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ATP6V1B1

ATPase H+ transporting V1 subunit B1

The ATP6V1B1 gene provides instructions for a key subunit of vacuolar H+-ATPase (V-ATPase), an enzyme essential for maintaining acid-base balance within the body. ATP6V1B1 is critical for forming part of the V-ATPase complex, which functions as a proton pump.

Chromosome 2p13.3 Autosomal recessive HGNC:853 Tier C
ATP6V1B1 2p13.3 p arm q arm 2

ATP6V1B1 is located on the short (p) arm of chromosome 2, at band 2p13.3. Arm ratio per GRCh38 - banding schematic.

Explore chromosome 2 in the library →

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Clinical tests that include this

Carrier Screening panel
ATP6V1B1 is 1 of 1,008 genes on this panel
Expanded carrier screening for recessive and X-linked conditions

Overview

The ATP6V1B1 gene encodes a subunit of the vacuolar H+-ATPase (V-ATPase), a large protein complex. V-ATPases are proton pumps that transport positively charged hydrogen atoms (protons) across cell membranes. This process is fundamental for regulating the relative acidity (pH) of cells and their surrounding environment, which is necessary for numerous biological reactions.

What the gene does

The V-ATPase containing the ATP6V1B1 subunit is specifically found in the inner ear and the nephrons of the kidneys. In the kidneys, nephrons filter waste products from the blood and reabsorb essential nutrients. The V-ATPase plays a crucial role in regulating the amount of acid excreted from the blood into the urine, thereby contributing to acid-base homeostasis. In the inner ear, this protein helps maintain the proper pH of the endolymph fluid, which is vital for auditory function. Impaired V-ATPase function due to ATP6V1B1 variants can lead to an inability of the kidneys to properly acidify urine and can affect inner ear function.

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Chromosome location

The ATP6V1B1 gene is located on chromosome 2 at position 2p13.3. This chromosomal location indicates its specific address within the human genome. The gene provides the genetic blueprint for a protein composed of 513 amino acids.

Protein structure

The ATP6V1B1 protein has a specific domain architecture, including a PDZ-binding motif located at amino acids 510-513. This motif is typically involved in protein-protein interactions, often linking membrane proteins to intracellular signalling pathways or cytoskeletal components.

Domain map · 513 amino acids
PDZ-binding (510-513)PDZ-binding510-5131~257513
Motif - short conserved sequence
🧬 Explore 3D structure on AlphaFold
UniProt:P15313Length:513 aaStructure:AlphaFold

Key variants

Variants within the ATP6V1B1 gene can alter the function of the encoded protein. These genetic changes can lead to impaired V-ATPase activity, affecting its ability to transport protons. Such alterations are typically inherited in an autosomal recessive pattern.

The table below shows the top 10 pathogenic or likely-pathogenic variants currently classified in ClinVar for ATP6V1B1.
View all on ClinVar →

Sample of pathogenic variants

10 pathogenic / likely-pathogenic variants from ClinVar, ranked by review status (expert-panel-reviewed first). This is a sample; recurrent founder variants in a specific population may not appear here - see the full ClinVar listing via the link above.

Variant (HGVS) Protein change Classification Evidence Associated condition
c.1143+2T>C
single nucleotide variant
 - Pathogenic/Likely pathogenic ★★☆☆ Renal tubular acidosis with progressive nerve deafness
c.1386C>A
single nucleotide variant
 p.Tyr462Ter Pathogenic/Likely pathogenic ★★☆☆ Renal tubular acidosis with progressive nerve deafness
c.27del
Deletion
 p.Leu12fs Pathogenic/Likely pathogenic ★★☆☆ Renal tubular acidosis with progressive nerve deafness
c.343_349del
Deletion
 p.Thr115fs Pathogenic/Likely pathogenic ★★☆☆ Renal tubular acidosis with progressive nerve deafness
c.408del
Deletion
 p.Pro137fs Pathogenic ★★☆☆ Renal tubular acidosis with progressive nerve deafness
c.448C>T
single nucleotide variant
 p.Gln150Ter Pathogenic/Likely pathogenic ★★☆☆ Renal tubular acidosis with progressive nerve deafness
c.481del
Deletion
 p.Glu161fs Pathogenic/Likely pathogenic ★★☆☆ Renal tubular acidosis with progressive nerve deafness
c.541C>T
single nucleotide variant
 p.Gln181Ter Pathogenic/Likely pathogenic ★★☆☆ Renal tubular acidosis with progressive nerve deafness
c.687+1G>A
single nucleotide variant
 - Pathogenic/Likely pathogenic ★★☆☆ Renal tubular acidosis with progressive nerve deafness
c.687+1G>T
single nucleotide variant
 - Pathogenic ★★☆☆ Renal tubular acidosis with progressive nerve deafness

Evidence stars indicate ClinVar review status. Individual variant interpretation should always be performed by a qualified clinical laboratory - many variants remain classified as Variants of Uncertain Significance (VUS) pending more research.

Associated conditions

Pathogenic variants in the ATP6V1B1 gene are associated with inherited conditions, such as Renal tubular acidosis type I (ATP6V1B1) (AR). This condition is characterised by metabolic acidosis (excess acid in the blood), bone weakness, and sensorineural hearing loss resulting from inner ear changes.

  • Renal tubular acidosis type I (ATP6V1B1)
    Renal
    AR
    Dedicated page coming soon

Inheritance pattern

Conditions caused by pathogenic ATP6V1B1 variants typically follow autosomal recessive inheritance.

♀ Carrier parent 1 altered copy ♂ Carrier parent 1 altered copy Affected Carrier Carrier Unaffected Affected Carrier Unaffected Circles = females · Squares = males

When both parents are carriers, each child has a 25% chance of being affected, 50% of being a carrier, and 25% of being unaffected.

Carrier frequency by population How common is heterozygous ATP6V1B1 carrier status across ancestry groups?

UK clinical status

The ATP6V1B1 gene is recognised within the NHS Genomic Medicine Service, indicating its clinical significance in the UK. It is listed on several green-status PanelApp panels, including DDG2P, Monogenic hearing loss (R67), Nephrocalcinosis or nephrolithiasis (R256), and Renal tubulopathies (R198).

Green-listed
High evidence · clinically actionable in NHS testing
Included in NHS GMS signed-off panels
Monogenic hearing loss · R67 NHS GMS → Nephrocalcinosis or nephrolithiasis · R256 NHS GMS → Renal tubulopathies · R198 NHS GMS → DDG2P NHS GMS →
NHS Genomic Medicine Service Jeen carrier screening

Sources: NHS GMS PanelApp · Genomics England PanelApp · NHS National Genomic Test Directory

Frequently asked questions

What is the primary function of the ATP6V1B1 gene?

The ATP6V1B1 gene provides instructions for a subunit of vacuolar H+-ATPase (V-ATPase), a proton pump critical for regulating the pH levels within cells and their surrounding environments, particularly in the kidneys and inner ear.

What conditions are associated with variants in the ATP6V1B1 gene?

Variants in the ATP6V1B1 gene are associated with Renal tubular acidosis type I (ATP6V1B1) (AR). This condition often presents with metabolic acidosis, bone weakness, and sensorineural hearing loss.

How is the ATP6V1B1 gene relevant to kidney function?

In the kidneys, the protein produced by the ATP6V1B1 gene is part of a V-ATPase in nephrons, helping to regulate the removal of acid from the blood into the urine. This process is essential for maintaining the body's proper acid-base balance.

References

  1. Mohebbi N, Vargas-Poussou R, Hegemann SC. Homozygous and compound heterozygous mutations in the ATP6V1B1 gene in patients with renal tubular acidosis and sensorineural hearing loss. Clinical genetics. 2013. PMID: 22509993
  2. Batlle D, Haque SK. Genetic causes and mechanisms of distal renal tubular acidosis. Nephrology, dialysis, transplantation : official publication of the European Dialysis and Transplant Association - European Renal Association. 2012. PMID: 23114896
  3. Alper SL. Familial renal tubular acidosis. Journal of nephrology. 2010. PMID: 21170890
  4. Sethi SK, Singh N, Gil H. Genetic studies in a family with distal renal tubular acidosis and sensorineural deafness. Indian pediatrics. 2009. PMID: 19478356
  5. Andreucci E, Bianchi B, Carboni I. Inner ear abnormalities in four patients with dRTA and SNHL: clinical and genetic heterogeneity. Pediatric nephrology (Berlin, Germany). 2009. PMID: 19639346
  6. Nikali K, Vanegas JJ, Burley MW. Extensive founder effect for distal renal tubular acidosis (dRTA) with sensorineural deafness in an isolated South American population. American journal of medical genetics. Part A. 2008. PMID: 18798332
  7. Gil H, Santos F, García E. Distal RTA with nerve deafness: clinical spectrum and mutational analysis in five children. Pediatric nephrology (Berlin, Germany). 2007. PMID: 17216496
  8. Stover EH, Borthwick KJ, Bavalia C. Novel ATP6V1B1 and ATP6V0A4 mutations in autosomal recessive distal renal tubular acidosis with new evidence for hearing loss. Journal of medical genetics. 2002. PMID: 12414817
Educational content. This page is not medical or genetic advice, is not individually reviewed by a clinician for each reader, and should not replace a consultation with a qualified healthcare professional or genetic counsellor. If you are considering genetic testing or acting on a test result, book a consultation.
Data sources Last updated 4 October 2026. Content compiled from HGNC · MedlinePlus Genetics · ClinGen · Genomics England PanelApp · NHS National Genomic Test Directory · ClinVar · UniProt · AlphaFold .