ATP9B

Summary

ATP9B (ATPase phospholipid transporting 9B, HGNC:13541) is a protein-coding gene on chromosome 18q23, encoding Probable phospholipid-transporting ATPase IIB (O43861).

Predicted to enable ATPase-coupled intramembrane lipid carrier activity. Predicted to be involved in endocytosis; phospholipid translocation; and retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum. Located in perinuclear region of cytoplasm and trans-Golgi network.

Source: NCBI Gene 374868 — automated summary from GO annotations (Alliance of Genome Resources).

At a glance

• GWAS associations: 5
• Clinical variants (ClinVar): 252 total — 4 pathogenic
• GTEx eGene: eQTL in 19 tissues, sQTL in 23 (q < 0.05)
• Constraint (gnomAD): pLI 0.00 (LoF-tolerant), LOEUF 0.86 (unconstrained)
• MANE Select transcript: NM_198531
• Notable: 252 clinical variants but no curated precision-oncology (CIViC) evidence yet

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:13541
Approved symbol	ATP9B
Name	ATPase phospholipid transporting 9B
Location	18q23
Locus type	gene with protein product
Status	Approved
Aliases	ATPIIB
Ensembl gene	ENSG00000166377
Ensembl biotype	protein_coding
OMIM	614446
Entrez	374868

Gene structure

Transcript identifiers

Ensembl transcripts: 61 — 30 protein_coding, 19 nonsense_mediated_decay, 9 retained_intron, 3 protein_coding_CDS_not_defined

MANE Select: ENST00000426216

Transcript support level (Ensembl TSL; 1 = fully mRNA-supported): TSL 1: 4, TSL 2: 4, TSL 3: 9, TSL 4: 5, TSL 5: 3

ENST00000426216, ENST00000307671, ENST00000490210, ENST00000585674, ENST00000586366, ENST00000586672, ENST00000586722, ENST00000586774, ENST00000587410, ENST00000587878, ENST00000587919, ENST00000588600, ENST00000588772, ENST00000588895, ENST00000588921, ENST00000589326, ENST00000589732, ENST00000589951, ENST00000590163, ENST00000590271, ENST00000590477, ENST00000590608, ENST00000591395, ENST00000591464, ENST00000591518, ENST00000899989, ENST00000899990, ENST00000899991, ENST00000899992, ENST00000899993, ENST00000899994, ENST00000899995, ENST00000940834, ENST00000940835, ENST00000940836, ENST00000963364, ENST00000963365, ENST00000963366, ENST00000963367, ENST00000963368, ENST00000963369, ENST00000963370, ENST00000981934, ENST00001041112, ENST00001041113, ENST00001041114, ENST00001041115, ENST00001041116, ENST00001041117, ENST00001041118, ENST00001041119, ENST00001041120, ENST00001041121, ENST00001041122, ENST00001111071, ENST00001111072, ENST00001111073, ENST00001112228, ENST00001124528, ENST00001124529, ENST00001131526

RefSeq mRNA: 2 — MANE Select: NM_198531 NM_001306085, NM_198531

CCDS: CCDS12014, CCDS77202

Canonical transcript exons

ENST00000426216 — 30 exons

Exon	Start	End
ENSE00002804876	79069394	79069529
ENSE00002907374	79377247	79378283
ENSE00003460183	79113241	79113354
ENSE00003500111	79110355	79110505
ENSE00003512812	79345775	79345839
ENSE00003522135	79347770	79347925
ENSE00003542338	79342268	79342366
ENSE00003566056	79345428	79345572
ENSE00003566891	79359354	79359462
ENSE00003573559	79126267	79126375
ENSE00003582657	79344265	79344354
ENSE00003586322	79306986	79307234
ENSE00003588591	79372825	79372882
ENSE00003605429	79213962	79214038
ENSE00003606422	79154504	79154555
ENSE00003608960	79329141	79329302
ENSE00003626646	79176813	79176907
ENSE00003632982	79375394	79375426
ENSE00003637813	79143802	79143860
ENSE00003642337	79337279	79337449
ENSE00003648208	79253381	79253541
ENSE00003649880	79096476	79096649
ENSE00003651762	79330012	79330104
ENSE00003659061	79277054	79277196
ENSE00003659967	79336628	79336711
ENSE00003661910	79193183	79193263
ENSE00003664371	79303604	79303716
ENSE00003676250	79348132	79348196
ENSE00003677118	79373898	79374101
ENSE00003683253	79206937	79207012

Expression profiles

Bgee: expression breadth ubiquitous, 263 present calls, max score 95.09.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 15.2445 / max 178.7572, expressed in 1801 samples.

Highest expression (Bgee): sural nerve, male germ line stem cell (sensu Vertebrata) in testis, colonic epithelium, calcaneal tendon, ventricular zone.

Genetic regulation across tissues (GTEx eQTL / sQTL)

ATP9B is an eGene in GTEx v10 — its expression is genetically regulated (eQTL) in 19 tissues and its splicing (sQTL) in 23 (q < 0.05). Strongest associations first; slope = normalized effect of the lead variant’s alternative allele.

showing 20 of 42 significant tissue × QTL associations:

Tissue	QTL	q-value	Slope	Lead variant
Whole Blood	eqtl	5.9e-50	+0.50	18:79077760:A:G
Testis	sqtl	1.5e-16	+0.89	18:79139804:C:T
Muscle Skeletal	eqtl	3.5e-14	-0.30	18:79147989:G:T
Adipose Subcutaneous	sqtl	8.8e-12	+0.47	18:79261380:A:G
Skin Sun Exposed Lower leg	sqtl	1.1e-10	+0.33	18:79385379:G:A
Spleen	eqtl	1.2e-10	+0.38	18:79059843:T:A
Cells EBV-transformed lymphocytes	eqtl	5.1e-10	+0.60	18:79061767:T:C
Artery Tibial	sqtl	3.7e-08	+0.48	18:79368978:A:AC
Breast Mammary Tissue	sqtl	5.5e-08	+0.51	18:79261380:A:G
Lung	eqtl	2.8e-07	-0.22	18:79098457:T:G
Colon Sigmoid	sqtl	4.5e-07	+0.52	18:79375472:A:G
Thyroid	sqtl	4.9e-07	-0.40	18:79352916:A:C
Esophagus Muscularis	sqtl	6.8e-07	+0.45	18:79349150:G:A
Brain Frontal Cortex BA9	eqtl	7.0e-07	+0.33	18:79330526:C:G
Cells Cultured fibroblasts	sqtl	1.4e-06	-0.57	18:79224827:C:T
Esophagus Gastroesophageal Junction	sqtl	1.5e-06	+0.51	18:79330526:C:G
Testis	eqtl	2.3e-06	-0.37	18:79031667:T:G
Nerve Tibial	eqtl	9.8e-06	+0.18	18:79100059:G:A
Lung	sqtl	1.4e-05	+0.39	18:79261380:A:G
Esophagus Mucosa	sqtl	1.9e-05	-0.48	18:79259645:C:A

FANTOM5 promoters

7 alternative TSS:

Promoter ID	TPM avg	Samples expressed
170890	12.8133	1793
170891	1.5245	597
170889	0.6003	252
208611	0.1777	76
170897	0.0646	28
170898	0.0407	18
170896	0.0234	5

Top tissues by expression

showing 100 of 288 tissues by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
sural nerve	UBERON:0015488	95.09	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	93.79	gold quality
colonic epithelium	UBERON:0000397	93.38	gold quality
calcaneal tendon	UBERON:0003701	93.06	gold quality
ventricular zone	UBERON:0003053	91.52	gold quality
adrenal tissue	UBERON:0018303	90.74	gold quality
right testis	UBERON:0004534	90.53	gold quality
left testis	UBERON:0004533	90.48	gold quality
testis	UBERON:0000473	89.79	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	88.91	gold quality
left ovary	UBERON:0002119	88.53	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	88.35	gold quality
ectocervix	UBERON:0012249	88.27	gold quality
tibial nerve	UBERON:0001323	88.07	gold quality
right ovary	UBERON:0002118	87.97	gold quality
ganglionic eminence	UBERON:0004023	87.87	gold quality
cervix squamous epithelium	UBERON:0006922	87.77	silver quality
lower esophagus mucosa	UBERON:0035834	87.73	gold quality
stromal cell of endometrium	CL:0002255	87.62	gold quality
ovary	UBERON:0000992	87.57	gold quality
endocervix	UBERON:0000458	87.45	gold quality
right uterine tube	UBERON:0001302	87.29	gold quality
skin of leg	UBERON:0001511	87.03	gold quality
stomach	UBERON:0000945	86.71	gold quality
body of stomach	UBERON:0001161	86.67	gold quality
skin of abdomen	UBERON:0001416	86.52	gold quality
mucosa of transverse colon	UBERON:0004991	86.45	gold quality
body of uterus	UBERON:0009853	86.45	gold quality
hindlimb stylopod muscle	UBERON:0004252	86.42	gold quality
spinal cord	UBERON:0002240	86.32	gold quality
vagina	UBERON:0000996	86.19	gold quality
right frontal lobe	UBERON:0002810	86.14	gold quality
left lobe of thyroid gland	UBERON:0001120	86.12	gold quality
popliteal artery	UBERON:0002250	86.08	gold quality
tibial artery	UBERON:0007610	86.07	gold quality
endothelial cell	CL:0000115	86.02	gold quality
thyroid gland	UBERON:0002046	85.96	gold quality
right lobe of thyroid gland	UBERON:0001119	85.93	gold quality
left uterine tube	UBERON:0001303	85.81	gold quality
adenohypophysis	UBERON:0002196	85.54	gold quality
upper lobe of left lung	UBERON:0008952	85.44	gold quality
gastrocnemius	UBERON:0001388	85.31	gold quality
minor salivary gland	UBERON:0001830	85.27	gold quality
muscle of leg	UBERON:0001383	85.18	gold quality
zone of skin	UBERON:0000014	85.12	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	85.04	gold quality
aorta	UBERON:0000947	84.94	gold quality
tonsil	UBERON:0002372	84.93	gold quality
bone marrow cell	CL:0002092	84.71	gold quality
upper lobe of lung	UBERON:0008948	84.69	gold quality
muscle layer of sigmoid colon	UBERON:0035805	84.66	gold quality
blood	UBERON:0000178	84.55	gold quality
monocyte	CL:0000576	84.52	gold quality
germinal epithelium of ovary	UBERON:0001304	84.50	silver quality
prefrontal cortex	UBERON:0000451	84.49	gold quality
adrenal gland	UBERON:0002369	84.47	gold quality
lower esophagus muscularis layer	UBERON:0035833	84.42	gold quality
lower esophagus	UBERON:0013473	84.41	gold quality
right hemisphere of cerebellum	UBERON:0014890	84.38	gold quality
mononuclear cell	CL:0000842	84.37	gold quality
CA1 field of hippocampus	UBERON:0003881	84.36	silver quality
leukocyte	CL:0000738	84.30	gold quality
cortical plate	UBERON:0005343	84.23	gold quality
mucosa of stomach	UBERON:0001199	84.20	gold quality
metanephros cortex	UBERON:0010533	84.16	gold quality
right adrenal gland cortex	UBERON:0035827	84.13	gold quality
right lung	UBERON:0002167	84.08	gold quality
pituitary gland	UBERON:0000007	83.98	gold quality
left adrenal gland cortex	UBERON:0035825	83.98	gold quality
esophagus	UBERON:0001043	83.92	gold quality
ascending aorta	UBERON:0001496	83.87	gold quality
saliva-secreting gland	UBERON:0001044	83.80	gold quality
left adrenal gland	UBERON:0001234	83.80	gold quality
thoracic aorta	UBERON:0001515	83.71	gold quality
cerebellar hemisphere	UBERON:0002245	83.70	gold quality
cerebellar cortex	UBERON:0002129	83.61	gold quality
mouth mucosa	UBERON:0003729	83.60	gold quality
right adrenal gland	UBERON:0001233	83.59	gold quality
primary visual cortex	UBERON:0002436	83.55	gold quality
granulocyte	CL:0000094	83.53	gold quality
Brodmann (1909) area 23	UBERON:0013554	83.50	gold quality
corpus callosum	UBERON:0002336	83.36	gold quality
left coronary artery	UBERON:0001626	83.35	gold quality
prostate gland	UBERON:0002367	83.34	gold quality
esophagus mucosa	UBERON:0002469	83.34	gold quality
subcutaneous adipose tissue	UBERON:0002190	83.20	gold quality
transverse colon	UBERON:0001157	83.18	gold quality
descending thoracic aorta	UBERON:0002345	83.17	gold quality
right atrium auricular region	UBERON:0006631	83.15	gold quality
right coronary artery	UBERON:0001625	83.06	gold quality
body of pancreas	UBERON:0001150	83.04	gold quality
omental fat pad	UBERON:0010414	82.92	gold quality
Brodmann (1909) area 9	UBERON:0013540	82.91	gold quality
right lobe of liver	UBERON:0001114	82.87	gold quality
peritoneum	UBERON:0002358	82.85	gold quality
tendon	UBERON:0000043	82.81	gold quality
adrenal cortex	UBERON:0001235	82.67	gold quality
small intestine Peyer’s patch	UBERON:0003454	82.55	gold quality
cingulate cortex	UBERON:0003027	82.53	gold quality
adipose tissue of abdominal region	UBERON:0007808	82.52	gold quality

Single-cell (SCXA)

Detected in 6 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	6.11
E-CURD-135	no	2928.00
E-HCAD-6	no	448.08
E-HCAD-8	no	442.67
E-MTAB-7249	no	271.29
E-GEOD-137537	no	5.64

HPA expression

RNA tissue specificity: Low tissue specificity

showing 60 of 80 HPA tissues / cells by nTPM:

Tissue / cell	Axis	nTPM	Protein (IHC)
Postcentral gyrus	tissue	154.9
Choroid plexus	tissue	141.6
Hippocampus	tissue	140.1	low
Nucleus accumbens	tissue	136.2
Locus coeruleus	tissue	115.3
Corpus callosum	tissue	34.4
Periaqueductal gray	tissue	33.9
Spinal cord	tissue	31.9
Midbrain	tissue	29.2
Medulla oblongata	tissue	29.2
Bone marrow	tissue	28.3	medium
Pons	tissue	27.9
Hypothalamus	tissue	27.9
Thalamus	tissue	27.6
Substantia nigra	tissue	27.0
Hippocampal formation	tissue	25.5
Superior colliculi	tissue	25.1
Septum	tissue	24.6
Cerebral cortex	tissue	23.9	medium
Motor cortex	tissue	23.9
Amygdala	tissue	23.3
Ventral forebrain	tissue	23.3
Basal ganglia	tissue	23.2	low
Somatosensory cortex	tissue	23.2
Prefrontal cortex	tissue	23.1
Entorhinal cortex	tissue	23.1
Putamen	tissue	22.7
Retrosplenial cortex	tissue	22.4
Temporal cortex	tissue	21.9
Occipital cortex	tissue	21.9
Retrosplenial and cingulate cortex	tissue	21.8
Insular cortex	tissue	21.7
Cerebellum	tissue	20.6	low
Olfactory bulb	tissue	20.3
Retina	tissue	17.5
Testis	tissue	16.8	medium
Caudate putamen	tissue	15.3
Parathyroid gland	tissue	13.3	low
Liver	tissue	13.2	not detected
Frontal cortex	tissue	13.1
Thyroid gland	tissue	10.8	high
Skin 1	tissue	10.3	medium
Endometrium 1	tissue	9.9	medium
Prostate	tissue	9.6	low
Stomach 1	tissue	9.5	not detected
Ovary	tissue	9.5	not detected
Salivary gland	tissue	9.5	medium
Kidney	tissue	9.4	medium
Lung	tissue	9.2	medium
Skeletal muscle	tissue	9.1	medium
Esophagus	tissue	8.8	medium
Pancreas	tissue	8.8	medium
Lymph node	tissue	8.5	low
Thymus	tissue	8.5
Epididymis	tissue	8.4	medium
Fallopian tube	tissue	8.4	medium
Placenta	tissue	8.3	high
Rectum	tissue	8.1	medium
Breast	tissue	8.0	medium
Spleen	tissue	7.9	low

Brain sub-regions (HPA Brain Atlas): detected in 192; highest nTPM — Somatosensory cortex, postcentral gyrus, ventral (white matter) (185.1), Flocculonodular lobe (181.2), Vermis (179.7), Parieto-temporal junction (white matter) (174.3), Cerebellar cortex (172.3).

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): CTNNBL1, MYB, MYF5, MYOD1, SPI1

miRNA regulators (miRDB)

Targeting ATP9B by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific).

showing 30 of 61 miRNAs:

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-4510	100.00	66.60	2050
HSA-MIR-6127	100.00	66.76	2188
HSA-MIR-6129	100.00	66.46	2080
HSA-MIR-6130	100.00	66.69	2012
HSA-MIR-6133	100.00	66.48	2064
HSA-MIR-3120-5P	100.00	65.56	965
HSA-MIR-3688-3P	99.97	72.02	2834
HSA-MIR-1250-3P	99.96	70.04	4038
HSA-MIR-4666A-3P	99.96	71.71	3434
HSA-MIR-545-3P	99.95	70.74	2783
HSA-MIR-4731-5P	99.89	67.23	2537
HSA-MIR-30A-3P	99.87	69.74	2928
HSA-MIR-30D-3P	99.87	69.92	2917
HSA-MIR-30E-3P	99.87	69.68	2942
HSA-MIR-221-5P	99.86	65.45	1052
HSA-MIR-8073	99.86	65.21	1118
HSA-MIR-378G	99.71	64.90	1106
HSA-MIR-3158-5P	99.65	67.51	1763
HSA-MIR-298	99.63	67.56	1916
HSA-MIR-7150	99.62	66.80	1322
HSA-MIR-1207-5P	99.49	69.11	2983
HSA-MIR-5571-5P	99.49	66.99	1764
HSA-MIR-6722-3P	99.45	67.62	1919
HSA-MIR-4427	99.34	70.33	1854
HSA-MIR-3606-5P	99.31	69.67	1168
HSA-MIR-4292	99.16	65.57	1767
HSA-MIR-6791-5P	99.16	65.92	1844
HSA-MIR-4763-3P	99.10	67.83	2649
HSA-MIR-661	99.09	65.94	2062
HSA-MIR-6868-5P	99.06	65.69	1284

Functional genomics

gnomAD constraint: pLI 2.77e-19, LOEUF 0.857, missense Z 0.619 — population loss-of-function intolerance (pLI ≥ 0.9 = LoF-intolerant; lower LOEUF = more constrained). gnomAD

Regional missense constraint (gnomAD RMC): no regional variation along ENST00000426216 — one region, missense o/e 1.00.

Literature-anchored findings (GeneRIF, showing 1)

• These results revealed that human human macrophage MHC receptor 1 on monocytes is a novel receptor specific for HLA-B44. (PMID:22525042)

Cross-species orthologs

6 orthologs

Organism	Symbol	Gene ID
danio_rerio	atp9b	ENSDARG00000062521
mus_musculus	Atp9b	ENSMUSG00000024566
rattus_norvegicus	Atp9b	ENSRNOG00000032039
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), ATP10A (ENSG00000206190)

Mouse-model phenotypes

Observed phenotypes of the mouse ortholog (MGI:1354757) from MGI (Alliance of Genome Resources) — knockout/mutant phenotypes, ranked by annotation count. 2 distinct phenotype terms.

Mouse phenotype (MP)	Records
abnormal vocalization	1
abnormal coat/hair pigmentation	1

Additional cross-species homologs

Sequence homologs in species beyond Ensembl Compara’s model organisms, by Diamond local protein alignment (% sequence identity; best hit per species). Lower-identity rows are more distant homologs. The matched accessions’ gene symbols aren’t in biobtree yet, so each row shows the UniProt accession.

Organism	UniProt	Identity	Method
Bos taurus	Q29449	96.0%	Diamond
Macaca fascicularis	Q9GKS6	88.7%	Diamond
Arabidopsis thaliana	Q9LK90	64.8%	Diamond
Schizosaccharomyces pombe 972h-	O94296	59.5%	Diamond
Saccharomyces cerevisiae S288C	P39524	59.5%	Diamond
Toxoplasma gondii GT1	S7VVK4	47.9%	Diamond

Genomic neighbors (locus context)

Genes flanking this one on the chromosome (NCBI/Entrez gene neighborhood). Positional context only — some neighbors share regulatory elements (bidirectional promoters, antisense/overlapping transcripts), but chromosomal adjacency is not itself a functional relationship (see Interactions for that).

Symbol	Type	Entrez
SALL3	protein-coding	27164
LINC01896	ncRNA	645321
NFATC1	protein-coding	4772

Protein

Protein identifiers

Probable phospholipid-transporting ATPase IIB — O43861 (reviewed: O43861)

Alternative names: ATPase class II type 9B

All UniProt accessions (12): O43861, B4DJ94, K7EII3, K7EJG1, K7EJP9, K7EJS3, K7EL57, K7EPH4, K7EQ39, K7EQQ5, K7ERE0, K7ES39

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Golgi apparatus. trans-Golgi network membrane.

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

Isoforms (2)

UniProt ID	Names	Canonical?
O43861-1	1	yes
O43861-2	2

RefSeq proteins (2): NP_001293014, NP_940933* (*=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
IPR059000	ATPase_P-type_domA	Domain

Pfam: PF00122, PF00702, PF16209, PF16212

UniProt features (58 total): binding site 20, topological domain 11, transmembrane region 10, sequence conflict 8, sequence variant 4, chain 1, region of interest 1, compositionally biased region 1, active site 1, splice variant 1

Structure

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-O43861-F1	79.49	0.29

Human Protein Atlas

Protein class: Enzymes, ENZYME proteins, Predicted membrane proteins, Predicted intracellular proteins, UniProt - Evidence at transcript level

Protein evidence: Evidence at protein level

Antibody reliability (HPA): IH approved

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)

Position	Role
468	4-aspartylphosphate intermediate

Ligand- & substrate-binding residues (20)

Position	Role
468	ATP
468	Mg(2+)
469	ATP
470	ATP
470	Mg(2+)
591	ATP
633	ATP
638	ATP
657	ATP
686	ATP
687	ATP
766	ATP
767	ATP
768	ATP
848	ATP
854	ATP
874	Mg(2+)
877	ATP
878	ATP
878	Mg(2+)

Function

Pathways and Gene Ontology

Reactome pathways

1 curated (TAS) of 3; 0 disease pathways. Curated-first; evidence = TAS (manually curated) vs IEA (electronic inference).

3 pathways:

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

MSigDB gene sets: 145 (showing top): IVANOVA_HEMATOPOIESIS_LATE_PROGENITOR, GOBP_VESICLE_MEDIATED_TRANSPORT, GOBP_REGULATION_OF_MEMBRANE_LIPID_DISTRIBUTION, GOBP_ORGANOPHOSPHATE_ESTER_TRANSPORT, GOCC_TRANS_GOLGI_NETWORK, RUTELLA_RESPONSE_TO_CSF2RB_AND_IL4_UP, FOSTER_TOLERANT_MACROPHAGE_UP, WANG_CISPLATIN_RESPONSE_AND_XPC_DN, GOBP_PHOSPHOLIPID_TRANSPORT, GOBP_MEMBRANE_ORGANIZATION, GRYDER_PAX3FOXO1_ENHANCERS_IN_TADS, GOBP_IMPORT_INTO_CELL, GOBP_LIPID_LOCALIZATION, GOBP_ENDOCYTOSIS, GRYDER_PAX3FOXO1_TOP_ENHANCERS

GO Biological Process (5): retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum (GO:0006890), endocytosis (GO:0006897), phospholipid translocation (GO:0045332), lipid transport (GO:0006869), phospholipid transport (GO:0015914)

GO Molecular Function (7): magnesium ion binding (GO:0000287), ATP binding (GO:0005524), ATP hydrolysis activity (GO:0016887), ATPase-coupled intramembrane lipid carrier activity (GO:0140326), nucleotide binding (GO:0000166), transporter activity (GO:0005215), metal ion binding (GO:0046872)

GO Cellular Component (7): endosome (GO:0005768), trans-Golgi network (GO:0005802), plasma membrane (GO:0005886), perinuclear region of cytoplasm (GO:0048471), Golgi apparatus (GO:0005794), endomembrane system (GO:0012505), membrane (GO:0016020)

Reactome top-level categories

2 top-level categories:

Category	Pathways
Ion channel transport	1
Transport of small molecules	1

GO top-level categories

31 GO namespaces:

Category	Terms
cellular anatomical structure	3
ATP-dependent activity	2
endomembrane system	2
cytoplasm	2
Golgi vesicle transport	1
vesicle budding from membrane	1
membrane invagination	1
import into cell	1
phospholipid transport	1
lipid translocation	1
transport	1
lipid localization	1
lipid transport	1
organophosphate ester transport	1
metal ion binding	1
adenyl ribonucleotide binding	1
purine ribonucleoside triphosphate binding	1
anion binding	1
ribonucleoside triphosphate phosphatase activity	1
intramembrane lipid carrier activity	1
nucleoside phosphate binding	1
heterocyclic compound binding	1
molecular_function	1
cation binding	1
cytoplasmic vesicle	1
Golgi apparatus subcompartment	1
membrane	1
cell periphery	1
intracellular membrane-bounded organelle	1
vacuole	1
plasma membrane	1

Experimentally-supported GO annotations

GO terms backed by direct experimental evidence (ECO experimental codes) — 2 of 19 annotations. The rest are phylogenetic / computational / electronic (IEA).

2 experimentally-supported GO terms:

GO term	NS	Evidence
perinuclear region of cytoplasm	CC	direct assay
trans-Golgi network	CC	direct assay

Protein interactions and networks

STRING

showing 15 of 574 interactions by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ATP9B	CDC50A	Q9NV96	624
ATP9B	CDC50B	Q3MIR4	604
ATP9B	SLC66A2	Q8N2U9	486
ATP9B	DOP1A	Q5JWR5	481
ATP9B	MON2	Q7Z3U7	452
ATP9B	NEO1	Q92859	441
ATP9B	DOP1B	Q9Y3R5	404
ATP9B	KCTD20	Q7Z5Y7	394
ATP9B	SALL3	Q9BXA9	370
ATP9B	RBFA	Q8N0V3	365
ATP9B	ZNF407	Q9C0G0	357
ATP9B	SMIM21	Q3B7S5	357
ATP9B	TXNL4A	P83876	356
ATP9B	EVA1C	P58658	346
ATP9B	ZNF75D	P51815	345

IntAct

Human interaction partners of ATP9B in IntAct, one row per partner (best MIscore; records = supporting IntAct interaction records).

2 partners by confidence:

Partner	Interaction type	MIscore	Records
ATP9A	association	0.350	1
AVPR2	association	0.350	1

BioGRID (24 interactions; top human partners by supporting records): ANKH (Affinity Capture-MS), ATP13A3 (Co-fractionation), ATP7B (Co-fractionation), ATP9A (Affinity Capture-MS), DDX58 (Affinity Capture-RNA), DVL2 (Affinity Capture-MS), HNRNPL (Affinity Capture-RNA), IGSF8 (Co-fractionation), KIAA1429 (Affinity Capture-RNA), MFSD5 (Affinity Capture-MS), NUDT21 (Affinity Capture-RNA), PARP3 (Proximity Label-MS), PDE2A (Affinity Capture-MS), PTK7 (Co-fractionation), SLC15A3 (Affinity Capture-MS)

Disease & clinical

Genetic variants

Variant evidence for ATP9B: 252 ClinVar records (4 pathogenic / likely pathogenic); 5 GWAS associations. Per-variant detail is on Sugi Variant.

ClinVar

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

Classification	Count (floor)
Pathogenic	4
Likely pathogenic	0
Uncertain significance	182
Likely benign	15
Benign	5

Top pathogenic / likely-pathogenic (4)

Showing all 4 pathogenic / likely-pathogenic ClinVar records, ranked by ClinVar review status (expert panel → multiple submitters → single submitter), then by number of submitting labs.

Variant ID	HGVS	Classification	Review	Submitters
1526633	GRCh37/hg19 18q22.1-23(chr18:64340599-77273893)x1	Pathogenic	criteria provided, single submitter	1
149476	GRCh38/hg38 18q22.3-23(chr18:72043906-80254936)x1	Pathogenic	no assertion criteria provided	1
242603	NC_000018.9:g.73376178_78077248del4701071	Pathogenic	no assertion criteria provided	1
564566	GRCh37/hg19 18q21.33-23(chr18:60416709-78014123)x1	Pathogenic	no assertion criteria provided	1

Per-variant reference — Sugi Variant

Explore ATP9B’s pathogenic and likely-pathogenic variants individually — each with its ClinVar classification and conditions, applied ACMG criteria (ClinGen expert panel, where curated), the calibrated in-silico predictors (AlphaMissense, REVEL, SaProt, conservation), gnomAD frequency, and the predictor-disagreement QC signal — on Sugi Variant.

SpliceAI

Top 10 splice-impact sites by Δscore (adjacent positions with the same effect merged into one range; 31 predictions of 4,263):

Position(s)	Effect	Δscore	Sites
18:79069530–79069531	donor_loss	1.0000	2
18:79113355–79113356	donor_loss	1.0000	6
18:79126265–79126266	acceptor_loss	1.0000	2
18:79126336	donor_gain	1.0000
18:79126376–79126377	donor_loss	1.0000	5
18:79206934	acceptor_gain	1.0000
18:79253542–79253543	donor_loss	1.0000	3
18:79277197–79277198	donor_loss	1.0000	5
18:79303598	acceptor_gain	1.0000
18:79303602–79303603	acceptor_loss	1.0000	5

AlphaMissense

3,334 missense substitutions predicted likely pathogenic (of 7,532 scored), across 817 residues. Top 20 hotspot residues, ranked by the number of likely-pathogenic substitutions (of those reachable by a single-nucleotide change), then by mean score:

Residue	Likely-pathogenic substitutions	Mean am_pathogenicity	Max am_pathogenicity
M478	9	0.986	0.999
M640	9	0.951	0.992
M881	9	0.924	0.995
D468	8	0.998	1.000
D878	8	0.998	0.999
D590	8	0.997	0.999
D742	8	0.996	0.999
D768	8	0.996	0.999
D249	8	0.992	0.997
D208	8	0.989	0.998
D270	8	0.989	0.997
D874	8	0.986	0.997
F633	8	0.985	0.999
D904	8	0.983	0.994
N877	8	0.977	0.999
N476	8	0.976	0.995
H937	8	0.976	0.992
S588	8	0.975	1.000
F312	8	0.974	0.997
D429	8	0.966	0.994

HPA cancer prognostics

RNA cancer specificity: Low cancer specificity

Human Protein Atlas survival analysis — favorable = higher expression predicts better survival.

1 prognostic cancer types:

Cancer	Prognostic	p-value
Kidney Renal Clear Cell Carcinoma (validation)	favorable	0.000974

Disease associations

OMIM: gene MIM:614446 | disease phenotypes: MIM:608572

GenCC curated gene-disease

Mondo (1): choanal atresia-hearing loss-cardiac defects-craniofacial dysmorphism syndrome (MONDO:0012064)

Orphanet (1): Burn-McKeown syndrome (Orphanet:1200)

GWAS associations

5 associations:

Study	Trait	p-value
GCST001942_18	Prostate cancer	2e-9
GCST006148_11	Frontotemporal dementia with GRN mutation	1e-6
GCST009391_1782	Metabolite levels	3e-6
GCST011983_19	Fasting glucose	4e-6
GCST006154_6	Frontotemporal dementia	6e-6

EFO canonical traits (from GWAS)

1 canonical traits:

EFO ID	Trait name
EFO:0009792	valine measurement

MeSH disease descriptors

1 disease descriptors:

Descriptor	Name	Tree numbers
C563682	Oculootofacial Dysplasia *(supp.)*

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (CPIC guideline: no)

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

29 total (human), top 29 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
bisphenol A	affects expression, decreases expression	2
sodium arsenite	decreases expression, increases abundance, increases expression	2
Arsenic	affects methylation, decreases expression, increases abundance	2
Benzo(a)pyrene	decreases expression	2
Aflatoxin B1	decreases methylation, affects methylation	2
Cadmium Chloride	increases abundance, increases expression	2
methylmercuric chloride	decreases expression	1
triphenyl phosphate	affects expression	1
uranyl acetate	affects expression	1
arsenite	affects binding, decreases reaction	1
1,6-hexamethylene diisocyanate	increases methylation	1
manganese chloride	decreases expression, increases abundance	1
aflatoxin B2	increases methylation	1
di-n-butylphosphoric acid	affects expression	1
CGP 52608	affects binding, increases reaction	1
bisphenol S	decreases methylation	1
Resveratrol	increases expression	1
Cadmium	increases abundance, increases expression	1
Cocaine	affects response to substance	1
Formaldehyde	decreases expression	1
Hydrogen Peroxide	increases expression	1
Manganese	decreases expression, increases abundance	1
Sarin	increases expression	1
Testosterone	decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
Uranium	affects expression	1
Valproic Acid	decreases methylation	1
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide	decreases expression	1
Cyclosporine	increases methylation	1

Cellosaurus cell lines

3 cell lines: 3 cancer cell line

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

Cellosaurus	Name	Category	Sex
CVCL_SE22	HAP1 ATP9B (-) 1	Cancer cell line	Male
CVCL_XL79	HAP1 ATP9B (-) 2	Cancer cell line	Male
CVCL_XL80	HAP1 ATP9B (-) 3	Cancer cell line	Male

Clinical trials (associated diseases)

Via MONDO — disease-level, not drug-specific.