Vps53 MGI Mouse Gene Detail - MGI:1915549 - VPS53 GARP complex subunit

Symbol

Vps53
Name

VPS53 GARP complex subunit
Synonyms

2010002A08Rik, 2310040I21Rik, 3100002B05Rik

Feature Type

protein coding gene
IDs

MGI:1915549
NCBI Gene: 68299
Alliance

gene page
Transcription Start Sites

6 TSS

Sequence Map

Chr11:75937052-76070464 bp, - strand
From NCBI annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 11, 45.92 cM, cytoband B4
Mapping Data

2 experiments

SNPs within 2kb

2908 from dbSNP Build 142
Strain Annotations

18

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_1915549	protein coding gene	Chr11:75937052-76070473 (-)
129S1/SvImJ	MGP_129S1SvImJ_G0018727	protein coding gene	Chr11:76839043-76997528 (-)
A/J	MGP_AJ_G0018693	protein coding gene	Chr11:73975615-74121299 (-)
AKR/J	MGP_AKRJ_G0018663	protein coding gene	Chr11:76215360-76353901 (-)
BALB/cJ	MGP_BALBcJ_G0018667	protein coding gene	Chr11:74355510-74501325 (-)
C3H/HeJ	MGP_C3HHeJ_G0018480	protein coding gene	Chr11:76234549-76383509 (-)
C57BL/6NJ	MGP_C57BL6NJ_G0019118	protein coding gene	Chr11:79262344-79406613 (-)
CAROLI/EiJ	MGP_CAROLIEiJ_G0016753	protein coding gene	Chr11:70989683-71121104 (-)
CAST/EiJ	MGP_CASTEiJ_G0018034	protein coding gene	Chr11:76637442-76780096 (-)
CBA/J	MGP_CBAJ_G0018450	protein coding gene	Chr11:82732399-82895953 (-)
DBA/2J	MGP_DBA2J_G0018559	protein coding gene	Chr11:73573030-73716488 (-)
FVB/NJ	MGP_FVBNJ_G0018549	protein coding gene	Chr11:73139341-73271869 (-)
LP/J	MGP_LPJ_G0018630	protein coding gene	Chr11:77420821-77573551 (-)
NOD/ShiLtJ	MGP_NODShiLtJ_G0018575	protein coding gene	Chr11:83238323-83396278 (-)
NZO/HlLtJ	MGP_NZOHlLtJ_G0019158	protein coding gene	Chr11:76423936-76562036 (-)
PWK/PhJ	MGP_PWKPhJ_G0017805	protein coding gene	Chr11:74294593-74437223 (-)
SPRET/EiJ	MGP_SPRETEiJ_G0017596	protein coding gene	Chr11:75994089-76129540 (-)
WSB/EiJ	MGP_WSBEiJ_G0018087	protein coding gene	Chr11:76248235-76386458 (-)

Human Ortholog

VPS53, VPS53 subunit of GARP complex

Vertebrate Orthologs

3

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

VPS53, VPS53 subunit of GARP complex
Synonyms

HCCS1, hVps53L, PCH2E, pp13624
Links

HGNC:25608

NCBI Gene ID: 55275

neXtProt AC: NX_Q5VIR6

UniProt: Q5VIR6
Chr Location

17p13.3; chr17:508503-721717 (-) GRCh38

MGI Vertebrate Homology

Vps53 stringent orthology
1 human;1 mouse;1 rat;1 zebrafish
HCOP

vertebrate homology predictions: VPS53
Gene Tree

Vps53

Diseases

1 with human VPS53 associations

				Human Disease	Mouse Models
				pontocerebellar hypoplasia type 2E IDs pontocerebellar hypoplasia type 2E DOID:0060271 OMIM:615851

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

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Phenotype Summary

7 phenotypes from 2 alleles in 2 genetic backgrounds
20 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
Chemically induced (other)

1
Endonuclease-mediated

2
Gene trapped

6
Targeted

5
Genomic Mutations

2 involving Vps53
Incidental Mutations

Mutagenetix , APF , CvDC
Find Mice (IMSR)

40 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

Mice homozygous for a knock-out allele exhibit embryonic lethality prior to E12.5 with trophoblast cell hyperplasia.

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All GO Annotations

24
GO References

8

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

706
cDNA Data

101

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GEO

Expression Atlas
Other Vertebrate Links

Xenbase vps53

ZFIN vps53

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All Sequences

105
RefSeq

5
UniProt

13
CCDS

CCDS25060.1

Ensembl

ENSMUSG00000017288 (Evidence)
NCBI Gene

68299

			Length	Strain/Species	Flank
genomic	68299	NCBI Gene Model \| MGI Sequence Detail	133413	C57BL/6J	± kb
transcript	NM_026664	RefSeq \| MGI Sequence Detail	2824	C57BL/6
polypeptide	Q8CCB4	UniProt \| EBI \| MGI Sequence Detail	832	Not Applicable

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UniProt

13 Sequences
Protein Ontology

PR:000017345 vacuolar protein sorting-associated protein 53

(term hierarchy)
InterPro Domains

IPR039766 Vacuolar protein sorting-associated protein 53

IPR031745 Vps53, C-terminal

IPR038260 Vps53, C-terminal domain superfamily

IPR007234 Vps53, N-terminal
GlyGen

Q8CCB4 1 site, 1 N-linked glycan (1 site)

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All nucleic 101

cDNA 101

Microarray probesets 7

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MGI:1913804, MGI:1917090

Summaries

All 49

Gene Ontology 8

Phenotypes 20
Earliest

J:137335 Roderick TH, Chromosomal inversions in studies of mammalian mutagenesis. Genetics. 1979 May;92(1 Pt 1 Suppl):s121-6
Latest

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

TSS for Vps53:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr109243	Chr11:76070422-76070475 (-)	15 bp
Tssr109242	Chr11:76065269-76065273 (-)	5,193 bp
Tssr109241	Chr11:76052292-76052332 (-)	18,152 bp
Tssr109240	Chr11:76045783-76045815 (-)	24,665 bp
Tssr109239	Chr11:76017526-76017530 (-)	52,936 bp
Tssr109238	Chr11:75960510-75960513 (-)	109,952 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 11/19/2024 MGI 6.24