Vps54 MGI Mouse Gene Detail - MGI:2178798 - VPS54 GARP complex subunit

Symbol

Vps54
Name

VPS54 GARP complex subunit
Synonyms

5330404P15Rik, mSLP8, Vps54l, wr

Feature Type

protein coding gene
IDs

MGI:2178798
NCBI Gene: 245944
Alliance

gene page
Transcription Start Sites

14 TSS

Sequence Map

Chr11:21189281-21271136 bp, + strand
From Ensembl annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 11, 13.89 cM, cytoband A3
Mapping Data

14 experiments

SNPs within 2kb

257 from dbSNP Build 142
Strain Annotations

18

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_2178798	protein coding gene	Chr11:21189032-21271136 (+)
129S1/SvImJ	MGP_129S1SvImJ_G0018071	protein coding gene	Chr11:18833648-18919831 (+)
A/J	MGP_AJ_G0018044	protein coding gene	Chr11:18165442-18248985 (+)
AKR/J	MGP_AKRJ_G0018008	protein coding gene	Chr11:18808356-18893918 (+)
BALB/cJ	MGP_BALBcJ_G0018012	protein coding gene	Chr11:18280637-18363870 (+)
C3H/HeJ	MGP_C3HHeJ_G0017826	protein coding gene	Chr11:18695462-18782349 (+)
C57BL/6NJ	MGP_C57BL6NJ_G0018464	protein coding gene	Chr11:19670615-19760583 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0016122	protein coding gene	Chr11:17119609-17199886 (+)
CAST/EiJ	MGP_CASTEiJ_G0017387	protein coding gene	Chr11:18684339-18776204 (+)
CBA/J	MGP_CBAJ_G0017800	protein coding gene	Chr11:20516875-20609617 (+)
DBA/2J	MGP_DBA2J_G0017910	protein coding gene	Chr11:18111385-18193640 (+)
FVB/NJ	MGP_FVBNJ_G0017902	protein coding gene	Chr11:17873507-17957207 (+)
LP/J	MGP_LPJ_G0017981	protein coding gene	Chr11:18983206-19069976 (+)
NOD/ShiLtJ	MGP_NODShiLtJ_G0017928	protein coding gene	Chr11:20931383-21020468 (+)
NZO/HlLtJ	MGP_NZOHlLtJ_G0018505	protein coding gene	Chr11:18893538-18977226 (+)
PWK/PhJ	MGP_PWKPhJ_G0017168	protein coding gene	Chr11:18123810-18208879 (+)
SPRET/EiJ	MGP_SPRETEiJ_G0016965	protein coding gene	Chr11:18609033-18701261 (+)
WSB/EiJ	MGP_WSBEiJ_G0017441	protein coding gene	Chr11:18541058-18628784 (+)

Human Ortholog

VPS54, VPS54 subunit of GARP complex

Vertebrate Orthologs

3

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

VPS54, VPS54 subunit of GARP complex
Synonyms

HCC8, hVps54L, PPP1R164, SLP-8p, VPS54L, WR
Links

HGNC:18652

NCBI Gene ID: 51542

neXtProt AC: NX_Q9P1Q0

UniProt: Q9P1Q0
Chr Location

2p15-p14; chr2:63892146-64019428 (-) GRCh38

MGI Vertebrate Homology

Vps54 stringent orthology
1 human;1 mouse;1 rat;1 zebrafish
HCOP

vertebrate homology predictions: VPS54
Gene Tree

Vps54

Diseases

2 with Vps54 mouse models

Human Disease

Mouse Models

amyotrophic lateral sclerosis type 1

IDs

View 1 model

Werdnig-Hoffmann disease

IDs

View 1 model

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

Mutations/Alleles

1 with disease annotations

References

3 with disease annotations

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Phenotype Summary

57 phenotypes from 3 alleles in 4 genetic backgrounds
129 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

238
Chemically induced (other)

1
Endonuclease-mediated

2
Gene trapped

233
Spontaneous

1
Transgenic

1
Genomic Mutations

1 involving Vps54
Incidental Mutations

Mutagenetix , APF , CvDC
Find Mice (IMSR)

284 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

Homozygous mutants show progressive ataxia, tremors, and limb paralysis with degeneration of motor nerve cells of brainstem and spinal cord and atrophy of skeletal muscle beginning about 3-weeks of age. Mutants are sterile and most die by 3-months of age.

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All GO Annotations

70
GO References

29

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	non-membrane-bounded 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

706
cDNA Data

104

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GEO

Expression Atlas
Other Vertebrate Links

Xenbase vps54

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All Sequences

67
RefSeq

11
UniProt

5
CCDS

CCDS24463.1, CCDS70147.1

Ensembl

ENSMUSG00000020128 (Evidence)
NCBI Gene

245944

			Length	Strain/Species	Flank
genomic	ENSMUSG00000020128	Ensembl Gene Model \| MGI Sequence Detail	81856	C57BL/6J	± kb
transcript	ENSMUST00000006221	Ensembl \| MGI Sequence Detail	4323	Not Applicable
polypeptide	ENSMUSP00000006221	Ensembl \| MGI Sequence Detail	977	Not Applicable

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UniProt

5 Sequences
Protein Ontology

PR:000017346 vacuolar protein sorting-associated protein 54

(term hierarchy)
PDB

3N1B, 3N1E
InterPro Domains

IPR039745 Vacuolar protein sorting-associated protein 54

IPR012501 Vacuolar protein sorting-associated protein 54, C-terminal

IPR019515 Vacuolar protein sorting-associated protein 54, N-terminal

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All nucleic 108

Genomic 1

cDNA 107

Microarray probesets 7

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MGD-MRK-15459, MGI:2443077, MGI:98964

Summaries

All 171

Diseases 3

Gene Ontology 29

Phenotypes 129
Earliest

J:5102 Duchen LW, et al., An hereditary motor neurone disease with progressive denervation of muscle in the mouse: the mutant 'wobbler'. J Neurol Neurosurg Psychiatry. 1968 Dec;31(6):535-42
Latest

J:328923 Junghans M, et al., ROS scavengers decrease gammaH2ax spots in motor neuronal nuclei of ALS model mice in vitro. Front Cell Neurosci. 2022;16:963169

TSS for Vps54:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr100558	Chr11:21188515-21188536 (+)	-755 bp
Tssr100559	Chr11:21188564-21188579 (+)	-709 bp
Tssr100560	Chr11:21188689-21188745 (+)	-564 bp
Tssr100561	Chr11:21188875-21188966 (+)	-360 bp
Tssr100562	Chr11:21189103-21189147 (+)	-156 bp
Tssr100563	Chr11:21189158-21189178 (+)	-113 bp
Tssr100564	Chr11:21189279-21189302 (+)	10 bp
Tssr100565	Chr11:21189973-21189977 (+)	694 bp
Tssr100566	Chr11:21192627-21192677 (+)	3,371 bp
Tssr100567	Chr11:21194301-21194307 (+)	5,023 bp
Tssr100568	Chr11:21205931-21205936 (+)	16,653 bp
Tssr100570	Chr11:21222145-21222180 (+)	32,882 bp
Tssr100571	Chr11:21233384-21233432 (+)	44,127 bp
Tssr3439	Chr11:21236493-21236506 (+)	47,219 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)
Citing These Resources Funding Information Warranty Disclaimer, Privacy Notice, Licensing, & Copyright Send questions and comments to User Support.	last database update 04/16/2024 MGI 6.23