Atp13a4 MGI Mouse Gene Detail - MGI:1924456

Symbol

Atp13a4
Name

ATPase type 13A4
Synonyms

4631413J11Rik, 9330174J19Rik

Feature Type

protein coding gene
IDs

MGI:1924456
NCBI Gene: 224079
Alliance

genome feature page
Transcription Start Sites

5 TSS

Sequence Map

Chr16:29214671-29363682 bp, - strand
From Ensembl annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 16, 20.24 cM
Mapping Data

2 experiments

SNPs within 2kb

3962 from dbSNP Build 142
Strain Annotations

18

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_1924456	protein coding gene	Chr16:29208685-29363682 (-)
129S1/SvImJ	ENSMUSG00200035885	protein coding gene	Chr16:26225243-26378018 (-)
A/J	ENSMUSG00195026981	protein coding gene	Chr16:25779589-25927166 (-)
AKR/J	ENSMUSG00220029835	protein coding gene	Chr16:26052938-26213564 (-)
BALB/cJ	ENSMUSG00180027265	protein coding gene	Chr16:26001618-26148247 (-)
C3H/HeJ	ENSMUSG00175037315	protein coding gene	Chr16:26149400-26294985 (-)
C57BL/6NJ	ENSMUSG00215013366	protein coding gene	Chr16:25897967-26164415 (-)
CAROLI/EiJ	MGP_CAROLIEiJ_G0020639	protein coding gene	Chr16:26447335-26578407 (-)
CAST/EiJ	ENSTCUG00005031834	protein coding gene	Chr16:26434223-26560185 (-)
CBA/J	ENSMUSG00210035525	protein coding gene	Chr16:26191477-26337054 (-)
DBA/2J	ENSMUSG00185018715	protein coding gene	Chr16:26106869-26252454 (-)
FVB/NJ	ENSMUSG00205013596	protein coding gene	Chr16:26118841-26264060 (-)
JF1/MsJ	ENSUMUG00000026720	protein coding gene	Chr16:26285796-26410940 (-)
LP/J	ENSMUSG00230029440	protein coding gene	Chr16:28676667-28823322 (-)
NOD/ShiLtJ	ENSMUSG00190032916	protein coding gene	Chr16:26285947-26440754 (-)
NZO/HlLtJ	ENSMUSG00225039132	protein coding gene	Chr16:31911561-32057114 (-)
PWK/PhJ	ENSLUMG00010029248	protein coding gene	Chr16:26124305-26249699 (-)
SPRET/EiJ	ENSMSPG00010017750	protein coding gene	Chr16:26089471-26225554 (-)
WSB/EiJ	no annotation

Human Ortholog

ATP13A4, ATPase 13A4

Vertebrate Orthologs

2

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

ATP13A4, ATPase 13A4
Links

HGNC:25422

NCBI Gene ID: 84239

UniProt: Q4VNC1
Chr Location

3q29; chr3:193398967-193593119 (-) GRCh38

MGI Vertebrate Homology

Atp13a4 stringent orthology
1 human;1 mouse;1 rat
HCOP

vertebrate homology predictions: ATP13A4
Gene Tree

Atp13a4

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Phenotype Summary

2 phenotypes from 1 allele in 1 genetic background
6 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

2
Endonuclease-mediated

2
Incidental Mutations

Mutagenetix , APF
Find Mice (IMSR)

60 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

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All GO Annotations

31
GO References

9

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

604
Tissues

6
cDNA Data

18
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 atp13a4

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All Sequences

91
RefSeq

35
UniProt

7
CCDS

CCDS49816.1, CCDS49817.1, CCDS59623.1

Ensembl

ENSMUSG00000038094 (Evidence)
NCBI Gene

224079

			Length	Strain/Species	Flank
genomic	ENSMUSG00000038094	Ensembl Gene Model \| MGI Sequence Detail	149012	C57BL/6J	± kb
transcript	ENSMUST00000182627	Ensembl \| MGI Sequence Detail	4238	Not Applicable
polypeptide	ENSMUSP00000138479	Ensembl \| MGI Sequence Detail	1193	Not Applicable

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UniProt

7 Sequences
Protein Ontology

PR:000031468 probable cation-transporting ATPase 13A4

(term hierarchy)
EC

7.2.2.-
InterPro Domains

IPR004014 Cation-transporting P-type ATPase, N-terminal

IPR036412 HAD-like superfamily

IPR023214 HAD superfamily

IPR047821 P5B-type ATPase

IPR047819 P5B-type ATPase, N-terminal

IPR001757 P-type ATPase

IPR059000 P-type ATPase, A domain

IPR008250 P-type ATPase, A domain superfamily

IPR023299 P-type ATPase, cytoplasmic domain N

IPR044492 P-type ATPase, haloacid dehalogenase domain

IPR018303 P-type ATPase, phosphorylation site

IPR006544 P-type ATPase, subfamily V

IPR023298 P-type ATPase, transmembrane domain superfamily
GlyGen

Q5XF90 2 sites, 2 N-linked glycans (2 sites)

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All nucleic 20

cDNA 18

Primer pair 2

Microarray probesets 3

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MGI:1918030

Summaries

All 36

Developmental Gene Expression 2

Gene Ontology 9

Phenotypes 6
Earliest

J:65060 Kawai J, et al., Functional annotation of a full-length mouse cDNA collection. Nature. 2001 Feb 8;409(6821):685-90
Latest

J:391708 van Veen S, et al., ATP13A4 gates extracellular polyamine levels to control excitatory synaptogenesis. Nat Commun. 2026 Aug 4;17(1)

TSS for Atp13a4:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr140685	Chr16:29363670-29363687 (-)	3 bp
Tssr140684	Chr16:29360359-29360376 (-)	3,314 bp
Tssr140683	Chr16:29360202-29360227 (-)	3,467 bp
Tssr140682	Chr16:29309229-29309275 (-)	54,430 bp
Tssr140681	Chr16:29260578-29260625 (-)	103,080 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 09/01/2026 MGI 6.24