000007.14Genomic Context describing neighboring genes Neighboring gene keratin 8 pseudogene 20 Neighboring gene CFAP144 pseudogene 1 Neighboring gene MPRA-validated peak6495 silencer Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:38925534-38926050 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:38926051-38926567 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25874 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr7:38989846-38991045 Neighboring gene POU6F2 antisense RNA 2 Neighboring gene MPRA-validated peak6496 silencer Neighboring gene NANOG hESC enhancer GRCh37_chr7:39082046-39082670 Neighboring gene POU class 6 homeobox 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:39298804-39299337 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:39310732-39311232 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:39311233-39311733 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:39349937-39350440 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:39350441-39350942 Neighboring gene uncharacterized LOC105375239 Neighboring gene small nucleolar RNA, H/ACA box 20B

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

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

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

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 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 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 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

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)

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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)

  1. NM_014396.4NP_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:571708
    CLH; Clathrin heavy chain repeat homology
    sd00039
    Location:138169
    7WD40; WD40 repeat [structural motif]
    cd16690
    Location:787841
    RING-H2_Vps41; RING finger, H2 subclass, found in vacuolar protein sorting-associated protein 41 (Vps41) and similar proteins
  2. NM_080631.4NP_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:546683
    CLH; Clathrin heavy chain repeat homology
    cd16690
    Location:762816
    RING-H2_Vps41; RING finger, H2 subclass, found in vacuolar protein sorting-associated protein 41 (Vps41) and similar proteins

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

  1. NC_000007.14 Reference GRCh38.p14 Primary Assembly

    Range
    38722974..38909191 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017011988.2XP_016867477.1  vacuolar protein sorting-associated protein 41 homolog isoform X1

RNA

  1. XR_007060008.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    38880029..39066224 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054357904.1XP_054213879.1  vacuolar protein sorting-associated protein 41 homolog isoform X1

RNA

  1. XR_008487564.1 RNA Sequence