Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	537
Gene name	ATPase H+ transporting accessory protein 1
Gene symbol	ATP6AP1
Synonyms (NCBI Gene)	16AATP6IP1ATP6S1Ac45CF2VATPS1XAP-3XAP3
Chromosome	X
Chromosome location	Xq28
Summary	This gene encodes a component of a multisubunit enzyme that mediates acidification of eukaryotic intracellular organelles. Vacuolar ATPase (V-ATPase) is comprised of a cytosolic V1 (site of the ATP catalytic site) and a transmembrane V0 domain. V-ATPase d

Show/Hide all (3)

SNP ID	Visualize variation	Clinical significance	Consequence
rs148803059	G>C	Conflicting-interpretations-of-pathogenicity	Missense variant, 5 prime UTR variant, coding sequence variant
rs878853276	T>C	Pathogenic	Missense variant, 5 prime UTR variant, coding sequence variant
rs1557196978	T>G	Pathogenic	Missense variant, 5 prime UTR variant, coding sequence variant

206

Show/Hide all (206)

miRTarBase ID	miRNA	Experiments	Reference
MIRT030317	hsa-miR-26b-5p	Microarray	19088304
MIRT051337	hsa-miR-15a-5p	CLASH	23622248
MIRT037865	hsa-miR-455-3p	CLASH	23622248
MIRT036538	hsa-miR-1226-5p	CLASH	23622248
MIRT689010	hsa-miR-6732-3p	HITS-CLIP	23313552
MIRT689009	hsa-miR-320e	HITS-CLIP	23313552
MIRT689008	hsa-miR-504-5p	HITS-CLIP	23313552
MIRT689007	hsa-miR-4690-3p	HITS-CLIP	23313552
MIRT689006	hsa-miR-5685	HITS-CLIP	23313552
MIRT689005	hsa-miR-4292	HITS-CLIP	23313552
MIRT689004	hsa-miR-6791-5p	HITS-CLIP	23313552
MIRT689003	hsa-miR-204-3p	HITS-CLIP	23313552
MIRT689002	hsa-miR-4646-5p	HITS-CLIP	23313552
MIRT689001	hsa-miR-1273f	HITS-CLIP	23313552
MIRT689000	hsa-miR-185-5p	HITS-CLIP	23313552
MIRT688999	hsa-miR-4306	HITS-CLIP	23313552
MIRT688998	hsa-miR-4644	HITS-CLIP	23313552
MIRT688997	hsa-miR-4747-5p	HITS-CLIP	23313552
MIRT688996	hsa-miR-5196-5p	HITS-CLIP	23313552
MIRT688995	hsa-miR-6878-5p	HITS-CLIP	23313552
MIRT688994	hsa-miR-6731-5p	HITS-CLIP	23313552
MIRT688993	hsa-miR-8085	HITS-CLIP	23313552
MIRT688992	hsa-miR-486-3p	HITS-CLIP	23313552
MIRT688991	hsa-miR-1237-5p	HITS-CLIP	23313552
MIRT688990	hsa-miR-4488	HITS-CLIP	23313552
MIRT688989	hsa-miR-4697-5p	HITS-CLIP	23313552
MIRT688988	hsa-miR-6846-5p	HITS-CLIP	23313552
MIRT688987	hsa-miR-6848-5p	HITS-CLIP	23313552
MIRT688986	hsa-miR-601	HITS-CLIP	23313552
MIRT688985	hsa-miR-92a-1-5p	HITS-CLIP	23313552
MIRT688984	hsa-miR-4425	HITS-CLIP	23313552
MIRT688983	hsa-miR-3147	HITS-CLIP	23313552
MIRT688982	hsa-miR-30c-1-3p	HITS-CLIP	23313552
MIRT688981	hsa-miR-30c-2-3p	HITS-CLIP	23313552
MIRT688980	hsa-miR-6788-5p	HITS-CLIP	23313552
MIRT688979	hsa-miR-1273h-5p	HITS-CLIP	23313552
MIRT688978	hsa-miR-30b-3p	HITS-CLIP	23313552
MIRT688977	hsa-miR-3689a-3p	HITS-CLIP	23313552
MIRT688976	hsa-miR-3689b-3p	HITS-CLIP	23313552
MIRT688975	hsa-miR-3689c	HITS-CLIP	23313552
MIRT688974	hsa-miR-6779-5p	HITS-CLIP	23313552
MIRT688973	hsa-miR-6780a-5p	HITS-CLIP	23313552
MIRT688972	hsa-miR-6843-3p	HITS-CLIP	23313552
MIRT688971	hsa-miR-6848-3p	HITS-CLIP	23313552
MIRT688970	hsa-miR-887-5p	HITS-CLIP	23313552
MIRT688969	hsa-miR-4727-3p	HITS-CLIP	23313552
MIRT512890	hsa-miR-6165	PAR-CLIP	23446348
MIRT512889	hsa-miR-4436a	PAR-CLIP	23446348
MIRT512888	hsa-miR-5000-3p	PAR-CLIP	23446348
MIRT512887	hsa-miR-196b-3p	PAR-CLIP	23446348
MIRT512886	hsa-miR-1286	PAR-CLIP	23446348
MIRT441146	hsa-miR-218-5p	HITS-CLIP	23212916
MIRT441146	hsa-miR-218-5p	HITS-CLIP	23212916
MIRT689010	hsa-miR-6732-3p	HITS-CLIP	23313552
MIRT689009	hsa-miR-320e	HITS-CLIP	23313552
MIRT689008	hsa-miR-504-5p	HITS-CLIP	23313552
MIRT689007	hsa-miR-4690-3p	HITS-CLIP	23313552
MIRT689006	hsa-miR-5685	HITS-CLIP	23313552
MIRT689005	hsa-miR-4292	HITS-CLIP	23313552
MIRT689004	hsa-miR-6791-5p	HITS-CLIP	23313552
MIRT689003	hsa-miR-204-3p	HITS-CLIP	23313552
MIRT689002	hsa-miR-4646-5p	HITS-CLIP	23313552
MIRT689001	hsa-miR-1273f	HITS-CLIP	23313552
MIRT689000	hsa-miR-185-5p	HITS-CLIP	23313552
MIRT688999	hsa-miR-4306	HITS-CLIP	23313552
MIRT688998	hsa-miR-4644	HITS-CLIP	23313552
MIRT688997	hsa-miR-4747-5p	HITS-CLIP	23313552
MIRT688996	hsa-miR-5196-5p	HITS-CLIP	23313552
MIRT688995	hsa-miR-6878-5p	HITS-CLIP	23313552
MIRT688994	hsa-miR-6731-5p	HITS-CLIP	23313552
MIRT688993	hsa-miR-8085	HITS-CLIP	23313552
MIRT688992	hsa-miR-486-3p	HITS-CLIP	23313552
MIRT688991	hsa-miR-1237-5p	HITS-CLIP	23313552
MIRT688990	hsa-miR-4488	HITS-CLIP	23313552
MIRT688989	hsa-miR-4697-5p	HITS-CLIP	23313552
MIRT688988	hsa-miR-6846-5p	HITS-CLIP	23313552
MIRT688987	hsa-miR-6848-5p	HITS-CLIP	23313552
MIRT688986	hsa-miR-601	HITS-CLIP	23313552
MIRT688985	hsa-miR-92a-1-5p	HITS-CLIP	23313552
MIRT688984	hsa-miR-4425	HITS-CLIP	23313552
MIRT688983	hsa-miR-3147	HITS-CLIP	23313552
MIRT688982	hsa-miR-30c-1-3p	HITS-CLIP	23313552
MIRT688981	hsa-miR-30c-2-3p	HITS-CLIP	23313552
MIRT688980	hsa-miR-6788-5p	HITS-CLIP	23313552
MIRT688979	hsa-miR-1273h-5p	HITS-CLIP	23313552
MIRT688978	hsa-miR-30b-3p	HITS-CLIP	23313552
MIRT688977	hsa-miR-3689a-3p	HITS-CLIP	23313552
MIRT688976	hsa-miR-3689b-3p	HITS-CLIP	23313552
MIRT688975	hsa-miR-3689c	HITS-CLIP	23313552
MIRT688974	hsa-miR-6779-5p	HITS-CLIP	23313552
MIRT688973	hsa-miR-6780a-5p	HITS-CLIP	23313552
MIRT688972	hsa-miR-6843-3p	HITS-CLIP	23313552
MIRT688971	hsa-miR-6848-3p	HITS-CLIP	23313552
MIRT688970	hsa-miR-887-5p	HITS-CLIP	23313552
MIRT688969	hsa-miR-4727-3p	HITS-CLIP	23313552
MIRT512890	hsa-miR-6165	PAR-CLIP	23446348
MIRT512889	hsa-miR-4436a	PAR-CLIP	23446348
MIRT512888	hsa-miR-5000-3p	PAR-CLIP	23446348
MIRT512887	hsa-miR-196b-3p	PAR-CLIP	23446348
MIRT512886	hsa-miR-1286	PAR-CLIP	23446348
MIRT808429	hsa-miR-1226	CLIP-seq
MIRT808430	hsa-miR-1273	CLIP-seq
MIRT808431	hsa-miR-1471	CLIP-seq
MIRT808432	hsa-miR-221	CLIP-seq
MIRT808433	hsa-miR-222	CLIP-seq
MIRT808434	hsa-miR-3171	CLIP-seq
MIRT808435	hsa-miR-3173-3p	CLIP-seq
MIRT808436	hsa-miR-4428	CLIP-seq
MIRT808437	hsa-miR-4731-3p	CLIP-seq
MIRT808438	hsa-miR-4733-3p	CLIP-seq
MIRT808439	hsa-miR-4801	CLIP-seq
MIRT808440	hsa-miR-499-3p	CLIP-seq
MIRT808441	hsa-miR-499a-3p	CLIP-seq
MIRT808442	hsa-miR-548ad	CLIP-seq
MIRT808443	hsa-miR-548v	CLIP-seq
MIRT1938790	hsa-miR-1206	CLIP-seq
MIRT1938791	hsa-miR-1825	CLIP-seq
MIRT1938792	hsa-miR-185	CLIP-seq
MIRT1938793	hsa-miR-1910	CLIP-seq
MIRT1938794	hsa-miR-199a-5p	CLIP-seq
MIRT1938795	hsa-miR-199b-5p	CLIP-seq
MIRT1938796	hsa-miR-3184	CLIP-seq
MIRT1938797	hsa-miR-423-5p	CLIP-seq
MIRT1938798	hsa-miR-4300	CLIP-seq
MIRT1938799	hsa-miR-4327	CLIP-seq
MIRT1938800	hsa-miR-4476	CLIP-seq
MIRT1938801	hsa-miR-920	CLIP-seq
MIRT1938802	hsa-miR-939	CLIP-seq
MIRT808429	hsa-miR-1226	CLIP-seq
MIRT808438	hsa-miR-4733-3p	CLIP-seq
MIRT808440	hsa-miR-499-3p	CLIP-seq
MIRT808441	hsa-miR-499a-3p	CLIP-seq
MIRT808429	hsa-miR-1226	CLIP-seq
MIRT808438	hsa-miR-4733-3p	CLIP-seq
MIRT808440	hsa-miR-499-3p	CLIP-seq
MIRT808441	hsa-miR-499a-3p	CLIP-seq
MIRT2435585	hsa-miR-1233	CLIP-seq
MIRT2435586	hsa-miR-1266	CLIP-seq
MIRT2435587	hsa-miR-1278	CLIP-seq
MIRT2435588	hsa-miR-150	CLIP-seq
MIRT2435589	hsa-miR-3692	CLIP-seq
MIRT2435590	hsa-miR-4270	CLIP-seq
MIRT2435591	hsa-miR-4441	CLIP-seq
MIRT2435592	hsa-miR-4518	CLIP-seq
MIRT2435593	hsa-miR-510	CLIP-seq
MIRT2435594	hsa-miR-562	CLIP-seq
MIRT2481444	hsa-miR-1205	CLIP-seq
MIRT2481445	hsa-miR-1224-3p	CLIP-seq
MIRT2435585	hsa-miR-1233	CLIP-seq
MIRT2481446	hsa-miR-1260	CLIP-seq
MIRT2481447	hsa-miR-1260b	CLIP-seq
MIRT2435586	hsa-miR-1266	CLIP-seq
MIRT2435587	hsa-miR-1278	CLIP-seq
MIRT2481448	hsa-miR-1280	CLIP-seq
MIRT2435588	hsa-miR-150	CLIP-seq
MIRT2481449	hsa-miR-1909	CLIP-seq
MIRT808432	hsa-miR-221	CLIP-seq
MIRT808433	hsa-miR-222	CLIP-seq
MIRT2481450	hsa-miR-3153	CLIP-seq
MIRT808434	hsa-miR-3171	CLIP-seq
MIRT808435	hsa-miR-3173-3p	CLIP-seq
MIRT2435589	hsa-miR-3692	CLIP-seq
MIRT2435590	hsa-miR-4270	CLIP-seq
MIRT2481451	hsa-miR-4286	CLIP-seq
MIRT2481452	hsa-miR-4419a	CLIP-seq
MIRT808436	hsa-miR-4428	CLIP-seq
MIRT2435591	hsa-miR-4441	CLIP-seq
MIRT2481453	hsa-miR-4477b	CLIP-seq
MIRT2481454	hsa-miR-4510	CLIP-seq
MIRT2435592	hsa-miR-4518	CLIP-seq
MIRT2481455	hsa-miR-4668-5p	CLIP-seq
MIRT808437	hsa-miR-4731-3p	CLIP-seq
MIRT2481456	hsa-miR-4760-3p	CLIP-seq
MIRT2481457	hsa-miR-4779	CLIP-seq
MIRT808439	hsa-miR-4801	CLIP-seq
MIRT2435593	hsa-miR-510	CLIP-seq
MIRT808443	hsa-miR-548v	CLIP-seq
MIRT2435594	hsa-miR-562	CLIP-seq
MIRT2481445	hsa-miR-1224-3p	CLIP-seq
MIRT2435585	hsa-miR-1233	CLIP-seq
MIRT2481446	hsa-miR-1260	CLIP-seq
MIRT2481447	hsa-miR-1260b	CLIP-seq
MIRT2435586	hsa-miR-1266	CLIP-seq
MIRT2435587	hsa-miR-1278	CLIP-seq
MIRT2481448	hsa-miR-1280	CLIP-seq
MIRT2435588	hsa-miR-150	CLIP-seq
MIRT808432	hsa-miR-221	CLIP-seq
MIRT808433	hsa-miR-222	CLIP-seq
MIRT808434	hsa-miR-3171	CLIP-seq
MIRT808435	hsa-miR-3173-3p	CLIP-seq
MIRT2435589	hsa-miR-3692	CLIP-seq
MIRT2435590	hsa-miR-4270	CLIP-seq
MIRT2481451	hsa-miR-4286	CLIP-seq
MIRT2481452	hsa-miR-4419a	CLIP-seq
MIRT808436	hsa-miR-4428	CLIP-seq
MIRT2435591	hsa-miR-4441	CLIP-seq
MIRT2481453	hsa-miR-4477b	CLIP-seq
MIRT2481454	hsa-miR-4510	CLIP-seq
MIRT2435592	hsa-miR-4518	CLIP-seq
MIRT808437	hsa-miR-4731-3p	CLIP-seq
MIRT2481456	hsa-miR-4760-3p	CLIP-seq
MIRT2481457	hsa-miR-4779	CLIP-seq
MIRT808439	hsa-miR-4801	CLIP-seq
MIRT2435593	hsa-miR-510	CLIP-seq
MIRT808443	hsa-miR-548v	CLIP-seq
MIRT2435594	hsa-miR-562	CLIP-seq

Show/Hide all (44)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000139	Component	Golgi membrane	NAS	32001091
GO:0001671	Function	ATPase activator activity	IBA
GO:0001671	Function	ATPase activator activity	IEA
GO:0005515	Function	Protein binding	IPI	29127204, 32353859, 32814053, 33060197, 33845483, 34232536, 34997207
GO:0005765	Component	Lysosomal membrane	NAS	32001091
GO:0005783	Component	Endoplasmic reticulum	IEA
GO:0005789	Component	Endoplasmic reticulum membrane	IEA
GO:0005886	Component	Plasma membrane	NAS	32001091
GO:0006811	Process	Monoatomic ion transport	IEA
GO:0006879	Process	Intracellular iron ion homeostasis	IMP	28296633
GO:0007035	Process	Vacuolar acidification	NAS	32001091
GO:0007042	Process	Lysosomal lumen acidification	NAS	32001091, 33065002
GO:0010008	Component	Endosome membrane	IEA
GO:0010008	Component	Endosome membrane	NAS	32001091
GO:0010008	Component	Endosome membrane	TAS
GO:0012505	Component	Endomembrane system	IEA
GO:0016020	Component	Membrane	IDA	33065002
GO:0016020	Component	Membrane	IEA
GO:0016469	Component	Proton-transporting two-sector ATPase complex	TAS	8733135
GO:0030641	Process	Regulation of cellular pH	IBA
GO:0030659	Component	Cytoplasmic vesicle membrane	IEA
GO:0030665	Component	Clathrin-coated vesicle membrane	IEA
GO:0030672	Component	Synaptic vesicle membrane	IEA
GO:0031267	Function	Small GTPase binding	IEA
GO:0031267	Function	Small GTPase binding	ISS
GO:0031410	Component	Cytoplasmic vesicle	IEA
GO:0033116	Component	Endoplasmic reticulum-Golgi intermediate compartment membrane	IEA
GO:0033176	Component	Proton-transporting V-type ATPase complex	IBA
GO:0033176	Component	Proton-transporting V-type ATPase complex	NAS	33065002
GO:0036035	Process	Osteoclast development	IEA
GO:0036035	Process	Osteoclast development	ISS
GO:0036295	Process	Cellular response to increased oxygen levels	IMP	28296633
GO:0045202	Component	Synapse	IEA
GO:0048388	Process	Endosomal lumen acidification	NAS	32001091
GO:0051452	Process	Intracellular pH reduction	NAS	32001091
GO:0061795	Process	Golgi lumen acidification	NAS	32001091
GO:0070062	Component	Extracellular exosome	HDA	19056867
GO:0097401	Process	Synaptic vesicle lumen acidification	IEA
GO:0098588	Component	Bounding membrane of organelle	IEA
GO:0099638	Process	Endosome to plasma membrane protein transport	IEA
GO:0099638	Process	Endosome to plasma membrane protein transport	ISS
GO:0141109	Function	Transporter activator activity	IEA
GO:1902600	Process	Proton transmembrane transport	IEA
GO:1902600	Process	Proton transmembrane transport	NAS	33065002

MIM	HGNC	e!Ensembl
300197	868	ENSG00000071553

Q15904

Protein name

V-type proton ATPase subunit S1 (V-ATPase subunit S1) (Protein XAP-3) (V-ATPase Ac45 subunit) (V-ATPase S1 accessory protein) (Vacuolar proton pump subunit S1)

Protein function

Accessory subunit of the proton-transporting vacuolar (V)-ATPase protein pump, which is required for luminal acidification of secretory vesicles (PubMed:33065002). Guides the V-type ATPase into specialized subcellular compartments, such as neuro

PDB

6WLW , 6WM2 , 6WM3 , 6WM4 , 7U4T , 7UNF

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF05827	ATP-synt_S1	321 → 468	Vacuolar ATP synthase subunit S1 (ATP6S1)	Family

Tissue specificity

TISSUE SPECIFICITY: widely expressed, with highest levels in brain and lowest in liver and duodenum. {ECO:0000269|PubMed:27231034}.

Sequence

MMAAMATARVRMGPRCAQALWRMPWLPVFLSLAAAAAAAAAEQQVPLVLWSSDRDLWAPA
ADTHEGHITSDLQLSTYLDPALELGPRNVLLFLQDKLSIEDFTAYGGVFGNKQDSAFSNL
ENALDLAPSSLVLPAVDWYAVSTLTTYLQEKLGASPLHVDLATLRELKLNASLPALLLIR
LPYTASSGLMAPREVLTGNDEVIGQVLSTLKSEDVPYTAALTAVRPSRVARDVAVVAGGL
GRQLLQKQPVSPVIHPPVSYNDTAPRILFWAQNFSVAYKDQWEDLTPLTFGVQELNLTGS
FWNDSFARLSLTYERLFGTTVTFKFILANRLYPVSARHWFTMERLEVHSNGSVAYFNASQ
VTGPSIYSFHCEYVSSLSKKGSLLVARTQPSPWQMMLQDFQIQAFNVMGEQFSYASDCAS
FFSPGIWMGLLTSLFMLFIFTYGLHMILSLKTMDRFDDHKGPTISLTQIV

Sequence length

470

Interactions

View interactions

	KEGG		Reactome
	Oxidative phosphorylation Metabolic pathways Lysosome Phagosome Vibrio cholerae infection Epithelial cell signaling in Helicobacter pylori infection Tuberculosis Hepatitis B Human papillomavirus infection Rheumatoid arthritis		Insulin receptor recycling Transferrin endocytosis and recycling Ion channel transport

Show/Hide Causal Diseases (1)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Immunodeficiency 47	Likely pathogenic; Pathogenic	rs2148221946, rs878853275, rs878853276, rs878853277, rs878853278, rs2523017845, rs2523016325, rs2523016265, rs2068680774, rs2068705545	RCV002248303 RCV000225137 RCV000225250 RCV000225332 RCV000225189 RCV003149154 RCV003485018 RCV003485019 RCV001171364 RCV001250487

Show/Hide Unknown Diseases (6)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
ALG2-congenital disorder of glycosylation	Conflicting classifications of pathogenicity	rs201620814	RCV005357969
ATP6AP1-related disorder	Uncertain significance; Benign; Likely benign; Conflicting classifications of pathogenicity	rs781797236, rs147496008, rs782690014, rs2523021401, rs782201766, rs148803059, rs201620814, rs1603384499	RCV004542177 RCV004543812 RCV004529215 RCV004529786 RCV004736426 RCV004543298 RCV004535837 RCV000991196
Decreased total lymphocyte count	Benign; Likely benign	rs140841742	RCV002227503
Decreased total neutrophil count	Benign; Likely benign	rs140841742	RCV002227503
Intellectual disability	Conflicting classifications of pathogenicity	rs148803059	RCV005625694
Nonpapillary renal cell carcinoma	Likely benign	rs143207881	RCV005898123

Show/Hide Text Mining Associations (30)

Disease Name	Relationship Type	References
Associations from Text MiningDisease associations identified through Pubtator
Adenocarcinoma of Lung	Associate	38177255
Agammaglobulinemia	Associate	37108612
Breast Neoplasms	Associate	3186693, 34228637, 36077333
Breast Neoplasms	Stimulate	8593862
Carcinogenesis	Associate	34228637
Carcinoma Hepatocellular	Associate	36651831
Central Nervous System Diseases	Associate	27231034
Cognition Disorders	Associate	32216104
Congenital Disorders of Glycosylation	Associate	32216104, 33407696, 35732497
Copper deficiency familial benign	Associate	32216104
COVID 19	Inhibit	34228637
COVID 19	Associate	34997207
Death	Associate	32216104
Dystonia	Associate	36651831
Ermine phenotype	Associate	32216104
Glioma	Associate	35266851, 36552760
Glycogen Storage Disease XIV	Associate	36651831, 37108612
Granular Cell Tumor	Associate	30166553, 35175560
Hernia Umbilical	Associate	35732497
Hydrocephalus	Associate	35732497
Hypospadias	Associate	35732497
Immunologic Deficiency Syndromes	Associate	27231034, 32216104, 35732497, 36651831
Liver Failure	Associate	32216104, 37108612
Lymphoma Follicular	Associate	34791836, 35482846
Lysosomal Storage Diseases	Associate	36651831
Neoplasms	Associate	26692014
Nervous System Diseases	Associate	35732497
Pectus Carinatum	Associate	35732497
Penis agenesis	Associate	35732497
Spinocerebellar Ataxias	Associate	32216104, 35732497, 36651831

ATP6AP1 (ATPase H+ transporting accessory protein 1)