ATP6V1G3

ATPase H+ transporting V1 subunit G3, the group of V-type ATPase subunits

Basic information

Region (hg38): 1:198523222-198540945

Links

ENSG00000151418 ∙ NCBI:127124 ∙ OMIM:618071 ∙ HGNC:18265 ∙ Uniprot:Q96LB4 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ATP6V1G3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ATP6V1G3 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			8	2		10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	8	2	0

Variants in ATP6V1G3

This is a list of pathogenic ClinVar variants found in the ATP6V1G3 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
1-198523401-G-C		not specified	Uncertain significance (Aug 04, 2023)
1-198523404-C-T		not specified	Uncertain significance (Jun 07, 2025)
1-198523432-T-C		not specified	Likely benign (Aug 13, 2021)
1-198523446-C-T		not specified	Uncertain significance (Dec 18, 2023)
1-198523453-G-T		not specified	Uncertain significance (Oct 29, 2024)
1-198523467-C-T		not specified	Uncertain significance (Feb 04, 2025)
1-198523494-T-C		not specified	Uncertain significance (Dec 22, 2023)
1-198523507-T-A		not specified	Uncertain significance (Feb 07, 2025)
1-198523512-C-T		not specified	Likely benign (Jul 22, 2024)
1-198523515-A-C		not specified	Uncertain significance (Feb 05, 2025)
1-198523519-T-C		not specified	Uncertain significance (Aug 15, 2023)
1-198529086-A-G		not specified	Uncertain significance (Dec 28, 2022)
1-198540629-T-G		not specified	Uncertain significance (Dec 27, 2023)
1-198540638-A-G		not specified	Uncertain significance (Nov 07, 2022)
1-198540642-G-C		not specified	Uncertain significance (Jan 27, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ATP6V1G3	protein_coding	protein_coding	ENST00000281087	3	17724

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.107	0.786	125393	0	11	125404	0.0000439

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.254	51	56.4	0.905	0.00000248	783
Missense in Polyphen		11	17.973	0.61203		262
Synonymous	0.585	15	18.2	0.825	7.83e-7	185
Loss of Function	1.26	2	5.05	0.396	2.80e-7	60

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000171	0.000171
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000475	0.0000441
Middle Eastern	0.00	0.00
South Asian	0.0000358	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalytic subunit of the peripheral V1 complex of vacuolar ATPase (V-ATPase). V-ATPase is responsible for acidifying a variety of intracellular compartments in eukaryotic cells.
• Pathway: mTOR signaling pathway - Homo sapiens (human);Synaptic vesicle cycle - Homo sapiens (human);Phagosome - Homo sapiens (human);Epithelial cell signaling in Helicobacter pylori infection - Homo sapiens (human);Oxidative phosphorylation - Homo sapiens (human);Collecting duct acid secretion - Homo sapiens (human);Vibrio cholerae infection - Homo sapiens (human);Rheumatoid arthritis - Homo sapiens (human);Signal Transduction;Transferrin endocytosis and recycling;Ion channel transport;Insulin receptor recycling;Signaling by Insulin receptor;ROS, RNS production in phagocytes;Innate Immune System;Immune System;Transport of small molecules;Iron uptake and transport;Signaling by Receptor Tyrosine Kinases (Consensus)

Recessive Scores

• pRec: 0.117

Intolerance Scores

• loftool: 0.711
• rvis_EVS: 1.1
• rvis_percentile_EVS: 91.93

Haploinsufficiency Scores

• pHI: 0.0962
• hipred: N
• hipred_score: 0.187

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Atp6v1g3

Gene ontology

• Biological process: insulin receptor signaling pathway;transferrin transport;ion transmembrane transport;proton transmembrane transport
• Cellular component: cytosol;plasma membrane;vacuolar proton-transporting V-type ATPase complex
• Molecular function: proton-exporting ATPase activity, phosphorylative mechanism;ATPase binding