ATP10B

protein-coding

ATPase phospholipid transporting 10B (putative), the group of ATPase phospholipid transporting

Gene summary

Enables glycosylceramide flippase activity and phosphatidylcholine flippase activity. Involved in lysosomal membrane organization. Located in endoplasmic reticulum; late endosome membrane; and lysosomal membrane. Part of phospholipid-translocating ATPase complex. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_025153.3

Inheritance

—

ClinVar variants

U:234B:21

Top phenotype

ATP10B-associated developmental disorder

gnomAD constraint

pLI —, LoF o/e 0.82

Max pathogenic AF

—

Genomic locus

chr5:160,563,120-160,852,214

External References & Databases

Ensembl (ENSG00000118322)

Transcript & Mutation Effects

hg38 • Region Span ~289.1 kb

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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 ATP10B variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 230

not providedTotal: 10

ATP10B-associated developmental disorderTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_025153.3. 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	Sum
synonymous			4 clinvar	2 clinvar		6
missense			224 clinvar	17 clinvar	2 clinvar	243
nonsense			3 clinvar			3
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	234	19	2	255

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 20 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_025153.3	RefSeq	NP_079429.2	22	MANE Select
ENST00000327245.10	Ensembl	ENSP00000313600.5	22	MANE Select
NM_001366652.1	RefSeq	NP_001353581.1	22	Standard
NM_001366653.2	RefSeq	NP_001353582.1	8	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Ion channel transport
Transport of small molecules
Ion transport by P-type ATPases

Biological Process

phospholipid translocation

Molecular Function

magnesium ion binding
phospholipid-translocating ATPase activity
protein binding
ATP binding

Cellular Component

endoplasmic reticulum
endoplasmic reticulum membrane
plasma membrane
integral component of membrane
cytoplasmic vesicle membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000327245
Coding exons: 22
Length: 289095
Individuals with no LoFs: 123384
Homozygous LoFs: 17
Heterozygous LoFs: 1432
Defined: 124833
p: 0.00582

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.0886	832	825	1.01	0.0000462	9586
Missense (PolyPhen)		263	320.93	0.8195		3827
Synonymous	-0.121	326	323	1.01	0.0000185	2857
Loss of Function	1.38	53	65.0	0.815	0.00000340	732

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0011	0.0010	notable
Latino/Admixed American	0.00091	0.00087	rare
Ashkenazi Jewish	0.00080	0.00070	rare
East Asian	0.00084	0.00078	rare
Finnish	0.035	0.034	notable
European (Non-Finnish)	0.0057	0.0054	notable
South Asian	0.0014	0.0013	notable
Other	0.0032	0.0030	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Catalytic component of a P4-ATPase flippase complex which catalyzes the hydrolysis of ATP coupled to the transport of aminophospholipids from the outer to the inner leaflet of various membranes and ensures the maintenance of asymmetric distribution of phospholipids. Phospholipid translocation seems also to be implicated in vesicle formation and in uptake of lipid signaling molecules (Probable). {ECO:0000305}.;

Recessive Scores

pRec: 0.0998

Intolerance Scores

LoFtool: 0.322
RVIS EVS: 1.38
RVIS percentile EVS: 94.52

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.194

Gene Damage Prediction

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