Atp6ap1 MGI Mouse Gene Detail - MGI:109629 - ATPase, H+ transporting, lysosomal accessory protein 1

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Atp6ap1 Gene Detail

Symbol

Atp6ap1
Name

ATPase, H+ transporting, lysosomal accessory protein 1
Synonyms

16A, AC45, Atp6ip1, Atp6s1, CF2, VATPS1, XAP-3

Feature Type

protein coding gene
IDs

MGI:109629
NCBI Gene: 54411
Alliance

gene page
Transcription Start Sites

3 TSS
Candidate for QTL

3 QTL

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Sequence Map

ChrX:73340753-73348297 bp, + strand
From NCBI annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome X, 37.96 cM
Mapping Data

3 experiments

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SNPs within 2kb

158 from dbSNP Build 142
Strain Annotations

18

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates	Select Strains
C57BL/6J	MGI_C57BL6J_109629	protein coding gene	ChrX:73340703-73348327 (+)
129S1/SvImJ	MGP_129S1SvImJ_G0035839	protein coding gene	ChrX:70095804-70104183 (+)
A/J	MGP_AJ_G0035820	protein coding gene	ChrX:70281175-70288883 (+)
AKR/J	MGP_AKRJ_G0035745	protein coding gene	ChrX:72183054-72190660 (+)
BALB/cJ	MGP_BALBcJ_G0035805	protein coding gene	ChrX:69304070-69315068 (+)
C3H/HeJ	MGP_C3HHeJ_G0035510	protein coding gene	ChrX:70571295-70578859 (+)
C57BL/6NJ	MGP_C57BL6NJ_G0036335	protein coding gene	ChrX:72256940-72264558 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0033179	protein coding gene	ChrX:69347203-69354885 (+)
CAST/EiJ	MGP_CASTEiJ_G0034801	protein coding gene	ChrX:55950594-55958177 (+)
CBA/J	MGP_CBAJ_G0035485	protein coding gene	ChrX:74252978-74261188 (+)
DBA/2J	MGP_DBA2J_G0035642	protein coding gene	ChrX:69740601-69748871 (+)
FVB/NJ	MGP_FVBNJ_G0035586	protein coding gene	ChrX:69084267-69091646 (+)
LP/J	MGP_LPJ_G0035727	protein coding gene	ChrX:70875861-70883529 (+)
NOD/ShiLtJ	MGP_NODShiLtJ_G0035624	protein coding gene	ChrX:76816911-76824630 (+)
NZO/HlLtJ	MGP_NZOHlLtJ_G0036357	protein coding gene	ChrX:69913091-69920668 (+)
PWK/PhJ	MGP_PWKPhJ_G0034500	protein coding gene	ChrX:53912340-53920496 (+)
SPRET/EiJ	MGP_SPRETEiJ_G0034334	protein coding gene	ChrX:56820731-56828365 (+)
WSB/EiJ	MGP_WSBEiJ_G0034942	protein coding gene	ChrX:69195616-69204648 (+)

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Human Ortholog

ATP6AP1, ATPase H+ transporting accessory protein 1

Vertebrate Orthologs

4

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

ATP6AP1, ATPase H+ transporting accessory protein 1
Synonyms

16A, Ac45, ATP6IP1, ATP6S1, CF2, VATPS1, XAP-3, XAP3
Links

HGNC:868

NCBI Gene ID: 537

neXtProt AC: NX_Q15904

UniProt: Q15904
Chr Location

Xq28; chrX:154428633-154436516 (+) GRCh38

MGI Vertebrate Homology

Atp6ap1 stringent orthology
1 human;1 mouse;1 rat;2 zebrafish
HCOP

vertebrate homology predictions: ATP6AP1
Gene Tree

Atp6ap1

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Diseases

1 with human ATP6AP1 associations

				Human Disease	Mouse Models
				immunodeficiency 47 IDs immunodeficiency 47 DOID:0112002 OMIM:300972 UMLS_CUI:C4310819

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

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Phenotype Summary

6 phenotypes from 2 alleles in 2 genetic backgrounds
1 images
12 phenotype references

Phenotype Overview

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

10
Endonuclease-mediated

1
Gene trapped

3
Targeted

6
Find Mice (IMSR)

9 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

A targeted mutation in this X-linked gene was made in male ES cells, but no viable chimeric mice were produced, suggesting a requirement for this gene in prenatal development.

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All GO Annotations

23
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

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

835
Tissues

100
cDNA Data

260
Literature Summary

3

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GEO

Expression Atlas
Other Vertebrate Links

Xenbase atp6ap1, atp6ap1.2

ZFIN atp6ap1a, atp6ap1b

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All Sequences

93
RefSeq

14
UniProt

14
CCDS

CCDS30226.1, CCDS90731.1

Ensembl

ENSMUSG00000019087 (Evidence)
NCBI Gene

54411

Representative Sequences				Length	Strain/Species	Flank
	genomic	54411	NCBI Gene Model \| MGI Sequence Detail	7545	C57BL/6J	± kb
	transcript	NM_001358380	RefSeq \| MGI Sequence Detail	2174	C57BL/6
	polypeptide	Q9R1Q9	UniProt \| EBI \| MGI Sequence Detail	463	Not Applicable

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UniProt

14 Sequences
Protein Ontology

PR:000004468 V-type proton ATPase subunit S1

(term hierarchy)
PDB

9BRA, 9BRQ, 9BRR, 9BRS, 9BRT, 9BRU, 9BRY, 9BRZ
InterPro Domains

IPR008388 V0 complex accessory subunit Ac45

IPR046755 V-type proton ATPase subunit S1, luminal domain

IPR046756 V-type proton ATPase subunit S1/VOA1, transmembrane domain
GlyGen

Q9R1Q9 10 sites, 13 N-linked glycans (6 sites), 1 O-linked glycan (1 site)

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All nucleic 268

Genomic 7

cDNA 261

Microarray probesets 3

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MGD-MRK-39628, MGI:2147865, MGI:2147998

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Summaries

All 48

Developmental Gene Expression 3

Gene Ontology 8

Phenotypes 12
Earliest

J:26634 Rivella S, et al., A comparative transcriptional map of a region of 250 kb on the human and mouse X chromosome between the G6PD and the FLN1 genes. Genomics. 1995 Aug 10;28(3):377-82
Latest

J:326541 Cyagen Biosciences Inc., Cyagen Biosciences Website. 2022;

TSS for Atp6ap1:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr161324	ChrX:73340726-73340784 (+)	2 bp
Tssr161325	ChrX:73343562-73343566 (+)	2,811 bp
Tssr161326	ChrX:73345992-73346007 (+)	5,247 bp

Atp6ap1 is Candidate Gene for:

QTL	Genetic Location*	Genome Location (GRCm39)	Reference	QTL Note
Bw19	ChrX, 24.88 cM	ChrX:46376920-52412327	J:91835	The correlation between gene expression and dietary interaction was examined in a population of (BALB/cStCrlfC3H/Nctr x VY/WffC3Hf/Nctr-A(vy)/a)F1 animals. A/a and A/A animals were placed on a 70% (calorie restricted) or 100% (non-restricted) diet andliver mRNA levels were assessed for over 18,000 genes using DNA microarrays. Twenty-eight known genes showing statistically significant differential expression between the 70% and 100% calorie diets and A/a and A/A genotypes mapped near known diabesity QTLs. These genes may be considered further for candidate genes. On mouse Chromosome X, Atp6ap1 (29.8 cM), Flna (29.8 cM), and Gdi1 (29.8 cM) all show differential expression between A/a and A/A animals on the restricted diet. Diabesity QTLs Bw19 (26.4 cM) and C10bw6 (32 cM) map near these candidate genes. Jarid1c (64 cM) shows differential expression between the restricted and unrestricted diets on the A/A background. Diabesity QTL Dob7 (59.5 cM) maps near Jarid1c.
C10bw6	ChrX, 30.84 cM		J:91835	The correlation between gene expression and dietary interaction was examined in a population of (BALB/cStCrlfC3H/Nctr x VY/WffC3Hf/Nctr-A(vy)/a)F1 animals. A/a and A/A animals were placed on a 70% (calorie restricted) or 100% (non-restricted) diet andliver mRNA levels were assessed for over 18,000 genes using DNA microarrays. Twenty-eight known genes showing statistically significant differential expression between the 70% and 100% calorie diets and A/a and A/A genotypes mapped near known diabesity QTLs. These genes may be considered further for candidate genes. On mouse Chromosome X, Atp6ap1 (29.8 cM), Flna (29.8 cM), and Gdi1 (29.8 cM) all show differential expression between A/a and A/A animals on the restricted diet. Diabesity QTLs Bw19 (26.4 cM) and C10bw6 (32 cM) map near these candidate genes. Jarid1c (64 cM) shows differential expression between the restricted and unrestricted diets on the A/A background. Diabesity QTL Dob7 (59.5 cM) maps near Jarid1c.
Dob7	ChrX, 57.38 cM		J:91835	The correlation between gene expression and dietary interaction was examined in a population of (BALB/cStCrlfC3H/Nctr x VY/WffC3Hf/Nctr-A(vy)/a)F1 animals. A/a and A/A animals were placed on a 70% (calorie restricted) or 100% (non-restricted) diet andliver mRNA levels were assessed for over 18,000 genes using DNA microarrays. Twenty-eight known genes showing statistically significant differential expression between the 70% and 100% calorie diets and A/a and A/A genotypes mapped near known diabesity QTLs. These genes may be considered further for candidate genes. On mouse Chromosome X, Atp6ap1 (29.8 cM), Flna (29.8 cM), and Gdi1 (29.8 cM) all show differential expression between A/a and A/A animals on the restricted diet. Diabesity QTLs Bw19 (26.4 cM) and C10bw6 (32 cM) map near these candidate genes. Jarid1c (64 cM) shows differential expression between the restricted and unrestricted diets on the A/A background. Diabesity QTL Dob7 (59.5 cM) maps near Jarid1c.

*cM position of peak correlated region/marker

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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