ATP6AP1L

pseudo

ATPase H+ transporting accessory protein 1 like (pseudogene)

Gene summary

Predicted to be located in bounding membrane of organelle; cytoplasmic vesicle membrane; and endomembrane system. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

N/A

Inheritance

—

ClinVar variants

—

Top phenotype

Inborn genetic diseases

gnomAD constraint

pLI —, LoF o/e 0.4

Max pathogenic AF

—

Genomic locus

chr5:82,295,449-82,318,300

External References & Databases

Ensembl (ENSG00000205464)

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ATP6AP1L variants in ClinVar

2 Conditions Cataloged

Inborn genetic diseasesTotal: 10

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript . Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB
synonymous
missense
nonsense
start loss
frameshift
splice donor/acceptor (+/-2bp)
Total	0	0	0	0	0

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 0 of 0 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
No transcripts match your selected source or search query.

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

ATP hydrolysis coupled proton transport
regulation of cellular pH

Molecular Function

proton-transporting ATP synthase activity, rotational mechanism
proton-transporting ATPase activity, rotational mechanism

Cellular Component

integral component of membrane
proton-transporting V-type ATPase, V1 domain
plasma membrane proton-transporting V-type ATPase complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000380167
Coding exons: 4
Length: 107516
Individuals with no LoFs: 125712
Homozygous LoFs: 1
Heterozygous LoFs: 33
Defined: 125746
p: 0.000135

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.338	115	126	0.915	0.00000725	1437
Missense (PolyPhen)		27	29.857	0.9043		425
Synonymous	0.955	47	56.1	0.838	0.00000339	457
Loss of Function	1.76	4	10.0	0.400	5.77e-7	97

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000067	0.000062	rare
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00017	0.00016	rare
Finnish	0.00028	0.00028	rare
European (Non-Finnish)	0.00018	0.00017	rare
South Asian	0.000042	0.000033	rare
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.279
RVIS EVS: 0.59
RVIS percentile EVS: 82.51

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Indispensability pred.: N
Indispensability score: 0.132

Gene Damage Prediction

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