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Vps41 Gene Detail
Summary
  • Symbol
    Vps41
  • Name
    VPS41 HOPS complex subunit
  • Synonyms
    mVam2, Vam2
  • Feature Type
    protein coding gene
  • IDs
    MGI:1929215
    NCBI Gene: 218035
  • Alliance
    genome feature page
  • Transcription Start Sites
    5 TSS
Location &
Maps
more
  • Sequence Map
    Chr13:18901462-19050981 bp, + strand
    From NCBI annotation of GRCm39
  • View this region in JBrowse
  • Genome Browsers
    Ensembl | UCSC | NCBI
  • Genetic Map
    Chromosome 13, 6.75 cM
  • Mapping Data
    3 experiments
Strain
Comparison
more
  • SNPs within 2kb
    4534 from dbSNP Build 142
  • Strain Annotations
    19
  • RFLP
    1
For selected strains:
Strain Gene Model ID Feature Type Coordinates Select Strains
C57BL/6J MGI_C57BL6J_1929215
 protein coding gene Chr13:18901456-19050981 (+)
129S1/SvImJ ENSMUSG00200013729
 protein coding gene Chr13:16140104-16293445 (+)
A/J ENSMUSG00195034052
 protein coding gene Chr13:15260192-15413822 (+)
AKR/J ENSMUSG00220026125
 protein coding gene Chr13:15176588-15449982 (+)
BALB/cJ ENSMUSG00180033241
 protein coding gene Chr13:15620890-15774506 (+)
C3H/HeJ ENSMUSG00175029077
 protein coding gene Chr13:15714458-15873384 (+)
C57BL/6NJ ENSMUSG00215015061
 protein coding gene Chr13:15657728-15809807 (+)
CAROLI/EiJ MGP_CAROLIEiJ_G0018250
 protein coding gene Chr13:14062940-14222376 (+)
CAST/EiJ ENSTCUG00005013509
 protein coding gene Chr13:15749314-16008920 (+)
CBA/J ENSMUSG00210029802
 protein coding gene Chr13:15574363-15727966 (+)
DBA/2J ENSMUSG00185012519
 protein coding gene Chr13:16275732-16429349 (+)
FVB/NJ ENSMUSG00205025351
 protein coding gene Chr13:15418060-15569144 (+)
JF1/MsJ ENSUMUG00000013267
 protein coding gene Chr13:15997177-16270691 (+)
LP/J ENSMUSG00230034021
 protein coding gene Chr13:25677634-25951000 (+)
NOD/ShiLtJ ENSMUSG00190020538
 protein coding gene Chr13:15548234-15701852 (+)
NZO/HlLtJ ENSMUSG00225032129
 protein coding gene Chr13:19420708-19572787 (+)
PWK/PhJ ENSLUMG00010026356
 protein coding gene Chr13:15008120-15278480 (+)
SPRET/EiJ ENSMSPG00010018673
 protein coding gene Chr13:14627334-14778387 (+)
WSB/EiJ ENSIUOG00005031770
 protein coding gene Chr13:14877809-15036873 (+)



Homology
more
  • Human Ortholog
    VPS41, VPS41 subunit of HOPS complex
  • Vertebrate Orthologs
    3
Vertebrate Orthology Source
Alliance of Genome Resources
  • Human Ortholog
    VPS41, VPS41 subunit of HOPS complex
  • Synonyms
    HVPS41, hVps41p, HVSP41, SCAR29
  • Links
    NCBI Gene ID: 27072
    UniProt: P49754

  • Chr Location
    7p14.1; chr7:38722974-38932394 (-)  GRCh38
Human Diseases
more
  • Diseases
    1 with human VPS41 associations

Human Disease Mouse Models
      
IDs
Click on a disease name to see all genes associated with that disease.

Mutations,
Alleles, and
Phenotypes
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  • Phenotype Summary
    11 phenotypes from 2 alleles in 1 genetic background
    16 phenotype references
Phenotype Overview

adipose tissue
behavior/neurological
cardiovascular system
cellular
craniofacial
digestive/alimentary system
embryo
endocrine/exocrine glands
growth/size/body
hearing/vestibular/ear
hematopoietic system
homeostasis/metabolism
integument
immune system
limbs/digits/tail
liver/biliary system
mortality/aging
muscle
nervous system
pigmentation
renal/urinary system
reproductive system
respiratory system
skeleton
taste/olfaction
neoplasm
vision/eye

Click cells to view annotations.
Embryos homozygous for a knock-out allele die by E9 exhibiting morphological and functional alteration of late endocytic compartments, and abnormal triploblastic development.
Gene Ontology
(GO)
Classifications
less
  • All GO Annotations
    77
  • GO References
    10
Molecular Function

carbohydrate derivative binding
cytoskeletal protein binding
DNA binding
enzyme regulator
hydrolase
ligase
lipid binding
oxidoreductase
RNA binding
signaling receptor activity
signaling receptor binding
transcription
transferase
transporter
Biological Process

carbohydrate derivative metabolism
cell differentiation
cell population proliferation
cellular component organization
DNA-templated transcription
establishment of localization
homeostatic process
immune system process
lipid metabolic process
programmed cell death
protein metabolic process
response to stimulus
signaling
system development
Cellular Component

cell projection
cytoplasmic vesicle
cytoskeleton
cytosol
endoplasmic reticulum
endosome
extracellular region
Golgi apparatus
mitochondrion
membraneless organelle
nucleus
organelle envelope
organelle lumen
plasma membrane
protein-containing complex
synapse
vacuole
Click cells to view annotations.
Expression
less
Expression Overview

early conceptus
embryo ectoderm
embryo endoderm
embryo mesoderm
embryo mesenchyme
extraembryonic component
alimentary system
auditory system
branchial arches
cardiovascular system
connective tissue
endocrine system
exocrine system
hemolymphoid system
integumental system
limbs
liver and biliary system
musculoskeletal system
nervous system
olfactory system
reproductive system
respiratory system
urinary system
visual system
Click cells to view annotations.


  • Assay Results
    608
  • Tissues
    7
  • cDNA Data
    170
  • Literature Summary
    2
  • Comparison Matrix
    Gene Expression + Phenotype
    • Sequences &
    Gene Models
    less
    Representative SequencesLengthStrain/SpeciesFlank
    genomic 218035 NCBI Gene Model | MGI Sequence Detail 149520 C57BL/6J ±  kb
    transcript NM_172120 RefSeq | MGI Sequence Detail 3212 ZRU/MplStud  
    polypeptide Q5KU39 UniProt | EBI | MGI Sequence Detail 853 Not Applicable  
    For the selected sequence
    Protein
    Information
    less
    • UniProt
      3 Sequences
    • Protein Ontology
      PR:000017340 vacuolar protein sorting-associated protein 41
      (term hierarchy)
    • InterPro Domains
      IPR000547 Clathrin, heavy chain/VPS, 7-fold repeat
      IPR011990 Tetratricopeptide-like helical domain superfamily
      IPR016902 Vacuolar protein sorting-associated protein 41
      IPR045111 Vacuolar protein sorting-associated protein Vps41/Vps8
      IPR057780 Vps41, beta-propeller
      IPR057779 Vps41, C-terminal RING finger
      IPR061510 Vps41, TPR-like region
      IPR036322 WD40-repeat-containing domain superfamily
      IPR015943 WD40/YVTN repeat-like-containing domain superfamily
      IPR001841 Zinc finger, RING-type
    Molecular
    Reagents
    less
    • All nucleic 171
      cDNA 170
      Other 1
      Antibodies 1

      Microarray probesets 4
    Other
    Accession IDs
    less
    MGI:2145205
    References
    more
    • Summaries
      All 49
      Developmental Gene Expression 2
      Gene Ontology 10
      Phenotypes 16
    • Earliest
      J:61187 Gwynn B, et al., Defects in the cappuccino (cno) gene on mouse chromosome 5 and human 4p cause Hermansky-Pudlak syndrome by an AP-3-independent mechanism. Blood. 2000 Dec 15;96(13):4227-35
    • Latest
      J:348149 Jain S, et al., Adaptor protein-3 produces synaptic vesicles that release phasic dopamine. Proc Natl Acad Sci U S A. 2023 Oct 17;120(42):e2309843120
    Contributing Projects:
    Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Models of Human Cancer database (MMHCdb) (formerly Mouse Tumor Biology (MTB)), Gene Ontology (GO)
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    Funding Information
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    Send questions and comments to User Support.     		last database update
    09/08/2026
    MGI 6.24     		The Jackson Laboratory