Vps4a MGI Mouse Gene Detail - MGI:1890520 - vacuolar protein sorting 4A

Symbol

Vps4a
Name

vacuolar protein sorting 4A
Synonyms

4930589C15Rik, MGC:11698

Feature Type

protein coding gene
IDs

MGI:1890520
NCBI Gene: 116733
Alliance

gene page
Transcription Start Sites

8 TSS

Sequence Map

Chr8:107757901-107772392 bp, + strand
From NCBI annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 8, 53.53 cM, cytoband D
Mapping Data

4 experiments

SNPs within 2kb

355 from dbSNP Build 142
Strain Annotations

18

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_1890520	protein coding gene	Chr8:107757854-107772392 (+)
129S1/SvImJ	MGP_129S1SvImJ_G0034092	protein coding gene	Chr8:109439457-109454992 (+)
A/J	MGP_AJ_G0034072	protein coding gene	Chr8:105055043-105069042 (+)
AKR/J	MGP_AKRJ_G0033998	protein coding gene	Chr8:108119407-108134061 (+)
BALB/cJ	MGP_BALBcJ_G0034065	protein coding gene	Chr8:105250348-105266181 (+)
C3H/HeJ	MGP_C3HHeJ_G0033777	protein coding gene	Chr8:108842346-108857960 (+)
C57BL/6NJ	MGP_C57BL6NJ_G0034585	protein coding gene	Chr8:113437243-113452501 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0031527	protein coding gene	Chr8:98161443-98174748 (+)
CAST/EiJ	MGP_CASTEiJ_G0033103	protein coding gene	Chr8:108368043-108384456 (+)
CBA/J	MGP_CBAJ_G0033750	protein coding gene	Chr8:117114292-117130389 (+)
DBA/2J	MGP_DBA2J_G0033905	protein coding gene	Chr8:104383162-104397924 (+)
FVB/NJ	MGP_FVBNJ_G0033850	protein coding gene	Chr8:103317365-103337631 (+)
LP/J	MGP_LPJ_G0033996	protein coding gene	Chr8:109622023-109640310 (+)
NOD/ShiLtJ	MGP_NODShiLtJ_G0033894	protein coding gene	Chr8:120231011-120245519 (+)
NZO/HlLtJ	MGP_NZOHlLtJ_G0034603	protein coding gene	Chr8:108046716-108062567 (+)
PWK/PhJ	MGP_PWKPhJ_G0032805	protein coding gene	Chr8:103805438-103820872 (+)
SPRET/EiJ	MGP_SPRETEiJ_G0032645	protein coding gene	Chr8:106759511-106777014 (+)
WSB/EiJ	MGP_WSBEiJ_G0033219	protein coding gene	Chr8:108766678-108782370 (+)

Human Ortholog

VPS4A, vacuolar protein sorting 4 homolog A

Vertebrate Orthologs

3

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

VPS4A, vacuolar protein sorting 4 homolog A
Synonyms

CIMDAG, SKD1, SKD1A, SKD2, VPS4, VPS4-1
Links

HGNC:13488

NCBI Gene ID: 27183

neXtProt AC: NX_Q9UN37

UniProt: Q9UN37
Chr Location

16q22.1; chr16:69311336-69326939 (+) GRCh38

MGI Vertebrate Homology

Vps4a stringent orthology
1 human;1 mouse;1 rat;1 zebrafish
HCOP

vertebrate homology predictions: VPS4A
Gene Tree

Vps4a

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Phenotype Summary

11 phenotypes from 1 allele in 1 genetic background
1 phenotype from multigenic genotypes
13 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

14
Endonuclease-mediated

1
Gene trapped

9
Targeted

4
Incidental Mutations

Mutagenetix , APF
Find Mice (IMSR)

17 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

Mouse embryonic fibroblasts from mice heterozygous for Vps4a and Vps4b null alleles exhibit exhibit increased endo/lysosomal organelles with large multi-membrane structures.

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All GO Annotations

103
GO References

22

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

817
Tissues

72
cDNA Data

90
Literature Summary

2

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GEO

Expression Atlas
Other Vertebrate Links

Xenbase vps4a

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All Sequences

44
RefSeq

2
UniProt

3
CCDS

CCDS40463.1

Ensembl

ENSMUSG00000031913 (Evidence)
NCBI Gene

116733

			Length	Strain/Species	Flank
genomic	116733	NCBI Gene Model \| MGI Sequence Detail	14492	C57BL/6J	± kb
transcript	NM_126165	RefSeq \| MGI Sequence Detail	2136	C57BL/6
polypeptide	Q8VEJ9	UniProt \| EBI \| MGI Sequence Detail	437	Not Applicable

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UniProt

3 Sequences
Protein Ontology

PR:000017342 vacuolar protein sorting-associated protein 4A

(term hierarchy)
EC

3.6.4.6
InterPro Domains

IPR041569 AAA ATPase, AAA+ lid domain

IPR003593 AAA+ ATPase domain

IPR003960 ATPase, AAA-type, conserved site

IPR003959 ATPase, AAA-type, core

IPR050304 Microtubule-severing AAA ATPase

IPR007330 MIT domain

IPR036181 MIT domain superfamily

IPR027417 P-loop containing nucleoside triphosphate hydrolase

IPR015415 Spastin/Vps4, C-terminal

IPR045253 Vacuolar protein sorting-associated protein 4, MIT domain
GlyGen

Q8VEJ9 3 sites, 3 N-linked glycans (3 sites)

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All nucleic 92

cDNA 90

Primer pair 2

Microarray probesets 3

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MGI:1925470, MGI:2142511, MGI:2145042

Summaries

All 59

Developmental Gene Expression 2

Gene Ontology 22

Phenotypes 13
Earliest

J:320408 Finken-Eigen M, et al., The VPS4 gene is involved in protein transport out of a yeast pre-vacuolar endosome-like compartment. Curr Genet. 1997 Jun;31(6):469-80
Latest

J:345621 Adams DJ, et al., Genetic determinants of micronucleus formation in vivo. Nature. 2024 Mar;627(8002):130-136

TSS for Vps4a:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr79275	Chr8:107757663-107757667 (+)	-236 bp
Tssr79276	Chr8:107757746-107757758 (+)	-149 bp
Tssr79277	Chr8:107757770-107757781 (+)	-125 bp
Tssr79278	Chr8:107757850-107757861 (+)	-45 bp
Tssr79279	Chr8:107757867-107757878 (+)	-28 bp
Tssr2680	Chr8:107757905-107757923 (+)	13 bp
Tssr79280	Chr8:107757927-107757982 (+)	54 bp
Tssr79281	Chr8:107757986-107757997 (+)	91 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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