Vps41 MGI Mouse Gene Detail - MGI:1929215 - VPS41 HOPS complex subunit

Symbol

Vps41
Name

VPS41 HOPS complex subunit
Synonyms

mVam2, Vam2

Feature Type

protein coding gene
IDs

MGI:1929215
NCBI Gene: 218035
Alliance

gene page
Transcription Start Sites

5 TSS

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

SNPs within 2kb

4534 from dbSNP Build 142
Strain Annotations

18
RFLP

1

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_1929215	protein coding gene	Chr13:18901456-19050981 (+)
129S1/SvImJ	MGP_129S1SvImJ_G0020256	protein coding gene	Chr13:15824461-15982410 (+)
A/J	MGP_AJ_G0020213	protein coding gene	Chr13:15622297-15773545 (+)
AKR/J	MGP_AKRJ_G0020187	protein coding gene	Chr13:15805952-15968121 (+)
BALB/cJ	MGP_BALBcJ_G0020199	protein coding gene	Chr13:15579319-15732055 (+)
C3H/HeJ	MGP_C3HHeJ_G0020002	protein coding gene	Chr13:15926804-16092808 (+)
C57BL/6NJ	MGP_C57BL6NJ_G0020643	protein coding gene	Chr13:16509230-16675334 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0018250	protein coding gene	Chr13:14062940-14222376 (+)
CAST/EiJ	MGP_CASTEiJ_G0019537	protein coding gene	Chr13:15669534-15828938 (+)
CBA/J	MGP_CBAJ_G0019966	protein coding gene	Chr13:17078652-17238825 (+)
DBA/2J	MGP_DBA2J_G0020085	protein coding gene	Chr13:15198456-15348972 (+)
FVB/NJ	MGP_FVBNJ_G0020067	protein coding gene	Chr13:14893104-15042050 (+)
LP/J	MGP_LPJ_G0020156	protein coding gene	Chr13:16113286-16280510 (+)
NOD/ShiLtJ	MGP_NODShiLtJ_G0020105	protein coding gene	Chr13:17435065-17599045 (+)
NZO/HlLtJ	MGP_NZOHlLtJ_G0020672	protein coding gene	Chr13:15615195-15768992 (+)
PWK/PhJ	MGP_PWKPhJ_G0019300	protein coding gene	Chr13:15251035-15407573 (+)
SPRET/EiJ	MGP_SPRETEiJ_G0019106	protein coding gene	Chr13:14748011-14909591 (+)
WSB/EiJ	MGP_WSBEiJ_G0019596	protein coding gene	Chr13:15644044-15805998 (+)

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

HGNC:12713

NCBI Gene ID: 27072

neXtProt AC: NX_P49754

UniProt: P49754
Chr Location

7p14.1; chr7:38722974-38932394 (-) GRCh38

MGI Vertebrate Homology

Vps41 stringent orthology
1 human;1 mouse;1 rat;1 zebrafish
HCOP

vertebrate homology predictions: VPS41
Protein SuperFamily

VPS41
Gene Tree

Vps41

Diseases

1 with human VPS41 associations

				Human Disease	Mouse Models
				autosomal recessive spinocerebellar ataxia 29 IDs autosomal recessive spinocerebellar ataxia 29 DOID:0070410 OMIM:619389

Click on a disease name to see all genes associated with that disease.

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Phenotype Summary

11 phenotypes from 2 alleles in 1 genetic background
15 phenotype references

Phenotype Overview

Blue squares indicate phenotypes directly attributed to mutations/alleles of this gene.

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.

All Mutations and Alleles

12
Gene trapped

9
Radiation induced

1
Targeted

2
Genomic Mutations

1 involving Vps41
Incidental Mutations

Mutagenetix , APF , CvDC
Find Mice (IMSR)

47 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

Embryos homozygous for a knock-out allele die by E9 exhibiting morphological and functional alteration of late endocytic compartments, and abnormal triploblastic development.

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All GO Annotations

52
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.

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Expression Overview

GXD's primary emphasis is on endogenous gene expression during development. Click on grid cells to view annotations.

Blue cells = expressed in wild-type.
Gray triangles = other expression annotations only
(e.g. absence of expression or data from mutants).

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

717
Tissues

7
cDNA Data

170
Literature Summary

2

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GEO

Expression Atlas
Other Vertebrate Links

Xenbase vps41

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All Sequences

58
RefSeq

4
UniProt

3
CCDS

CCDS26257.1

Ensembl

ENSMUSG00000041236 (Evidence)
NCBI Gene

218035

			Length	Strain/Species	Flank
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

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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

IPR036322 WD40-repeat-containing domain superfamily

IPR015943 WD40/YVTN repeat-like-containing domain superfamily

IPR001841 Zinc finger, RING-type

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All nucleic 171

cDNA 170

Other 1

Microarray probesets 4

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MGI:2145205

Summaries

All 47

Developmental Gene Expression 2

Gene Ontology 10

Phenotypes 15
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

TSS for Vps41:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr118499	Chr13:18901459-18901486 (+)	11 bp
Tssr118500	Chr13:18901850-18901857 (+)	392 bp
Tssr4003	Chr13:18929268-18929282 (+)	27,813 bp
Tssr118501	Chr13:18965587-18965605 (+)	64,134 bp
Tssr118502	Chr13:19026311-19026333 (+)	124,860 bp

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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