Vps39 MGI Mouse Gene Detail - MGI:2443189 - VPS39 HOPS complex subunit

Symbol

Vps39
Name

VPS39 HOPS complex subunit
Synonyms

A230065P22Rik, mVam6, Vam6, Vam6P

Feature Type

protein coding gene
IDs

MGI:2443189
NCBI Gene: 269338
Alliance

gene page
Transcription Start Sites

7 TSS

Sequence Map

Chr2:120146942-120183618 bp, - strand
From NCBI annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 2, 60.31 cM
Mapping Data

2 experiments

SNPs within 2kb

881 from dbSNP Build 142
Strain Annotations

18

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_2443189	protein coding gene	Chr2:120146942-120183618 (-)
129S1/SvImJ	MGP_129S1SvImJ_G0026364	protein coding gene	Chr2:123177863-123216021 (-)
A/J	MGP_AJ_G0026325	protein coding gene	Chr2:118128137-118167111 (-)
AKR/J	MGP_AKRJ_G0026304	protein coding gene	Chr2:121426500-121466881 (-)
BALB/cJ	MGP_BALBcJ_G0026338	protein coding gene	Chr2:118373473-118410716 (-)
C3H/HeJ	MGP_C3HHeJ_G0026084	protein coding gene	Chr2:121902325-121940506 (-)
C57BL/6NJ	MGP_C57BL6NJ_G0026785	protein coding gene	Chr2:127193271-127230787 (-)
CAROLI/EiJ	MGP_CAROLIEiJ_G0024165	protein coding gene	Chr2:113147201-113189065 (-)
CAST/EiJ	MGP_CASTEiJ_G0025546	protein coding gene	Chr2:122215177-122253128 (-)
CBA/J	MGP_CBAJ_G0026060	protein coding gene	Chr2:131641358-131685664 (-)
DBA/2J	MGP_DBA2J_G0026199	protein coding gene	Chr2:117520465-117557316 (-)
FVB/NJ	MGP_FVBNJ_G0026161	protein coding gene	Chr2:116356482-116393082 (-)
LP/J	MGP_LPJ_G0026300	protein coding gene	Chr2:123437039-123476159 (-)
NOD/ShiLtJ	MGP_NODShiLtJ_G0026180	protein coding gene	Chr2:135954165-135995607 (-)
NZO/HlLtJ	MGP_NZOHlLtJ_G0026840	protein coding gene	Chr2:121551739-121590962 (-)
PWK/PhJ	MGP_PWKPhJ_G0025282	protein coding gene	Chr2:117121849-117158775 (-)
SPRET/EiJ	MGP_SPRETEiJ_G0025081	protein coding gene	Chr2:120742477-120779660 (-)
WSB/EiJ	MGP_WSBEiJ_G0025615	protein coding gene	Chr2:122389552-122427010 (-)

Human Ortholog

VPS39, VPS39 subunit of HOPS complex

Vertebrate Orthologs

3

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

VPS39, VPS39 subunit of HOPS complex
Synonyms

hVam6p, TLP, VAM6
Links

HGNC:20593

NCBI Gene ID: 23339

neXtProt AC: NX_Q96JC1

UniProt: Q96JC1
Chr Location

15q15.1; chr15:42158701-42208307 (-) GRCh38

MGI Vertebrate Homology

Vps39 stringent orthology
1 human;1 mouse;1 rat;1 zebrafish
HCOP

vertebrate homology predictions: VPS39
Gene Tree

Vps39

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Phenotype Summary

2 phenotypes from 1 allele in 1 genetic background
11 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

8
Chemically induced (other)

1
Gene trapped

2
Radiation induced

1
Targeted

4
Genomic Mutations

2 involving Vps39
Incidental Mutations

Mutagenetix , APF
Find Mice (IMSR)

50 strains or lines available

Mice exhibit embryonic lethality between E2.5 and E7.5.

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All GO Annotations

26
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

1020
Tissues

74
cDNA Data

101
Literature Summary

3

Images

Tissue x Stage Matrix

Other Mouse Links

Allen Institute

GEO

Expression Atlas
Other Vertebrate Links

Xenbase vps39

ZFIN vps39

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All Sequences

79
RefSeq

11
UniProt

8
CCDS

CCDS16619.1, CCDS38210.1

Ensembl

ENSMUSG00000027291 (Evidence)
NCBI Gene

269338

			Length	Strain/Species	Flank
genomic	269338	NCBI Gene Model \| MGI Sequence Detail	36677	C57BL/6J	± kb
transcript	NR_027618	RefSeq \| MGI Sequence Detail	4432	C57BL/6
polypeptide	Q8R5L3	UniProt \| EBI \| MGI Sequence Detail	886	Not Applicable

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UniProt

8 Sequences
Protein Ontology

PR:000017339 Vam6/Vps39-like protein

(term hierarchy)
InterPro Domains

IPR001180 Citron homology (CNH) domain

IPR000547 Clathrin, heavy chain/VPS, 7-fold repeat

IPR019452 Vacuolar sorting protein 39/Transforming growth factor beta receptor-associated domain 1

IPR019453 Vacuolar sorting protein 39/Transforming growth factor beta receptor-associated domain 2

IPR032914 Vam6/VPS39/TRAP1 family

IPR036322 WD40-repeat-containing domain superfamily

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All nucleic 103

cDNA 101

Primer pair 2

Microarray probesets 3

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MGI:3035039

Summaries

All 43

Developmental Gene Expression 3

Gene Ontology 8

Phenotypes 11
Earliest

J:109968 Roderick TH, et al., Nineteen paracentric chromosomal inversions in mice. Genetics. 1974 Jan;76(1):109-17
Latest

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

TSS for Vps39:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr25857	Chr2:120183575-120183624 (-)	18 bp
Tssr25856	Chr2:120183480-120183502 (-)	127 bp
Tssr25855	Chr2:120183466-120183477 (-)	146 bp
Tssr25854	Chr2:120183453-120183464 (-)	159 bp
Tssr25853	Chr2:120182503-120182511 (-)	1,111 bp
Tssr25852	Chr2:120159162-120159179 (-)	24,447 bp
Tssr25851	Chr2:120158930-120158939 (-)	24,683 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 12/17/2024 MGI 6.24