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	525
Gene name	ATPase H+ transporting V1 subunit B1
Gene symbol	ATP6V1B1
Synonyms (NCBI Gene)	ATP6B1DRTA2RTA1BVATBVMA2VPP3
Chromosome	2
Chromosome location	2p13.3
Summary	This gene encodes a component of vacuolar ATPase (V-ATPase), a multisubunit enzyme that mediates acidification of eukaryotic intracellular organelles. V-ATPase dependent organelle acidification is necessary for such intracellular processes as protein sort

Show/Hide all (19)

SNP ID	Visualize variation	Clinical significance	Consequence
rs121964879	C>T	Pathogenic	Genic upstream transcript variant, stop gained, coding sequence variant
rs121964880	T>C	Likely-pathogenic, pathogenic	Coding sequence variant, missense variant
rs121964881	G>A	Pathogenic	Coding sequence variant, missense variant
rs145536062	C>T	Pathogenic-likely-pathogenic, likely-pathogenic	Coding sequence variant, stop gained
rs145735762	C>G,T	Conflicting-interpretations-of-pathogenicity, uncertain-significance	Missense variant, coding sequence variant
rs527738649	T>C	Likely-benign, conflicting-interpretations-of-pathogenicity	Genic upstream transcript variant, coding sequence variant, missense variant
rs531239712	G>A,C	Uncertain-significance, conflicting-interpretations-of-pathogenicity	Coding sequence variant, missense variant
rs727504746	G>A	Pathogenic	Splice donor variant
rs781838938	C>G,T	Pathogenic	Coding sequence variant, missense variant
rs781969081	C>-,CC	Pathogenic	Frameshift variant, coding sequence variant
rs782138777	C>T	Pathogenic	Coding sequence variant, stop gained
rs782152033	C>-	Pathogenic	Frameshift variant, coding sequence variant
rs782723581	G>A,T	Pathogenic	Splice donor variant
rs1064797052	A>-	Pathogenic	Coding sequence variant, frameshift variant
rs1553419751	G>T	Likely-pathogenic	Stop gained, coding sequence variant
rs1553420702	G>C	Pathogenic	Splice donor variant
rs1572919267	G>C	Pathogenic	Splice acceptor variant
rs1572922954	G>C	Likely-pathogenic	Splice acceptor variant
rs1572924733	C>G	Likely-pathogenic	Coding sequence variant, stop gained

Show/Hide all (38)

miRTarBase ID	miRNA	Experiments	Reference
MIRT568914	hsa-miR-1321	PAR-CLIP	20371350
MIRT568912	hsa-miR-4739	PAR-CLIP	20371350
MIRT568913	hsa-miR-4756-5p	PAR-CLIP	20371350
MIRT568911	hsa-miR-1247-3p	PAR-CLIP	20371350
MIRT568910	hsa-miR-4537	PAR-CLIP	20371350
MIRT568909	hsa-miR-4419a	PAR-CLIP	20371350
MIRT568908	hsa-miR-4510	PAR-CLIP	20371350
MIRT568907	hsa-miR-6127	PAR-CLIP	20371350
MIRT568906	hsa-miR-6129	PAR-CLIP	20371350
MIRT568905	hsa-miR-6130	PAR-CLIP	20371350
MIRT568904	hsa-miR-6133	PAR-CLIP	20371350
MIRT568903	hsa-miR-6827-5p	PAR-CLIP	20371350
MIRT568902	hsa-miR-149-3p	PAR-CLIP	20371350
MIRT568901	hsa-miR-4728-5p	PAR-CLIP	20371350
MIRT568900	hsa-miR-6785-5p	PAR-CLIP	20371350
MIRT568899	hsa-miR-6883-5p	PAR-CLIP	20371350
MIRT568898	hsa-miR-3175	PAR-CLIP	20371350
MIRT568914	hsa-miR-1321	PAR-CLIP	20371350
MIRT568912	hsa-miR-4739	PAR-CLIP	20371350
MIRT568913	hsa-miR-4756-5p	PAR-CLIP	20371350
MIRT568911	hsa-miR-1247-3p	PAR-CLIP	20371350
MIRT568910	hsa-miR-4537	PAR-CLIP	20371350
MIRT568909	hsa-miR-4419a	PAR-CLIP	20371350
MIRT568908	hsa-miR-4510	PAR-CLIP	20371350
MIRT568907	hsa-miR-6127	PAR-CLIP	20371350
MIRT568906	hsa-miR-6129	PAR-CLIP	20371350
MIRT568905	hsa-miR-6130	PAR-CLIP	20371350
MIRT568904	hsa-miR-6133	PAR-CLIP	20371350
MIRT568903	hsa-miR-6827-5p	PAR-CLIP	20371350
MIRT568902	hsa-miR-149-3p	PAR-CLIP	20371350
MIRT568901	hsa-miR-4728-5p	PAR-CLIP	20371350
MIRT568900	hsa-miR-6785-5p	PAR-CLIP	20371350
MIRT568899	hsa-miR-6883-5p	PAR-CLIP	20371350
MIRT568898	hsa-miR-3175	PAR-CLIP	20371350
MIRT809088	hsa-miR-4264	CLIP-seq
MIRT809089	hsa-miR-4760-3p	CLIP-seq
MIRT809090	hsa-miR-4797-3p	CLIP-seq
MIRT809091	hsa-miR-935	CLIP-seq

Show/Hide all (56)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000166	Function	Nucleotide binding	IEA
GO:0000221	Component	Vacuolar proton-transporting V-type ATPase, V1 domain	IDA	33065002
GO:0000221	Component	Vacuolar proton-transporting V-type ATPase, V1 domain	IEA
GO:0001503	Process	Ossification	IMP	16433694
GO:0003091	Process	Renal water homeostasis	IEA
GO:0003096	Process	Renal sodium ion transport	IEA
GO:0005515	Function	Protein binding	IPI	32814053
GO:0005524	Function	ATP binding	IEA
GO:0005737	Component	Cytoplasm	IEA
GO:0005737	Component	Cytoplasm	ISS	14585495
GO:0005829	Component	Cytosol	IEA
GO:0005829	Component	Cytosol	TAS
GO:0005886	Component	Plasma membrane	IEA
GO:0005902	Component	Microvillus	IEA
GO:0005902	Component	Microvillus	ISS	14585495
GO:0006693	Process	Prostaglandin metabolic process	IEA
GO:0006811	Process	Monoatomic ion transport	IEA
GO:0006885	Process	Regulation of pH	IEA
GO:0006885	Process	Regulation of pH	IMP	9916796
GO:0006885	Process	Regulation of pH	IMP	12414817
GO:0007035	Process	Vacuolar acidification	IBA
GO:0007605	Process	Sensory perception of sound	IMP	9916796
GO:0007605	Process	Sensory perception of sound	IMP	20622307
GO:0010468	Process	Regulation of gene expression	IEA
GO:0015078	Function	Proton transmembrane transporter activity	IEA
GO:0015078	Function	Proton transmembrane transporter activity	ISS	14585495
GO:0016020	Component	Membrane	IEA
GO:0016241	Process	Regulation of macroautophagy	NAS	22982048
GO:0016323	Component	Basolateral plasma membrane	IEA
GO:0016323	Component	Basolateral plasma membrane	ISS	14585495
GO:0016324	Component	Apical plasma membrane	IDA	16769747, 16928804, 29993276
GO:0016324	Component	Apical plasma membrane	IEA
GO:0016328	Component	Lateral plasma membrane	IEA
GO:0016328	Component	Lateral plasma membrane	ISS	14585495
GO:0016471	Component	Vacuolar proton-transporting V-type ATPase complex	IMP	12414817
GO:0030534	Process	Adult behavior	IEA
GO:0033180	Component	Proton-transporting V-type ATPase, V1 domain	IEA
GO:0035812	Process	Renal sodium excretion	IEA
GO:0042048	Process	Olfactory behavior	IEA
GO:0042472	Process	Inner ear morphogenesis	IMP	19639346
GO:0044877	Function	Protein-containing complex binding	IEA
GO:0045851	Process	PH reduction	IMP	16769747, 20622307
GO:0046034	Process	ATP metabolic process	IEA
GO:0046034	Process	ATP metabolic process	IEA
GO:0046961	Function	Proton-transporting ATPase activity, rotational mechanism	IBA
GO:0046961	Function	Proton-transporting ATPase activity, rotational mechanism	IEA
GO:0055064	Process	Chloride ion homeostasis	IEA
GO:0055074	Process	Calcium ion homeostasis	IMP	20622307
GO:0055075	Process	Potassium ion homeostasis	IEA
GO:0070062	Component	Extracellular exosome	HDA	19056867, 19199708, 23533145
GO:0070072	Process	Vacuolar proton-transporting V-type ATPase complex assembly	IMP	16769747
GO:0097254	Process	Renal tubular secretion	IMP	12414817
GO:0097401	Process	Synaptic vesicle lumen acidification	IEA
GO:0098850	Component	Extrinsic component of synaptic vesicle membrane	IEA
GO:1902600	Process	Proton transmembrane transport	IEA
GO:1902600	Process	Proton transmembrane transport	IMP	12414817, 16769747

MIM	HGNC	e!Ensembl
192132	853	ENSG00000116039

P15313

Protein name

V-type proton ATPase subunit B, kidney isoform (V-ATPase subunit B 1) (Endomembrane proton pump 58 kDa subunit) (Vacuolar proton pump subunit B 1)

Protein function

Non-catalytic subunit of the V1 complex of vacuolar(H+)-ATPase (V-ATPase), a multisubunit enzyme composed of a peripheral complex (V1) that hydrolyzes ATP and a membrane integral complex (V0) that translocates protons (PubMed:16769747). V-ATPase

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF02874	ATP-synt_ab_N	44 → 110	ATP synthase alpha/beta family, beta-barrel domain	Domain
PF00006	ATP-synt_ab	167 → 393	ATP synthase alpha/beta family, nucleotide-binding domain	Domain

Tissue specificity

TISSUE SPECIFICITY: Kidney; localizes to early distal nephron, encompassing thick ascending limbs and distal convoluted tubules (at protein level) (PubMed:16769747, PubMed:29993276). Expressed in the cochlea and endolymphatic sac (PubMed:9916796). {ECO:00

Sequence

MAMEIDSRPGGLPGSSCNLGAAREHMQAVTRNYITHPRVTYRTVCSVNGPLVVLDRVKFA
QYAEIVHFTLPDGTQRSGQVLEVAGTKAIVQVFEGTSGIDARKTTCEFTGDILRTPVSED
MLGRVFNGSGKPIDKGPVVMAEDFLDINGQPINPHSRIYPEEMIQTGISPIDVMNSIARG
QKIPIFSAAGLPHNEIAAQICRQAGLVKKSKAVLDYHDDNFAIVFAAMGVNMETARFFKS
DFEQNGTMGNVCLFLNLANDPTIERIITPRLALTTAEFLAYQCEKHVLVILTDMSSYAEA
LREVSAAREEVPGRRGFPGYMYTDLATIYERAGRVEGRGGSITQIPILTMPNDDITHPIP
DLTGFITEGQIYVDRQLHNRQIYPPINVLPSLSRLMKSAIGEGMTRKDHGDVSNQLYACY
AIGKDVQAMKAVVGEEALTSEDLLYLEFLQKFEKNFINQGPYENRSVFESLDLGWKLLRI
FPKEMLKRIPQAVIDEFYSREGALQDLAPDTAL

Sequence length

513

Interactions

View interactions

	KEGG		Reactome
	Oxidative phosphorylation Metabolic pathways Phagosome mTOR signaling pathway Synaptic vesicle cycle Collecting duct acid secretion Vibrio cholerae infection Epithelial cell signaling in Helicobacter pylori infection Human papillomavirus infection Rheumatoid arthritis		ROS and RNS production in phagocytes Insulin receptor recycling Transferrin endocytosis and recycling Amino acids regulate mTORC1 Ion channel transport

269

Show/Hide Causal Diseases (14)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Abnormality of the genitourinary system	Likely pathogenic	rs2104827591	RCV001814505
ATP6V1B1-related disorder	Likely pathogenic; Pathogenic	rs1680488861, rs781969081, rs1572919267	RCV003408066 RCV003411471 RCV003413587
Distal renal tubular acidosis	Pathogenic; Likely pathogenic	rs781838938, rs121964880, rs782152033	RCV001849357 RCV001849262 RCV001849427
Gastric cancer	Likely pathogenic; Pathogenic	rs121964881	RCV005887475
Malignant tumor of urinary bladder	Likely pathogenic	rs1363121734	RCV005935043
Nephrocalcinosis	Likely pathogenic; Pathogenic	rs121964880, rs1572919267	RCV000662318 RCV000852376
Nephrolithiasis	Likely pathogenic; Pathogenic	rs121964880	RCV000662318
Ovarian serous cystadenocarcinoma	Likely pathogenic; Pathogenic	rs121964881	RCV005887476
Polydactyly, postaxial, type A1	Pathogenic	rs1572919267	RCV000852376
Rare genetic deafness	Pathogenic	rs727504746	RCV000156046
Renal tubular acidosis	Pathogenic	rs1288346981	RCV001328240
Renal tubular acidosis with progressive nerve deafness	Pathogenic; Likely pathogenic	rs2104834712, rs1553415274, rs2104831698, rs2104834809, rs782484337, rs1680488861, rs1558681020, rs782151715, rs2104834299, rs1679840748, rs2104825177, rs1553416787, rs727504746, rs2466301518, rs2466285143 View all (28 more)	RCV002504641 RCV001785889 RCV001801011 RCV001843327 RCV001843691 RCV002486620 RCV005031907 RCV005025515 RCV002484808 RCV003226511 RCV005607011 RCV002222881 RCV001271396 RCV002470029 RCV002470410 RCV003388161 RCV005028012 RCV003226722 RCV003226723 RCV000763500 RCV000013011 RCV000013013 RCV000013014 RCV000013015 RCV003337746 RCV003338028 RCV005030108 RCV005030161 RCV005030315 RCV003991234 RCV003991255 RCV000986767 RCV001271397 RCV000671126 RCV000670148 RCV000670146 RCV002221248 RCV005624429 RCV000986768 RCV001836093 RCV001827329 RCV002484268 RCV001836175 RCV001785799 RCV001251495
Renal tubular acidosis, distal, 3, with or without sensorineural hearing loss	Likely pathogenic	rs2466287299	RCV004763657
Renal tubulopathies	Pathogenic	rs782152033	RCV006252567

Show/Hide Unknown Diseases (6)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Cervical cancer	Benign	rs797042448	RCV005919739
Clear cell carcinoma of kidney	Likely benign	rs782584396	RCV005921095
Hearing impairment	Uncertain significance; Conflicting classifications of pathogenicity	rs782166295, rs727505222	RCV001375316 RCV001375115
Lung cancer	Uncertain significance	rs377624239	RCV005909153
Nonpapillary renal cell carcinoma	Likely benign	rs782205270	RCV005912759
Usher syndrome	Uncertain significance	rs2104831947	RCV001375105

Show/Hide Text Mining Associations (23)

Disease Name	Relationship Type	References
Associations from Text MiningDisease associations identified through Pubtator
Acidosis	Associate	38447554
Acidosis Renal Tubular	Associate	12414817, 12566520, 19478356, 20622307, 23923981, 24252324, 24975934, 25285676, 26208211, 26453614, 26571219, 28188436, 28233610, 29202719, 29627839 View all (7 more)
Breast Neoplasms	Associate	33000417
Carcinoma Ovarian Epithelial	Associate	36999629
Chromosome Aberrations	Associate	26453614
Deafness	Associate	12414817
Disease	Associate	28233610
Drug Related Side Effects and Adverse Reactions	Associate	33000417
Fanconi Syndrome	Associate	28188436
Growth Disorders	Associate	30230413, 38445406
Hearing Loss	Associate	12414817, 20622307
Hearing Loss Sensorineural	Associate	10577919, 19478356, 20622307, 23923981, 24252324, 24975934, 28188436, 29627839, 30558562, 38445406
Hypokalemia	Associate	30558562
Hypoxia	Associate	35711425
Kidney Calculi	Associate	26453614
Kidney Diseases	Associate	26208211, 36408280
Neoplasms	Associate	33000417, 36999629
Nephrocalcinosis	Associate	28893421, 35612621
Nephrolithiasis	Associate	28893421
Osteopetrosis	Associate	12566520
Ovarian Neoplasms	Associate	36999629
Renal Insufficiency Chronic	Associate	28233610
Renal tubular acidosis distal autosomal recessive	Associate	12414817

ATP6V1B1 (ATPase H+ transporting V1 subunit B1)