ATP10A

Summary

ATP10A (ATPase phospholipid transporting 10A (putative), HGNC:13542) is a protein-coding gene on chromosome 15q12, encoding Phospholipid-transporting ATPase VA (O60312). Catalytic component of P4-ATPase flippase complex, which catalyzes the hydrolysis of ATP coupled to the transport of phosphatidylcholine (PC) from the outer to the inner leaflet of the plasma membrane.

The protein encoded by this gene belongs to the family of P-type cation transport ATPases, and to the subfamily of aminophospholipid-transporting ATPases. The aminophospholipid translocases transport phosphatidylserine and phosphatidylethanolamine from one side of a bilayer to another. This gene is maternally expressed. It maps within the most common interval of deletion responsible for Angelman syndrome, also known as ‘happy puppet syndrome’.

Source: NCBI Gene 57194 — RefSeq curated summary.

At a glance

• GWAS associations: 10
• Clinical variants (ClinVar): 547 total — 166 pathogenic, 6 likely-pathogenic
• Phenotypes (HPO): 27
• Dosage sensitivity (ClinGen): haploinsufficiency no evidence, triplosensitivity no evidence
• MANE Select transcript: NM_024490

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:13542
Approved symbol	ATP10A
Name	ATPase phospholipid transporting 10A (putative)
Location	15q12
Locus type	gene with protein product
Status	Approved
Aliases	ATPVA, ATPVC, KIAA0566
Ensembl gene	ENSG00000206190
Ensembl biotype	protein_coding
OMIM	605855
Entrez	57194

Gene structure

Transcript identifiers

Ensembl transcripts: 19 — 7 protein_coding, 5 protein_coding_CDS_not_defined, 4 retained_intron, 3 nonsense_mediated_decay

ENST00000356865, ENST00000389967, ENST00000553577, ENST00000555450, ENST00000555756, ENST00000555815, ENST00000619904, ENST00000620538, ENST00000673676, ENST00000673679, ENST00000673680, ENST00000673716, ENST00000673747, ENST00000673763, ENST00000673805, ENST00000673849, ENST00000673898, ENST00000674021, ENST00000674138

RefSeq mRNA: 1 — MANE Select: NM_024490 NM_024490

CCDS: CCDS32178

Canonical transcript exons

ENST00000555815 — 21 exons

Exon	Start	End
ENSE00001494339	25713674	25714241
ENSE00001494344	25718182	25718399
ENSE00001494345	25721657	25721909
ENSE00001494346	25723891	25724021
ENSE00001494347	25725951	25726082
ENSE00001494348	25727160	25727266
ENSE00001494350	25736056	25736141
ENSE00001494351	25781019	25781223
ENSE00001507396	25716730	25716924
ENSE00003495637	25694819	25695146
ENSE00003539032	25683286	25683486
ENSE00003542861	25680994	25681074
ENSE00003551054	25680810	25680914
ENSE00003553606	25680121	25680308
ENSE00003574514	25687703	25687828
ENSE00003634563	25678712	25679974
ENSE00003635537	25707976	25708102
ENSE00003636489	25701916	25702100
ENSE00003651044	25708197	25708300
ENSE00003683512	25691715	25691791
ENSE00003897378	25862648	25863327

Expression profiles

Bgee: expression breadth ubiquitous, 229 present calls, max score 93.77.

FANTOM5 (CAGE): breadth broad, TPM avg 2.8487 / max 79.9423, expressed in 818 samples.

FANTOM5 promoters (7 alternative TSS)

Promoter ID	TPM avg	Samples expressed
149019	2.0108	722
149017	0.5122	256
149018	0.1462	60
149015	0.1293	25
149016	0.0245	13
149021	0.0160	2
149020	0.0096	3

Top tissues by expression

282 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
endothelial cell	CL:0000115	93.77	gold quality
descending thoracic aorta	UBERON:0002345	93.76	gold quality
thoracic aorta	UBERON:0001515	92.94	gold quality
ascending aorta	UBERON:0001496	92.85	gold quality
aorta	UBERON:0000947	92.62	gold quality
popliteal artery	UBERON:0002250	92.51	gold quality
tibial artery	UBERON:0007610	92.51	gold quality
dorsal motor nucleus of vagus nerve	UBERON:0002870	92.10	gold quality
inferior olivary complex	UBERON:0002127	92.05	gold quality
renal glomerulus	UBERON:0000074	91.13	gold quality
metanephric glomerulus	UBERON:0004736	91.00	gold quality
left coronary artery	UBERON:0001626	90.45	gold quality
coronary artery	UBERON:0001621	90.06	gold quality
right coronary artery	UBERON:0001625	90.03	gold quality
lower esophagus muscularis layer	UBERON:0035833	88.47	gold quality
lower esophagus	UBERON:0013473	88.37	gold quality
granulocyte	CL:0000094	87.98	gold quality
blood vessel layer	UBERON:0004797	87.54	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	87.17	gold quality
upper lobe of left lung	UBERON:0008952	85.18	gold quality
epithelial cell of pancreas	CL:0000083	84.66	silver quality
visceral pleura	UBERON:0002401	84.43	gold quality
upper lobe of lung	UBERON:0008948	84.36	gold quality
right frontal lobe	UBERON:0002810	84.12	gold quality
right adrenal gland	UBERON:0001233	84.05	gold quality
substantia nigra	UBERON:0002038	84.00	gold quality
right adrenal gland cortex	UBERON:0035827	83.97	gold quality
midbrain	UBERON:0001891	83.64	gold quality
adrenal cortex	UBERON:0001235	83.43	gold quality
left adrenal gland	UBERON:0001234	83.30	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-CURD-119	yes	34.43
E-HCAD-35	yes	26.10
E-ANND-3	no	4.05

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

53 targeting ATP10A, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-3185	99.99	68.12	1959
HSA-MIR-4803	99.98	71.99	3117
HSA-MIR-19A-3P	99.98	75.33	2762
HSA-MIR-19B-3P	99.98	75.44	2754
HSA-MIR-302C-5P	99.97	72.56	3642
HSA-MIR-3143	99.93	71.96	3104
HSA-MIR-4697-3P	99.89	67.09	1123
HSA-MIR-137-3P	99.87	74.74	2401
HSA-MIR-205-5P	99.81	70.05	1557
HSA-MIR-4677-5P	99.70	70.09	1940
HSA-MIR-494-3P	99.70	71.45	2795
HSA-MIR-518A-5P	99.70	69.01	2209
HSA-MIR-527	99.70	69.01	2209
HSA-MIR-4729	99.69	72.18	4233
HSA-MIR-7152-5P	99.60	69.33	2094
HSA-MIR-6513-3P	99.59	69.77	1102
HSA-MIR-4261	99.59	70.30	3415
HSA-MIR-1252-3P	99.55	67.71	2862
HSA-MIR-4753-5P	99.54	68.51	1356
HSA-MIR-543	99.52	69.03	2595
HSA-MIR-143-3P	99.49	69.05	1457
HSA-MIR-4770	99.49	69.09	1451
HSA-MIR-6083	99.47	68.73	2393
HSA-MIR-147B-5P	99.45	70.62	2432
HSA-MIR-150-3P	99.43	70.51	920
HSA-MIR-3182	99.40	68.15	2454
HSA-MIR-377-3P	99.37	70.18	1905

Functional genomics

ClinGen dosage: haploinsufficiency 0 (no evidence), triplosensitivity 0 (no evidence). ClinGen Gene Dosage Map

Literature-anchored findings (GeneRIF, showing 6)

• ATP10A gene is imprinted, with preferential expression from the maternal allele in human brain. (PMID:11353404)
• report the generation of the complete genomic structure (PMID:12105293)
• In the analysis of a four-marker haplotype located in ATP10C, a statistically significant difference was observed in the frequency of one haplotype between male autism patients and controls (PMID:18186074)
• monoallelic expression of human ATP10A is variable in the population and is influenced by both gender and common genetic variation (PMID:18726118)
• has been proven that hypocaloric diets induce changes in the DNA methylation pattern in PBMCs (CpG18 of ATP10A and CpG 21 of WT1) and that some of these markers could be used as early indicators of response to metabolic effects of weight-loss programs (PMID:21209057)
• results suggest that enhanced PC flipping activity due to exogenous ATP10A expression alters the lipid composition at the plasma membrane (PMID:25947375)

Cross-species orthologs

6 orthologs

Organism	Symbol	Gene ID
danio_rerio	atp10a	ENSDARG00000061039
mus_musculus	Atp10a	ENSMUSG00000025324
rattus_norvegicus	Atp10a	ENSRNOG00000056228
drosophila_melanogaster	CG31729	FBGN0051729
caenorhabditis_elegans	tat-5	WBGENE00009498
caenorhabditis_elegans		WBGENE00017174

Paralogs (13): ATP9A (ENSG00000054793), ATP11B (ENSG00000058063), ATP11A (ENSG00000068650), ATP8B1 (ENSG00000081923), ATP11C (ENSG00000101974), ATP8B4 (ENSG00000104043), ATP10B (ENSG00000118322), ATP8A1 (ENSG00000124406), ATP8B3 (ENSG00000130270), ATP8A2 (ENSG00000132932), ATP8B2 (ENSG00000143515), ATP10D (ENSG00000145246), ATP9B (ENSG00000166377)

Protein

Protein identifiers

Phospholipid-transporting ATPase VA — O60312 (reviewed: O60312)

Alternative names: ATPase class V type 10A, Aminophospholipid translocase VA, P4-ATPase flippase complex alpha subunit ATP10A

All UniProt accessions (7): A0A669KAW0, A0A669KAY1, A0A669KB44, A0A669KBE2, A0A669KBH6, O60312, H0YJI4

UniProt curated annotations — full annotation on UniProt →

Function. Catalytic component of P4-ATPase flippase complex, which catalyzes the hydrolysis of ATP coupled to the transport of phosphatidylcholine (PC) from the outer to the inner leaflet of the plasma membrane. Initiates inward plasma membrane bending and recruitment of Bin/amphiphysin/Rvs (BAR) domain-containing proteins involved in membrane tubulation and cell trafficking. Facilitates ITGB1/beta1 integrin endocytosis, delaying cell adhesion and cell spreading on extracellular matrix. Has low flippase activity toward glucosylceramide (GlcCer).

Subunit / interactions. Component of a P4-ATPase flippase complex which consists of a catalytic alpha subunit ATP10A and an accessory beta subunit TMEM30A.

Subcellular location. Cell membrane. Endoplasmic reticulum membrane.

Tissue specificity. Widely expressed, with highest levels in kidney, followed by lung, brain, prostate, testis, ovary and small intestine.

Post-translational modifications. Autophosphorylated at the conserved aspartate of the P-type ATPase signature sequence.

Activity regulation. Inhibited under hypotonic conditions.

Similarity. Belongs to the cation transport ATPase (P-type) (TC 3.A.3) family. Type IV subfamily.

Isoforms (2)

UniProt ID	Names	Canonical?
O60312-1	1	yes
O60312-2	2

RefSeq proteins (1): NP_077816* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001757	P_typ_ATPase	Family
IPR006539	P-type_ATPase_IV	Family
IPR008250	ATPase_P-typ_transduc_dom_A_sf	Homologous_superfamily
IPR018303	ATPase_P-typ_P_site	PTM
IPR023214	HAD_sf	Homologous_superfamily
IPR023298	ATPase_P-typ_TM_dom_sf	Homologous_superfamily
IPR023299	ATPase_P-typ_cyto_dom_N	Homologous_superfamily
IPR032630	P_typ_ATPase_c	Domain
IPR032631	P-type_ATPase_N	Domain
IPR036412	HAD-like_sf	Homologous_superfamily
IPR044492	P_typ_ATPase_HD_dom	Domain

Pfam: PF13246, PF16209, PF16212

Enzyme classification (BRENDA):

• EC 7.6.2.1 — P-type phospholipid transporter (BRENDA: 22 organisms, 260 substrates, 62 inhibitors, 53 Km, 0 kcat entries)

Substrate kinetics (BRENDA)

4 substrates with measured Km, best-characterized 4. Km ranges are aggregated across organisms/conditions.

Substrate	Km (mM)	Measurements
ATP	0.016–2.215	41
P-NITROPHENYL PHOSPHATE	1.17–1.46	3
ACETYL PHOSPHATE	1.03–1.31	2
1-PALMITOYL-2-OLEOYL-SN-GLYCERO-3-PHOSPHO-L-SERI	0.111	1

Catalyzed reactions (Rhea), 2 shown:

• a 1,2-diacyl-sn-glycero-3-phosphocholine(out) + ATP + H2O = a 1,2-diacyl-sn-glycero-3-phosphocholine(in) + ADP + phosphate + H(+) (RHEA:38583)
• a beta-D-glucosyl-(1<->1’)-N-acylsphing-4-enine(out) + ATP + H2O = a beta-D-glucosyl-(1<->1’)-N-acylsphing-4-enine(in) + ADP + phosphate + H(+) (RHEA:66036)

UniProt features (67 total): binding site 18, sequence variant 12, topological domain 11, transmembrane region 10, region of interest 4, compositionally biased region 4, splice variant 2, mutagenesis site 2, chain 1, active site 1, modified residue 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-O60312-F1	71.30	0.32

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Catalytic / active sites (1): 427 (4-aspartylphosphate intermediate)

Ligand- & substrate-binding residues (18): 427; 427; 428; 429; 429; 700; 742; 766; 809; 889; 890; 891 …

Post-translational modifications (1): 466

Mutagenesis-validated functional residues (2):

Position	Phenotype
98–99	decreases pc-flipping activity.
203	impairs pc-flipping activity.

Function

Pathways and Gene Ontology

Reactome pathways

3 pathways

ID	Pathway
R-HSA-936837	Ion transport by P-type ATPases
R-HSA-382551	Transport of small molecules
R-HSA-983712	Ion channel transport

MSigDB gene sets: 305 (showing top): GOBP_REGULATION_OF_CELL_MORPHOGENESIS, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GOBP_PLASMA_MEMBRANE_ORGANIZATION, GOBP_REGULATION_OF_MEMBRANE_LIPID_DISTRIBUTION, BOYLAN_MULTIPLE_MYELOMA_D_DN, ATGTTAA_MIR302C, GOBP_ORGANOPHOSPHATE_ESTER_TRANSPORT, CAIRO_HEPATOBLASTOMA_CLASSES_DN, LEE_NAIVE_T_LYMPHOCYTE, ONKEN_UVEAL_MELANOMA_UP, FOSTER_TOLERANT_MACROPHAGE_UP, TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_10D_UP, GOBP_ENDOMEMBRANE_SYSTEM_ORGANIZATION, GOBP_REGULATION_OF_PLASMA_MEMBRANE_ORGANIZATION, GOBP_PHOSPHOLIPID_TRANSPORT

GO Biological Process (7): regulation of cell shape (GO:0008360), monoatomic ion transmembrane transport (GO:0034220), phospholipid translocation (GO:0045332), positive regulation of membrane tubulation (GO:1903527), lipid transport (GO:0006869), phospholipid transport (GO:0015914), lipid translocation (GO:0034204)

GO Molecular Function (11): magnesium ion binding (GO:0000287), ATP binding (GO:0005524), ATP hydrolysis activity (GO:0016887), phosphatidylcholine floppase activity (GO:0090554), ATPase-coupled intramembrane lipid carrier activity (GO:0140326), phosphatidylcholine flippase activity (GO:0140345), glycosylceramide flippase activity (GO:0140351), nucleotide binding (GO:0000166), transporter activity (GO:0005215), protein binding (GO:0005515), metal ion binding (GO:0046872)

GO Cellular Component (6): endoplasmic reticulum (GO:0005783), endoplasmic reticulum membrane (GO:0005789), plasma membrane (GO:0005886), membrane (GO:0016020), phospholipid-translocating ATPase complex (GO:1990531), endomembrane system (GO:0012505)

Reactome top-level categories

Rollup of top-2 pathways:

Category	Pathways
Ion channel transport	1
Transport of small molecules	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
lipid transport	2
ATP-dependent activity	2
phosphatidylcholine intramembrane carrier activity	2
cellular anatomical structure	2
regulation of cell morphogenesis	1
regulation of biological quality	1
monoatomic ion transport	1
transmembrane transport	1
phospholipid transport	1
lipid translocation	1
positive regulation of cellular component organization	1
plasma membrane tubulation	1
regulation of membrane tubulation	1
transport	1
lipid localization	1
organophosphate ester transport	1
regulation of membrane lipid distribution	1
metal ion binding	1
adenyl ribonucleotide binding	1
purine ribonucleoside triphosphate binding	1
ribonucleoside triphosphate phosphatase activity	1
floppase activity	1
intramembrane lipid carrier activity	1
glycerophospholipid flippase activity	1
sphingolipid intramembrane carrier activity	1
flippase activity	1
nucleoside phosphate binding	1
heterocyclic compound binding	1
molecular_function	1
binding	1
cation binding	1
cytoplasm	1
endomembrane system	1
intracellular membrane-bounded organelle	1
organelle membrane	1
nuclear outer membrane-endoplasmic reticulum membrane network	1
endoplasmic reticulum subcompartment	1
membrane	1
cell periphery	1
transporter complex	1

Protein interactions and networks

STRING

1004 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ATP10A	MKRN3	Q13064	895
ATP10A	UBE3A	P78355	883
ATP10A	SNRPN	P14648	867
ATP10A	MAGEL2	Q9UJ55	853
ATP10A	NDN	Q99608	829
ATP10A	GABRB3	P28472	825
ATP10A	OCA2	Q04671	739
ATP10A	TUBGCP5	Q96RT8	659
ATP10A	GABRG3	Q99928	647
ATP10A	NIPA2	Q8N8Q9	615
ATP10A	CDC50A	Q9NV96	614
ATP10A	GABRA5	P31644	609
ATP10A	NPAP1	Q9NZP6	606
ATP10A	NIPA1	Q7RTP0	603
ATP10A	BMP8A	Q7Z5Y6	566

IntAct

6 interactions, top by confidence:

A	B	Type	Score
ATP10A	TMEM30A	psi-mi:“MI:0915”(physical association)	0.660
ATP10A	HSPA8	psi-mi:“MI:0915”(physical association)	0.400
DYRK1A	TEX13D	psi-mi:“MI:0914”(association)	0.350

BioGRID (6): ATP10A (Biochemical Activity), ATP10A (Affinity Capture-RNA), ATP10A (Affinity Capture-MS), HSPA8 (Affinity Capture-MS), ATP10A (Affinity Capture-MS), ATP10A (Affinity Capture-MS)

ESM2 similar proteins: A0A131MCZ8, A3KMI0, A6H8T7, A7T1N0, B1AWN4, B7ZC32, D3ZEY4, D3ZSI8, F4INY4, G0S196, O36028, O54827, O60312, O60353, O60423, O62852, O94823, P21441, P22717, P32660, P34586, P49619, P49620, Q01063, Q03603, Q09891, Q12675, Q2NKY8, Q38SD2, Q39017, Q3UHC2, Q5BJS0, Q5CZZ9, Q5R607, Q5ZI74, Q6P158, Q6P5D3, Q6P5E8, Q6UQ17, Q7L2E3

Diamond homologs: A1A4J6, A3FIN4, B1AWN4, C7EXK4, D4AA47, D4ABB8, F1Q4S1, G0S196, G2X7W6, G5EBH1, O36028, O43520, O43861, O54827, O60312, O60423, O94296, O94823, P32660, P39524, P40527, P57792, P70704, P98195, P98196, P98197, P98198, P98199, P98200, P98204, P98205, Q09891, Q10309, Q12675, Q148W0, Q29449, Q37145, Q5BL50, Q6DFW5, Q6UQ17

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

547 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	166
Likely pathogenic	6
Uncertain significance	247
Likely benign	60
Benign	33

Top pathogenic / likely-pathogenic (30)

Variant ID	HGVS	Classification
144574	GRCh38/hg38 15q11.2-13.1(chr15:23462288-28275170)x1	Pathogenic
144586	GRCh38/hg38 15q11.2-13.1(chr15:23319714-28275170)x3	Pathogenic
144600	GRCh38/hg38 15q11.2-13.1(chr15:23319714-28347620)x1	Pathogenic
144613	GRCh38/hg38 15q11.2-13.1(chr15:22358243-28481444)x1	Pathogenic
144667	GRCh38/hg38 15q11.2-13.1(chr15:23462288-28314291)x1	Pathogenic
145034	GRCh38/hg38 15q11.2-13.1(chr15:23439508-28154050)x1	Pathogenic
145322	GRCh38/hg38 15q11.2-13.1(chr15:23462288-28694922)x1	Pathogenic
145368	GRCh38/hg38 15q11.2-13.1(chr15:22358243-28481444)x3	Pathogenic
145389	GRCh38/hg38 15q11.2-13.1(chr15:23410917-28275170)x1	Pathogenic
145987	GRCh38/hg38 15q11.2-13.1(chr15:23328044-28154050)x1	Pathogenic
146184	GRCh38/hg38 15q11.2-13.1(chr15:23462305-28275167)x3	Pathogenic
146185	GRCh38/hg38 15q11.2-13.1(chr15:23319714-28275167)x3	Pathogenic
146448	GRCh38/hg38 15q11.2-13.1(chr15:22358243-28481444)x1	Pathogenic
146597	GRCh38/hg38 15q11.2-13.1(chr15:23319714-28314256)x1	Pathogenic
146634	GRCh38/hg38 15q11.2-13.1(chr15:23462105-28290061)x1	Pathogenic
147585	GRCh38/hg38 15q11.2-13.1(chr15:23411789-28280314)x3	Pathogenic
147819	GRCh38/hg38 15q11.2-13.1(chr15:23462305-28314256)x1	Pathogenic
147960	GRCh38/hg38 15q11.2-13.1(chr15:23462305-28694952)x3	Pathogenic
148004	GRCh38/hg38 15q11.2-13.1(chr15:23319714-28314256)x3	Pathogenic
148318	GRCh38/hg38 15q11.2-13.1(chr15:23422864-28280314)x3	Pathogenic
148320	GRCh38/hg38 15q11.2-13.1(chr15:23422864-28280314)x1	Pathogenic
148846	GRCh38/hg38 15q11.2-12(chr15:23319714-25980547)x3	Pathogenic
148891	GRCh38/hg38 15q11.2-13.1(chr15:23422864-28314256)x1	Pathogenic
149074	GRCh38/hg38 15q11.2-13.1(chr15:22358243-28481444)x4	Pathogenic
149075	GRCh38/hg38 15q11.2-13.1(chr15:22358243-28481444)x3	Pathogenic
149915	GRCh38/hg38 15q11.2-13.1(chr15:23462288-28446301)x1	Pathogenic
150279	GRCh38/hg38 15q11.2-13.1(chr15:23319714-28446301)x3	Pathogenic
150488	GRCh38/hg38 15q11.2-13.1(chr15:23410917-28446301)x1	Pathogenic
150851	GRCh38/hg38 15q11.2-13.1(chr15:23999707-28314256)x1	Pathogenic
151262	GRCh38/hg38 15q11.2-13.1(chr15:23375044-28300209)x1	Pathogenic

SpliceAI

4807 predictions. Top by Δscore:

Variant	Effect	Δscore
15:25680989:CTT:C	donor_loss	1.0000
15:25680990:TTA:T	donor_loss	1.0000
15:25680991:TA:T	donor_loss	1.0000
15:25680992:A:AC	donor_gain	1.0000
15:25680992:ACCA:A	donor_loss	1.0000
15:25680993:C:CA	donor_loss	1.0000
15:25680993:C:CC	donor_gain	1.0000
15:25681072:TTC:T	acceptor_gain	1.0000
15:25681075:C:CC	acceptor_gain	1.0000
15:25701913:TA:T	donor_loss	1.0000
15:25701915:C:CT	donor_loss	1.0000
15:25708100:AACC:A	acceptor_loss	1.0000
15:25708101:ACCTA:A	acceptor_loss	1.0000
15:25708102:CCTA:C	acceptor_loss	1.0000
15:25708103:C:T	acceptor_loss	1.0000
15:25708104:T:A	acceptor_loss	1.0000
15:25708195:A:AC	donor_gain	1.0000
15:25708196:C:CC	donor_gain	1.0000
15:25708196:CT:C	donor_gain	1.0000
15:25708196:CTCT:C	donor_gain	1.0000
15:25708199:T:A	donor_gain	1.0000
15:25708300:ACTA:A	acceptor_loss	1.0000
15:25708301:C:CC	acceptor_gain	1.0000
15:25708301:CTA:C	acceptor_loss	1.0000
15:25708302:T:G	acceptor_loss	1.0000
15:25710972:C:A	donor_gain	1.0000
15:25714237:CTCAC:C	acceptor_gain	1.0000
15:25714238:TCAC:T	acceptor_gain	1.0000
15:25714239:CAC:C	acceptor_gain	1.0000
15:25714239:CACC:C	acceptor_gain	1.0000

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000014689 (15:25817190 C>T), RS1000042674 (15:25739029 T>C), RS1000044705 (15:25776582 A>G), RS1000053587 (15:25827261 A>G,T), RS1000053637 (15:25862226 G>T), RS1000057866 (15:25733887 A>G), RS1000058353 (15:25704642 T>G), RS1000072100 (15:25810400 C>A), RS1000085143 (15:25848247 T>C), RS1000116750 (15:25704893 G>A,C), RS1000117011 (15:25770061 A>G), RS1000122794 (15:25690876 A>G), RS1000136014 (15:25674174 A>G), RS1000149745 (15:25699699 T>A,C), RS1000155303 (15:25760741 G>A)

Disease associations

OMIM: gene MIM:605855 | disease phenotypes: MIM:176270, MIM:608636, MIM:105830, MIM:612269, MIM:600131, MIM:604233

GenCC curated gene-disease

Mondo (10): cerebral palsy (MONDO:0006497), Prader-Willi syndrome (MONDO:0008300), 15q11q13 microduplication syndrome (MONDO:0012081), Angelman syndrome (MONDO:0007113), autism spectrum disorder (MONDO:0005258), epilepsy, childhood absence, susceptibility to, 5 (MONDO:0012843), epilepsy, childhood absence, susceptibility to, 1 (MONDO:0020759), childhood absence epilepsy (MONDO:0010826), generalized epilepsy with febrile seizures plus (MONDO:0018214), neurodevelopmental disorder (MONDO:0700092)

Orphanet (6): Prader-Willi syndrome (Orphanet:739), 15q11q13 microduplication syndrome (Orphanet:238446), Angelman syndrome (Orphanet:72), Childhood absence epilepsy (Orphanet:64280), Genetic epilepsy with febrile seizure plus (Orphanet:36387), NON RARE IN EUROPE: Autism (Orphanet:106)

HPO phenotypes

27 total (28 of 27 shown, HPO-id order):

HPO	Term
HP:0000154	Wide mouth
HP:0000303	Mandibular prognathia
HP:0000708	Atypical behavior
HP:0000710	Hyperorality
HP:0000736	Short attention span
HP:0000748	Inappropriate laughter
HP:0000752	Hyperactivity
HP:0001010	Hypopigmentation of the skin
HP:0001250	Seizure
HP:0001251	Ataxia
HP:0001344	Absent speech
HP:0001513	Obesity
HP:0001999	Abnormal facial shape
HP:0002136	Broad-based gait
HP:0002307	Drooling
HP:0002353	EEG abnormality
HP:0002465	Poor speech
HP:0002591	Polyphagia
HP:0004485	Cessation of head growth
HP:0005599	Hypopigmentation of hair
HP:0006979	Sleep-wake cycle disturbance
HP:0007730	Iris hypopigmentation
HP:0008872	Feeding difficulties in infancy
HP:0008947	Floppy infant
HP:0031936	Delayed ability to walk
HP:0040082	Happy demeanor
HP:0410263	Brain imaging abnormality
HP:0100021	Cerebral palsy

GWAS associations

10 associations (top):

Study	Trait	p-value
GCST001208_6	Insulin resistance/response	7.000000e-06
GCST001208_8	Insulin resistance/response	4.000000e-07
GCST001538_21	Immune reponse to smallpox (secreted IFN-alpha)	6.000000e-09
GCST006627_63	Diastolic blood pressure	1.000000e-09
GCST008514_23	Peginterferon alfa-2a treatment response in chronic hepatitis B infection	8.000000e-06
GCST008755_4	Phenylephrine infusion rate during anesthesia	2.000000e-06
GCST010002_162	Refractive error	4.000000e-11
GCST010302_18	Cutaneous melanoma or hair colour	2.000000e-08
GCST010724_25	HOMA-B (corrected for HOMA-IR)	6.000000e-09
GCST010724_26	HOMA-B (corrected for HOMA-IR)	6.000000e-09

EFO canonical traits (6, from GWAS)

EFO ID	Trait name
EFO:0004645	response to vaccine
EFO:0004873	cytokine measurement
EFO:0006336	diastolic blood pressure
EFO:0010103	response to peginterferon alfa-2a
EFO:0003924	hair color
EFO:0004469	HOMA-B

MeSH disease descriptors (6)

Descriptor	Name	Tree numbers
D017204	Angelman Syndrome	C10.228.662.075; C16.131.077.095; C16.131.260.040; C16.320.180.040; C16.320.447.250
D002547	Cerebral Palsy	C10.228.140.140.254
D065886	Neurodevelopmental Disorders	F03.625
D011218	Prader-Willi Syndrome	C10.597.606.360.690; C16.131.077.730; C16.131.260.700; C16.320.180.700; C16.320.447.500; C18.654.726.750.500.740
C565808	Generalized Epilepsy with Febrile Seizures Plus (supp.)
C531619	Happy puppet syndrome (formerly) (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

PharmGKB clinical annotations

1 annotations.

Variant	Type	Level	Drugs	Phenotypes
rs12595802	Efficacy	3	duloxetine	Major Depressive Disorder

PharmGKB variants

2 variants.

Variant	Genes	Level	Score	#Clin annots	Drugs
rs12595802	ATP10A	3	0.00	1	duloxetine
rs12913988	ATP10A		0.00	0

GtoPdb / IUPHAR curated pharmacology

(IUPHAR/BPS Guide to Pharmacology — expert-curated)

Target class: transporter — P4 P-type ATPases: Phospholipid-transporting ATPases

CTD chemical–gene interactions

34 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
TL8-506	affects cotreatment, increases expression	1
triphenyl phosphate	affects expression	1
bisphenol A	increases methylation	1
deoxynivalenol	decreases expression	1
terbufos	increases methylation	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
sodium arsenite	increases expression	1
zinc chromate	decreases expression, increases abundance	1
benzo(e)pyrene	increases methylation	1
S-(1,2-dichlorovinyl)cysteine	affects cotreatment, decreases expression, affects response to substance, increases expression	1
di-n-butylphosphoric acid	affects expression	1
chromium hexavalent ion	decreases expression, increases abundance	1
abrine	decreases expression	1
bisphenol S	affects cotreatment, decreases methylation	1
jinfukang	affects cotreatment, decreases expression	1
(+)-JQ1 compound	decreases expression	1
Fulvestrant	affects cotreatment, decreases methylation	1
Benzo(a)pyrene	affects methylation, decreases methylation, increases methylation	1
Calcitriol	decreases expression	1
Cisplatin	decreases expression, affects cotreatment	1
Fonofos	increases methylation	1
Estradiol	affects cotreatment, increases expression	1
Lipopolysaccharides	affects cotreatment, decreases expression, affects response to substance, increases expression	1
Methapyrilene	increases methylation	1
Parathion	increases methylation	1
Phthalic Acids	increases methylation	1
Polychlorinated Biphenyls	affects expression	1
Progesterone	affects cotreatment, increases expression	1
Dihydrotestosterone	increases expression	1
Testosterone	decreases expression	1

Cellosaurus cell lines

1 cell lines: 1 cancer cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_B1EM	Abcam A-549 ATP10A KO	Cancer cell line	Male

Clinical trials (associated diseases)

300 trials via MONDO — disease-level, not drug-specific.

Trial	Phase	Status	Title
NCT00154830	PHASE4	COMPLETED	Alterations of Functional Activities and Leg Stiffness After Hamstring Lengthening in Cerebral Palsy Children
NCT00432055	PHASE4	COMPLETED	Effects of Botulinum Toxin Type A in Adults With Cerebral Palsy
NCT00549471	PHASE4	TERMINATED	Improvement After Botulinum Toxin Injections to the Arms in Children With Cerebral Palsy
NCT00752934	PHASE4	TERMINATED	Does Oral Baclofen Improve Care and Comfort in Spastic Children in Nursing Homes?
NCT00964639	PHASE4	COMPLETED	Postoperative Pain in Children With Cerebral Palsy After Pelvic and Femoral Osteotomies
NCT01386255	PHASE4	WITHDRAWN	Placebo Controlled Study of Baclofen for GERD in Children With Cerebral Palsy
NCT02546999	PHASE4	COMPLETED	Does Botulinum Toxin A Make Walking Easier in Children With Cerebral Palsy?
NCT02633241	PHASE4	COMPLETED	A Pilot Study of Dexmedetomidine-Propofol in Children Undergoing Magnetic Resonance Imaging
NCT03117322	PHASE4	COMPLETED	Synbiotic, Prebiotics and Probiotics in Children With Cerebral Palsy and Constipation
NCT03648658	PHASE4	UNKNOWN	Paracetamol Study in Patients With Low Muscle Mass
NCT04074265	PHASE4	COMPLETED	Peri-operative Use of a Pain Injection in Pediatric Patients With Cerebral Palsy
NCT04273737	PHASE4	TERMINATED	Amantadine in Treating Cognitive & Motor Impairments in Adolescents and Adults With Cerebral Palsy
NCT04523935	PHASE4	COMPLETED	Excessive Crying in Children With Cerebral Palsy and Communication Deficits
NCT05887765	PHASE4	COMPLETED	Effect of Systematic Dexamethasone on the Duration of Popliteal Nerve Block for Anesthesia After Pediatric Ankle Surgery
NCT06176430	PHASE4	UNKNOWN	Comparison of Twice Weekly Versus Daily Iron Therapy in Treating Anemia in Children With Cerebral Palsy
NCT06189781	PHASE4	RECRUITING	Pain Injection Versus Epidural Anesthesia for Hip Surgery in Pediatric Patients With Cerebral Palsy
NCT00014989	PHASE3	COMPLETED	Beneficial Effects of Antenatal Magnesium Sulfate (BEAM Trial)
NCT00065949	PHASE3	UNKNOWN	Magnesium Sulfate to Prevent Brain Injury in Premature Infants
NCT00367068	PHASE3	COMPLETED	Dutch National ITB Study in Children With Cerebral Palsy
NCT00491894	PHASE3	COMPLETED	Safety and Efficacy Study of Oral Glycopyrrolate Liquid for the Treatment of Pathologic (Chronic Moderate to Severe) Drooling in Pediatric Patients 3 to 18 Years of Age With Cerebral Palsy or Other Neurologic Conditions
NCT00632528	PHASE3	COMPLETED	MEOPA to Improve Physical Therapy Results After Multilevel Surgery
NCT00822029	PHASE3	TERMINATED	Use of Oral Bisphosphonates in the Treatment of Osteoporosis of Non-walking Children With Cerebral Palsy
NCT00922077	PHASE3	COMPLETED	Individualized Neurodevelopmental Treatment
NCT01249417	PHASE3	COMPLETED	Dysport® Pediatric Lower Limb Spasticity Study
NCT01251380	PHASE3	COMPLETED	Dysport® Pediatric Lower Limb Spasticity Follow-on Study
NCT01437644	PHASE3	COMPLETED	The Post-Operative Pain in Cerebral Palsy (POPPIES) Trial
NCT01492608	PHASE3	COMPLETED	Magnesium Sulphate for Preterm Birth (MASP Study)
NCT01603602	PHASE3	COMPLETED	BOTOX® Treatment in Pediatric Upper Limb Spasticity
NCT01603615	PHASE3	COMPLETED	BOTOX® Open-Label Treatment in Pediatric Upper Limb Spasticity
NCT01603628	PHASE3	COMPLETED	BOTOX® Treatment in Pediatric Lower Limb Spasticity
NCT01603641	PHASE3	COMPLETED	BOTOX® Open-Label Treatment in Pediatric Lower Limb Spasticity
NCT01633736	PHASE3	UNKNOWN	Targeted Hip Strength Training in Children With Cerebral Palsy (CP)
NCT01898520	PHASE3	COMPLETED	A Safety, Efficacy and Tolerability Study of Sativex for the Treatment of Spasticity in Children Aged 8 to 18 Years
NCT01929434	PHASE3	COMPLETED	Efficacy of Stem Cell Transplantation Compared to Rehabilitation Treatment of Patients With Cerebral Paralysis
NCT02002884	PHASE3	COMPLETED	Dose-response Study of Efficacy and Safety of Botulinum Toxin Type A to Treat Spasticity of the Arm(s) or of Arm(s) and Leg(s) in Cerebral Palsy
NCT02270736	PHASE3	COMPLETED	Clinical Study to Investigate the Efficacy and Safety of NT 201 Compared to Placebo in the Treatment of Chronic Troublesome Drooling Associated With Neurological Disorders and/or Intellectual Disability
NCT02839785	PHASE3	TERMINATED	Analgesia and Physiotherapy in Children With Cerebral Palsy (ANTALKINECP)
NCT03110341	PHASE3	UNKNOWN	Effect of Erythropoietin in Premature Infants on White Matter Lesions and Neurodevelopmental Outcome
NCT03302871	PHASE3	COMPLETED	Integrated Management Enhances Functional Gains in Children With Cerebral Palsy Treated by BoNT-A
NCT03306212	PHASE3	COMPLETED	Efficacy of Intermittent Serial Casting on Spastic Wrist Flexion Deformity