ATP10D

protein-coding

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

Gene summary

Enables glycosylceramide flippase activity. Predicted to be involved in phospholipid translocation. Located in endoplasmic reticulum and plasma membrane. Part of phospholipid-translocating ATPase complex. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_020453.4

Inheritance

—

ClinVar variants

U:171B:12

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.61

Max pathogenic AF

—

Genomic locus

chr4:47,485,275-47,593,486

External References & Databases

Ensembl (ENSG00000145246)

Transcript & Mutation Effects

hg38 • Region Span ~108.2 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 ATP10D variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 170

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_020453.4. 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			5 clinvar			5
missense			164 clinvar	11 clinvar	1 clinvar	176
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	171	11	1	183

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 29 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_020453.4	RefSeq	NP_065186.3	22	MANE Select
ENST00000273859.8	Ensembl	ENSP00000273859.3	22	MANE Select
ENST00000503288.6	Ensembl	ENSP00000421536.1	5	Standard
ENST00000504445.1	Ensembl	ENSP00000420909.1	9	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

cation transport
ion transmembrane transport
phospholipid translocation

Molecular Function

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

Cellular Component

nucleoplasm
endoplasmic reticulum
endoplasmic reticulum membrane
plasma membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000273859
Coding exons: 22
Length: 108199
Individuals with no LoFs: 125483
Homozygous LoFs: 0
Heterozygous LoFs: 265
Defined: 125748
p: 0.00105

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.662	714	766	0.933	0.0000392	9341
Missense (PolyPhen)		244	308.83	0.79007		3812
Synonymous	-0.194	288	284	1.01	0.0000149	2775
Loss of Function	3.01	42	69.0	0.608	0.00000402	781

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00025	0.00025	rare
Latino/Admixed American	0.00064	0.00064	rare
Ashkenazi Jewish	0.0049	0.0049	notable
East Asian	0.0017	0.0017	notable
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00098	0.00097	rare
South Asian	0.0014	0.0014	notable
Other	0.00099	0.00098	rare

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: 0.0945

Intolerance Scores

LoFtool: 0.284
RVIS EVS: 0.3
RVIS percentile EVS: 72.02

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.230

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High