ABCA13

Summary

ABCA13 (ATP binding cassette subfamily A member 13, HGNC:14638) is a protein-coding gene on chromosome 7p12.3, encoding ATP-binding cassette sub-family A member 13 (Q86UQ4). May mediate the cholesterol and gangliosides transport from the plasma membrane to intracellular vesicles in an ATP hydrolysis dependent manner, thus playing a role in their internalization by endocytic retrograde transport and may also participate in the endocytosis of synaptic….

In human, the ATP-binding cassette (ABC) family of transmembrane transporters has at least 48 genes and 7 gene subfamilies. This gene is a member of ABC gene subfamily A (ABCA). Genes within the ABCA family typically encode several thousand amino acids. Like other ABC transmembrane transporter proteins, this protein has 12 or more transmembrane alpha-helix domains that likely arrange to form a single central chamber with multiple substrate binding sites. It is also predicted to have two large extracellular domains and two nucleotide binding domains as is typical for ABCA proteins. Alternative splice variants have been described but their biological validity has not been demonstrated.

Source: NCBI Gene 154664 — RefSeq curated summary.

At a glance

• Gene–disease (curated): schizophrenia (Limited, GenCC)
• GWAS associations: 6
• Clinical variants (ClinVar): 944 total — 4 pathogenic, 3 likely-pathogenic
• Phenotypes (HPO): 1
• MANE Select transcript: NM_152701

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:14638
Approved symbol	ABCA13
Name	ATP binding cassette subfamily A member 13
Location	7p12.3
Locus type	gene with protein product
Status	Approved
Aliases	FLJ33876, FLJ33951
Ensembl gene	ENSG00000179869
Ensembl biotype	protein_coding
OMIM	607807
Entrez	154664

Gene structure

Transcript identifiers

Ensembl transcripts: 8 — 4 protein_coding, 2 nonsense_mediated_decay, 1 retained_intron, 1 protein_coding_CDS_not_defined

ENST00000411975, ENST00000417403, ENST00000435451, ENST00000435803, ENST00000453246, ENST00000484268, ENST00000544596, ENST00000611776

RefSeq mRNA: 1 — MANE Select: NM_152701 NM_152701

CCDS: CCDS47584

Canonical transcript exons

ENST00000435803 — 62 exons

Exon	Start	End
ENSE00000976692	48580224	48580374
ENSE00000976693	48587154	48587288
ENSE00000976694	48594710	48594813
ENSE00001249564	48644617	48644754
ENSE00001249616	48645417	48647497
ENSE00001259713	48271787	48276565
ENSE00001290325	48410520	48410677
ENSE00001299557	48507872	48508049
ENSE00001306979	48403683	48403879
ENSE00001308191	48528236	48528345
ENSE00001308534	48520041	48520294
ENSE00001311855	48278094	48279920
ENSE00001316565	48412353	48412583
ENSE00001320475	48483076	48483163
ENSE00001323784	48524248	48524440
ENSE00001326386	48511084	48511199
ENSE00001327434	48506336	48506390
ENSE00001329780	48489236	48489344
ENSE00001330941	48516725	48516881
ENSE00001336488	48481036	48481154
ENSE00001336489	48471530	48471599
ENSE00001336491	48466956	48467045
ENSE00001336493	48455037	48455286
ENSE00001336494	48427766	48427871
ENSE00001336514	48309947	48310141
ENSE00001336515	48298366	48298487
ENSE00001336517	48297232	48297311
ENSE00001336520	48295700	48295863
ENSE00001336524	48287960	48288078
ENSE00001336526	48281343	48281452
ENSE00001336542	48234018	48234151
ENSE00001336543	48229825	48229955
ENSE00001336544	48227262	48227425
ENSE00001336545	48219354	48219505
ENSE00001336547	48198237	48198360
ENSE00001401899	48221281	48221309
ENSE00001596752	48171458	48171552
ENSE00001800408	48192959	48193052
ENSE00003461865	48268980	48269094
ENSE00003478921	48240867	48241066
ENSE00003480385	48367794	48367908
ENSE00003486930	48249212	48249351
ENSE00003499975	48387822	48387959
ENSE00003505050	48245863	48246030
ENSE00003509286	48352181	48352487
ENSE00003517219	48317157	48317296
ENSE00003518145	48245512	48245612
ENSE00003522494	48376441	48376572
ENSE00003523873	48248239	48248444
ENSE00003523897	48314232	48314409
ENSE00003531953	48372168	48372497
ENSE00003562290	48374347	48374416
ENSE00003578890	48391921	48392139
ENSE00003609453	48239241	48239405
ENSE00003615961	48338365	48338455
ENSE00003633654	48244576	48244703
ENSE00003640713	48335422	48335535
ENSE00003645852	48389040	48389220
ENSE00003652092	48643288	48643393
ENSE00003667529	48313067	48313231
ENSE00003675117	48615285	48615377
ENSE00003681430	48350643	48350819

Expression profiles

Bgee: expression breadth ubiquitous, 126 present calls, max score 98.47.

FANTOM5 (CAGE): breadth broad, TPM avg 2.5612 / max 1128.8566, expressed in 239 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
78592	2.4196	186
78597	0.0664	36
78598	0.0377	17
204433	0.0208	9
78599	0.0167	12

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
bronchial epithelial cell	CL:0002328	98.47	gold quality
bronchus	UBERON:0002185	97.39	gold quality
epithelium of nasopharynx	UBERON:0001951	95.50	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	94.97	gold quality
mucosa of paranasal sinus	UBERON:0005030	94.59	gold quality
nasal cavity epithelium	UBERON:0005384	94.07	gold quality
nasal cavity mucosa	UBERON:0001826	91.58	gold quality
bone marrow cell	CL:0002092	91.15	gold quality
bone marrow	UBERON:0002371	86.77	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	78.64	gold quality
trabecular bone tissue	UBERON:0002483	77.65	gold quality
trachea	UBERON:0003126	75.27	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	74.84	gold quality
right uterine tube	UBERON:0001302	73.84	gold quality
oviduct epithelium	UBERON:0004804	67.78	gold quality
left lobe of thyroid gland	UBERON:0001120	65.56	gold quality
thyroid gland	UBERON:0002046	64.26	gold quality
tibial nerve	UBERON:0001323	62.68	gold quality
right lobe of thyroid gland	UBERON:0001119	62.24	gold quality
monocyte	CL:0000576	61.73	gold quality
leukocyte	CL:0000738	61.09	gold quality
stromal cell of endometrium	CL:0002255	60.20	gold quality
esophagus mucosa	UBERON:0002469	60.07	gold quality
upper leg skin	UBERON:0004262	57.76	gold quality
blood	UBERON:0000178	57.55	gold quality
right lung	UBERON:0002167	56.60	gold quality
right testis	UBERON:0004534	56.48	gold quality
fallopian tube	UBERON:0003889	56.33	gold quality
lower esophagus mucosa	UBERON:0035834	56.21	gold quality
testis	UBERON:0000473	56.14	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-MTAB-9801	yes	697.49
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

77 targeting ABCA13, 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-3613-3P	100.00	76.36	7965
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-513B-5P	99.99	69.96	2150
HSA-MIR-4482-3P	99.98	72.50	3147
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-568	99.98	69.86	2084
HSA-MIR-3688-3P	99.97	72.02	2834
HSA-MIR-4267	99.96	66.53	2368
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-6835-3P	99.93	70.49	2904
HSA-MIR-335-3P	99.93	73.36	4958
HSA-MIR-219A-5P	99.91	73.36	735
HSA-MIR-4782-3P	99.88	73.31	735
HSA-MIR-6766-3P	99.88	73.38	732
HSA-MIR-3121-3P	99.82	71.96	3630
HSA-MIR-4495	99.82	72.08	3080
HSA-MIR-3681-5P	99.82	66.88	387
HSA-MIR-636	99.80	69.58	1500
HSA-MIR-7856-5P	99.75	69.99	2901
HSA-MIR-6885-3P	99.75	70.36	3187
HSA-MIR-4719	99.73	72.10	3329
HSA-MIR-8084	99.73	69.57	1760
HSA-MIR-4729	99.69	72.18	4233
HSA-MIR-12124	99.68	69.17	2700
HSA-MIR-7-5P	99.67	70.53	1809
HSA-MIR-1284	99.67	73.56	1353
HSA-MIR-1303	99.65	69.77	1662
HSA-MIR-3158-5P	99.65	67.51	1763
HSA-MIR-6849-5P	99.64	66.00	352

Literature-anchored findings (GeneRIF, showing 9)

• Description of a new gene that maps to chromosome 7. (PMID:12697998)
• ABCA13 is a candidate gene in schizophrenia, bipolar disorder, and depression (PMID:19944402)
• No copy number variation including ABCA13 was identified in schizophrenia, bipolar disorder, or major depressive disorder samples, nor in the controls. (PMID:23250005)
• An alternative human ABCA13 transcript and protein. (PMID:23266639)
• The results of this study demonstrated that common genetic variants at ABCA13 are unlikely to be related to the pathogenesis of schizophrenia in the Han Chinese population. (PMID:23910238)
• CIAPIN1 and ABCA13 may be novel markers of poor outcome in pre-chemotherapy serous carcinoma effusions. (PMID:25889687)
• Rare missense variants within a single gene, abca13, form yin yang haplotypes. (PMID:25898927)
• ABCA13 gene may contain overlapping common genetic risk factors for both major depressive disorder and schizophrenia in the Han Chinese population. (PMID:27712136)
• ATP-binding cassette transporter 13 mRNA expression level in schizophrenia patients. (PMID:33299069)

Cross-species orthologs

16 orthologs

Organism	Symbol	Gene ID
danio_rerio	abca5	ENSDARG00000074041
mus_musculus	Abca13	ENSMUSG00000004668
rattus_norvegicus	Abca13	ENSRNOG00000025645
drosophila_melanogaster	Eato	FBGN0028539
drosophila_melanogaster	CG1494	FBGN0031169
drosophila_melanogaster	Abca3	FBGN0031170
drosophila_melanogaster	CG1801	FBGN0031171
drosophila_melanogaster	CG8908	FBGN0034493
drosophila_melanogaster	CG6052	FBGN0036747
drosophila_melanogaster	CG31213	FBGN0051213
drosophila_melanogaster	ldd	FBGN0083956
drosophila_melanogaster	CG43672	FBGN0263747
caenorhabditis_elegans		WBGENE00000019
caenorhabditis_elegans	abt-2	WBGENE00000020
caenorhabditis_elegans		WBGENE00000022
caenorhabditis_elegans	abt-5	WBGENE00000023

Paralogs (11): ABCA7 (ENSG00000064687), ABCA2 (ENSG00000107331), ABCA8 (ENSG00000141338), ABCA12 (ENSG00000144452), ABCA9 (ENSG00000154258), ABCA6 (ENSG00000154262), ABCA10 (ENSG00000154263), ABCA5 (ENSG00000154265), ABCA1 (ENSG00000165029), ABCA3 (ENSG00000167972), ABCA4 (ENSG00000198691)

Protein

Protein identifiers

ATP-binding cassette sub-family A member 13 — Q86UQ4 (reviewed: Q86UQ4)

All UniProt accessions (6): A0A0A0MT16, Q86UQ4, F5H7B7, H0Y4D2, H7BZI9, H7C0U5

UniProt curated annotations — full annotation on UniProt →

Function. May mediate the cholesterol and gangliosides transport from the plasma membrane to intracellular vesicles in an ATP hydrolysis dependent manner, thus playing a role in their internalization by endocytic retrograde transport and may also participate in the endocytosis of synaptic vesicle in cortical neurons.

Subcellular location. Cytoplasmic vesicle membrane.

Tissue specificity. Significantly expressed in the bone marrow, trachea, testis, thyroid and lung as well as in skin fibroblasts.

Miscellaneous. May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay.

Similarity. Belongs to the ABC transporter superfamily.

Isoforms (7)

UniProt ID	Names	Canonical?
Q86UQ4-1	1	yes
Q86UQ4-2	2
Q86UQ4-3	3
Q86UQ4-4	4
Q86UQ4-5	5
Q86UQ4-6	6
Q86UQ4-7	7

RefSeq proteins (1): NP_689914* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR003439	ABC_transporter-like_ATP-bd	Domain
IPR003593	AAA+_ATPase	Domain
IPR013525	ABC2_TM	Domain
IPR026082	ABCA	Family
IPR027417	P-loop_NTPase	Homologous_superfamily
IPR056264	R2_ABCA1-4-like	Domain

Pfam: PF00005, PF12698, PF23321

Catalyzed reactions (Rhea), 1 shown:

• cholesterol(in) + ATP + H2O = cholesterol(out) + ADP + phosphate + H(+) (RHEA:39051)

UniProt features (53 total): sequence variant 20, transmembrane region 14, splice variant 7, sequence conflict 7, domain 2, binding site 2, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

No AlphaFold model available for Q86UQ4 — AlphaFold DB does not currently provide models for proteins above ~3000 aa.

Functional residue map

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

Ligand- & substrate-binding residues (2): 3875–3882; 4754–4761

Function

Pathways and Gene Ontology

Reactome pathways

3 pathways

ID	Pathway
R-HSA-6798695	Neutrophil degranulation
R-HSA-168249	Innate Immune System
R-HSA-168256	Immune System

MSigDB gene sets: 101 (showing top): REACTOME_INNATE_IMMUNE_SYSTEM, GOBP_POSITIVE_REGULATION_OF_ENDOCYTOSIS, GOCC_VACUOLAR_MEMBRANE, GOCC_SECRETORY_GRANULE, IVANOVA_HEMATOPOIESIS_MATURE_CELL, GOBP_POSITIVE_REGULATION_OF_STEROL_TRANSPORT, GOBP_VESICLE_MEDIATED_TRANSPORT, GOBP_POSITIVE_REGULATION_OF_LIPID_TRANSPORT, GOBP_SYNAPTIC_VESICLE_RECYCLING, GOBP_REGULATION_OF_VESICLE_MEDIATED_TRANSPORT, KEGG_ABC_TRANSPORTERS, GOBP_ORGANIC_HYDROXY_COMPOUND_TRANSPORT, SENGUPTA_NASOPHARYNGEAL_CARCINOMA_DN, GOBP_REGULATION_OF_ENDOCYTOSIS, GOBP_REGULATION_OF_STEROL_TRANSPORT

GO Biological Process (5): lipid transport (GO:0006869), positive regulation of cholesterol transport (GO:0032376), ceramide transport (GO:0035627), positive regulation of synaptic vesicle endocytosis (GO:1900244), transmembrane transport (GO:0055085)

GO Molecular Function (6): lipid carrier activity (GO:0005319), ATP binding (GO:0005524), ATP hydrolysis activity (GO:0016887), ATPase-coupled transmembrane transporter activity (GO:0042626), ABC-type transporter activity (GO:0140359), nucleotide binding (GO:0000166)

GO Cellular Component (7): plasma membrane (GO:0005886), secretory granule membrane (GO:0030667), azurophil granule membrane (GO:0035577), intracellular vesicle (GO:0097708), membrane (GO:0016020), cytoplasmic vesicle membrane (GO:0030659), cytoplasmic vesicle (GO:0031410)

Reactome top-level categories

Rollup of top-2 pathways:

Category	Pathways
Innate Immune System	1
Immune System	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
transport	2
ATP-dependent activity	2
lipid localization	1
cholesterol transport	1
positive regulation of sterol transport	1
regulation of cholesterol transport	1
lipid transport	1
nitrogen compound transport	1
positive regulation of endocytosis	1
synaptic vesicle endocytosis	1
regulation of synaptic vesicle endocytosis	1
positive regulation of synaptic vesicle recycling	1
cellular process	1
molecular carrier activity	1
adenyl ribonucleotide binding	1
purine ribonucleoside triphosphate binding	1
ribonucleoside triphosphate phosphatase activity	1
primary active transmembrane transporter activity	1
ATP hydrolysis activity	1
ATPase-coupled transmembrane transporter activity	1
nucleoside phosphate binding	1
heterocyclic compound binding	1
membrane	1
cell periphery	1
secretory granule	1
cytoplasmic vesicle membrane	1
bounding membrane of organelle	1
lysosomal membrane	1
secretory granule membrane	1
azurophil granule	1
intracellular anatomical structure	1
vesicle	1
intracellular membrane-bounded organelle	1
cellular anatomical structure	1
vesicle membrane	1
cytoplasmic vesicle	1
cytoplasm	1
intracellular vesicle	1

Protein interactions and networks

STRING

1266 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ABCA13	ABCD4	O14678	580
ABCA13	PHETA1	Q8N4B1	548
ABCA13	CUX2	O14529	547
ABCA13	TSPEAR	Q8WU66	521
ABCA13	PCLO	Q9Y6V0	520
ABCA13	DRD4	P21917	500
ABCA13	SNRNP70	P08621	492
ABCA13	ABCC9	O60706	489
ABCA13	ABCF2	Q9UG63	475
ABCA13	DAOA	P59103	464
ABCA13	PPP3CC	P48454	460
ABCA13	ZNF573	Q86YE8	452
ABCA13	PRODH	O43272	445
ABCA13	COL19A1	Q14993	445
ABCA13	DAO	P14920	443

IntAct

8 interactions, top by confidence:

A	B	Type	Score
	ESYT2	psi-mi:“MI:0914”(association)	0.350
	E2F3	psi-mi:“MI:0914”(association)	0.350
NEK4	E2F8	psi-mi:“MI:0914”(association)	0.350
CUL3	PXDNL	psi-mi:“MI:0914”(association)	0.350
P		psi-mi:“MI:0914”(association)	0.350
ATG16L1	ESYT2	psi-mi:“MI:0914”(association)	0.350
KLHL22	TRAV18	psi-mi:“MI:0914”(association)	0.350

BioGRID (26): HAGH (Co-fractionation), ABCA13 (Biochemical Activity), ABCA13 (Affinity Capture-RNA), ABCA13 (Affinity Capture-MS), ABCA13 (Affinity Capture-MS), ABCA13 (Affinity Capture-MS), ABCA13 (Affinity Capture-MS), ABCA13 (Affinity Capture-MS), HIST1H2BH (Cross-Linking-MS (XL-MS)), HIST1H1C (Cross-Linking-MS (XL-MS)), VDAC1 (Cross-Linking-MS (XL-MS)), ABCA13 (Affinity Capture-MS), HSP90AB1 (Cross-Linking-MS (XL-MS)), PMS1 (Cross-Linking-MS (XL-MS)), ABCA13 (Co-fractionation)

ESM2 similar proteins: A0JPP4, A6H7F9, A7WNB0, C0HMB7, C6KI89, E9Q355, E9Q876, F5HGK9, O36397, O75969, O77797, P01586, P03319, P04823, P06740, P14683, P25140, P28907, Q00997, Q02484, Q15846, Q2TAV2, Q2YDM0, Q3TBN1, Q3ZRW6, Q3ZRW7, Q3ZRW9, Q499E0, Q5BK38, Q5BKX0, Q5CCK0, Q5RBQ2, Q5RDR5, Q5RII3, Q5SSE9, Q5VAN0, Q68FB2, Q6AY76, Q6DFY8, Q6UWF9

Diamond homologs: A0A0G2K1Q8, C0SPB4, E9PU17, E9PX95, E9Q876, F1MWM0, O35600, O52618, O95477, P08720, P0A9U1, P0A9U2, P0DXG8, P0DXU5, P0DXU7, P19844, P22040, P23703, P26050, P30750, P32010, P36879, P37624, P41233, P41234, P44785, P50332, P54592, P55476, P63355, P63356, P70970, P72335, P78363, P94374, P94440, Q05067, Q0I5E9, Q0TLD2, Q13ZJ1

SIGNOR signaling

1 interactions.

A	Effect	B	Mechanism
ABCA13	“up-regulates quantity”	cholesterol	relocalization

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	4
Likely pathogenic	3
Uncertain significance	724
Likely benign	110
Benign	39

Top pathogenic / likely-pathogenic (7)

Variant ID	HGVS	Classification
145645	GRCh38/hg38 7p13-12.1(chr7:44571949-53699760)x1	Pathogenic
147754	GRCh38/hg38 7p14.1-12.1(chr7:40020598-50543500)x1	Pathogenic
419105	NM_152701.5(ABCA13):c.4338dup (p.Pro1447fs)	Pathogenic
441541	GRCh37/hg19 7p21.3-12.1(chr7:11048840-52863626)x3	Pathogenic
210065	NM_152701.5(ABCA13):c.11473+2T>C	Likely pathogenic
3024159	NM_152701.5(ABCA13):c.12064C>T (p.Arg4022Ter)	Likely pathogenic
3024201	NM_152701.5(ABCA13):c.2510del (p.Leu837fs)	Likely pathogenic

SpliceAI

11702 predictions. Top by Δscore:

Variant	Effect	Δscore
7:48198233:CTAG:C	acceptor_loss	1.0000
7:48198235:A:AG	acceptor_gain	1.0000
7:48198236:G:GG	acceptor_gain	1.0000
7:48198359:CGGT:C	donor_loss	1.0000
7:48198360:GGTAA:G	donor_loss	1.0000
7:48198361:G:GA	donor_loss	1.0000
7:48198361:G:GG	donor_gain	1.0000
7:48198362:T:TC	donor_loss	1.0000
7:48227260:A:AC	acceptor_loss	1.0000
7:48227260:A:AG	acceptor_gain	1.0000
7:48227260:AGAT:A	acceptor_gain	1.0000
7:48227260:AGATG:A	acceptor_gain	1.0000
7:48227261:G:GA	acceptor_gain	1.0000
7:48227261:G:GT	acceptor_loss	1.0000
7:48227261:GAT:G	acceptor_gain	1.0000
7:48227261:GATG:G	acceptor_gain	1.0000
7:48227261:GATGG:G	acceptor_gain	1.0000
7:48227423:GAA:G	donor_gain	1.0000
7:48227426:G:GG	donor_gain	1.0000
7:48227449:C:CG	donor_gain	1.0000
7:48234149:G:GT	donor_gain	1.0000
7:48240856:C:A	acceptor_gain	1.0000
7:48240864:TA:T	acceptor_loss	1.0000
7:48240865:A:G	acceptor_loss	1.0000
7:48240865:AGGT:A	acceptor_gain	1.0000
7:48240866:GGT:G	acceptor_gain	1.0000
7:48240866:GGTG:G	acceptor_gain	1.0000
7:48240866:GGTGT:G	acceptor_gain	1.0000
7:48241045:A:G	donor_gain	1.0000
7:48241062:AAGAT:A	donor_gain	1.0000

AlphaMissense

33689 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
7:48352265:G:C	R3489P	0.994
7:48594719:A:C	S4884R	0.992
7:48594721:C:A	S4884R	0.992
7:48594721:C:G	S4884R	0.992
7:48317218:G:C	W3307C	0.990
7:48317218:G:T	W3307C	0.990
7:48350819:A:C	S3461R	0.989
7:48352182:T:A	S3461R	0.989
7:48352182:T:G	S3461R	0.989
7:48317216:T:A	W3307R	0.988
7:48317216:T:C	W3307R	0.988
7:48587251:C:A	A4868D	0.986
7:48528246:T:C	L4752P	0.985
7:48587250:G:C	A4868P	0.985
7:48317244:G:T	G3316V	0.984
7:48594717:C:A	P4883H	0.984
7:48615309:C:G	C4923W	0.984
7:48352255:T:G	Y3486D	0.983
7:48352282:A:C	S3495R	0.983
7:48352284:C:A	S3495R	0.983
7:48352284:C:G	S3495R	0.983
7:48587236:G:C	R4863P	0.983
7:48594714:A:T	E4882V	0.982
7:48352399:G:C	A3534P	0.981
7:48372429:A:C	S3689R	0.981
7:48372431:C:A	S3689R	0.981
7:48372431:C:G	S3689R	0.981
7:48580278:T:G	C4803W	0.981
7:48587281:T:C	L4878P	0.981
7:48594798:T:A	V4910E	0.981

dbSNP variants (sampled 300 via entrez): RS1000004995 (7:48597814 C>T), RS1000007849 (7:48196572 C>T), RS1000025969 (7:48421301 A>G), RS1000026649 (7:48441051 C>G,T), RS1000026909 (7:48394851 A>C,G), RS1000028961 (7:48517388 T>C), RS1000033608 (7:48475160 C>A), RS1000037606 (7:48235663 A>G), RS1000041255 (7:48182809 A>G), RS1000042530 (7:48323614 A>G,T), RS1000047203 (7:48471186 G>C), RS1000062697 (7:48603961 G>T), RS1000065737 (7:48176587 A>G), RS1000069270 (7:48639637 G>A), RS1000078728 (7:48441481 C>T)

Disease associations

OMIM: gene MIM:607807 | disease phenotypes: MIM:181500, MIM:190300

GenCC curated gene-disease

Disease	Classification	Inheritance
schizophrenia	Limited	Unknown

Mondo (2): schizophrenia (MONDO:0005090), essential tremor (MONDO:0003233)

Orphanet (2): NON RARE IN EUROPE: Schizophrenia (Orphanet:3140), NON RARE IN EUROPE: Hereditary essential tremor (Orphanet:862)

HPO phenotypes

1 total (1 of 1 shown, HPO-id order):

HPO	Term
HP:0100753	Schizophrenia

GWAS associations

6 associations (top):

Study	Trait	p-value
GCST002685_13	Refractive astigmatism	4.000000e-06
GCST002793_2	Vein graft stenosis in coronary artery bypass grafting	5.000000e-06
GCST003134_24	Cerebrospinal fluid clusterin levels	9.000000e-06
GCST003875_2	Gut microbiota (bacterial taxa)	4.000000e-14
GCST004642_4	QT interval (ambient particulate matter interaction)	2.000000e-06
GCST90093090_6	DHEAS levels	8.000000e-06

EFO canonical traits (6, from GWAS)

EFO ID	Trait name
EFO:0007051	vein graft stenosis
EFO:0007874	gut microbiome measurement
EFO:0007883	taxonomic microbiome measurement
EFO:0004682	QT interval
EFO:0008255	particulate matter air pollution measurement
EFO:0007001	dehydroepiandrosterone sulphate measurement

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
D020329	Essential Tremor	C10.228.662.350

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

GtoPdb / IUPHAR curated pharmacology

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

Target class: transporter — ABCA subfamily

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, increases expression, decreases methylation	6
Cadmium Chloride	decreases reaction, increases abundance, increases palmitoylation, decreases expression, increases expression	3
Cadmium	decreases expression, decreases reaction, increases abundance, increases palmitoylation	2
Phenylmercuric Acetate	affects cotreatment, increases expression	2
fluorene-9-bisphenol	decreases expression	1
urushiol	increases expression	1
kojic acid	decreases expression	1
trichostatin A	increases expression	1
sodium arsenite	increases expression	1
2-bromopalmitate	decreases reaction, increases abundance, increases palmitoylation	1
S-(1,2-dichlorovinyl)cysteine	affects response to substance, increases expression	1
CGP 52608	increases reaction, affects binding	1
2-palmitoylglycerol	increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	1
clothianidin	increases expression	1
abrine	increases expression	1
dorsomorphin	affects cotreatment, increases expression	1
jinfukang	affects cotreatment, increases expression	1
NSC 689534	affects binding, increases expression	1
Temozolomide	increases expression	1
Arbutin	decreases expression	1
Benzo(a)pyrene	decreases expression	1
Caffeine	increases phosphorylation	1
Cisplatin	affects cotreatment, increases expression	1
Colchicine	affects response to substance	1
Copper	affects binding, increases expression	1
Lipopolysaccharides	affects response to substance, increases expression	1
Nickel	decreases expression	1
Tobacco Smoke Pollution	decreases expression	1

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT00000374	PHASE4	COMPLETED	Treatment for First-Episode Schizophrenia
NCT00001656	PHASE4	COMPLETED	Comparison of Clozapine vs Olanzapine in Childhood-Onset Psychotic Disorders
NCT00007774	PHASE4	COMPLETED	To Determine if Olanzapine is More Cost Effective Than Haloperidol for the Treatment of Schizophrenia
NCT00014001	PHASE4	COMPLETED	CATIE- Schizophrenia Trial
NCT00018668	PHASE4	COMPLETED	Antipsychotic Response in Schizophrenia
NCT00034801	PHASE4	COMPLETED	Olanzapine Versus Active Comparator in the Treatment of Depression in Patients With Schizophrenia
NCT00034905	PHASE4	COMPLETED	A Comparison of Seroquel vs. Risperidone in Schizophrenia
NCT00036088	PHASE4	COMPLETED	Olanzapine Versus An Active Comparator in the Treatment of Schizophrenia
NCT00044187	PHASE4	COMPLETED	The Assessment of a Weight-Gain Agent for the Treatment of Olanzapine-Associated Anti-Obesity Agent in Patients With Schizophrenia, Schizophreniform Disorder, Schizoaffective Disorder, and Bipolar I Disorder
NCT00044655	PHASE4	COMPLETED	Switching Medication to Treat Schizophrenia
NCT00048828	PHASE4	COMPLETED	Treating Drug-Resistant Childhood Schizophrenia
NCT00053703	PHASE4	COMPLETED	Treatment of Early Onset Schizophrenia Spectrum Disorders (TEOSS)
NCT00056498	PHASE4	COMPLETED	Risperidone Treatment in Schizophrenia Patients Who Are Currently Taking Clozapine
NCT00061802	PHASE4	COMPLETED	Efficacy and Safety of Two Atypical Antipsychotics vs. Placebo in Patients With an Acute Exacerbation of Either Schizophrenia or Schizoaffective Disorder
NCT00080327	PHASE4	COMPLETED	Study of Three Doses of Aripiprazole in Patients With Acute Schizophrenia
NCT00088049	PHASE4	COMPLETED	Study of Olanzapine vs. Aripiprazole in the Treatment of Schizophrenia
NCT00090012	PHASE4	COMPLETED	Comparison of Continuing Olanzapine to Switching to Quetiapine in Overweight or Obese Patients With Schizophrenia and Schizoaffective Disorder
NCT00100776	PHASE4	COMPLETED	Efficacy of High Dose Olanzapine for the Treatment of Schizophrenia and Schizoaffective Disorder
NCT00103571	PHASE4	COMPLETED	Olanzapine Versus Aripiprazole in the Treatment of Acutely Ill Patients With Schizophrenia
NCT00108368	PHASE4	COMPLETED	The Effects of Risperidone and Olanzapine on Thinking
NCT00114595	PHASE4	COMPLETED	Ethyl-Eicosapentaenoic Acid and Tardive Dyskinesia
NCT00130923	PHASE4	COMPLETED	Risperidone Long-acting Versus Oral Risperidone in Patients With Schizophrenia and Alcohol Use Disorder
NCT00137020	PHASE4	COMPLETED	Clinical Effect Of Cross Titration Of Antipsychotics With Ziprasidone In Schizophrenia Or Schizoaffective Disorder
NCT00140166	PHASE4	COMPLETED	Treatment of Acute Schizophrenia With Vitamin Therapy
NCT00145847	PHASE4	COMPLETED	Naltrexone Treatment of Alcohol Abuse in Schizophrenia
NCT00148564	PHASE4	COMPLETED	Energy Homeostasis Under Treatment With Atypical Antipsychotics
NCT00156715	PHASE4	COMPLETED	Efficacy of Quetiapine in the Treatment of Patients With Schizophrenia and a Comorbid Substance Use Disorder
NCT00158223	PHASE4	COMPLETED	Effectiveness of Pimozide in Augmenting the Effects of Clozapine in the Treatment of Schizophrenia
NCT00159081	PHASE4	COMPLETED	One Year Drug Treatment in First-Episode Schizophrenia
NCT00159120	PHASE4	COMPLETED	Maintenance Treatment vs. Stepwise Drug Discontinuation in First-Episode Schizophrenia
NCT00159133	PHASE4	COMPLETED	Prodrome-Based Early Intervention With Antipsychotics vs. Benzodiazepines in First-Episode Schizophrenia
NCT00159757	PHASE4	TERMINATED	12 Week Open, Non-Comparative Switch Study Of Oral Ziprazidone In Previously Treated Schizophrenic Patients
NCT00167817	PHASE4	COMPLETED	Effect of Switch to Aripiprazole on Health and Smoking Parameters in Patients With Schizophrenia: A Pilot Study
NCT00169026	PHASE4	TERMINATED	Alcoholism and Schizophrenia: Effects of Clozapine
NCT00169039	PHASE4	TERMINATED	Clozapine Versus Chlorpromazine for Treatment-Unresponsive Schizophrenia
NCT00169065	PHASE4	COMPLETED	Effectiveness of Clozapine Versus Olanzapine for Treatment-resistant Schizophrenia
NCT00169091	PHASE4	TERMINATED	Clozapine Versus Haloperidol for Treating the First Episode of Schizophrenia
NCT00176423	PHASE4	COMPLETED	Efficacy Study of Galantamine for Cognitive Impairments in Schizophrenia
NCT00176436	PHASE4	COMPLETED	Atomoxetine for Treatment of Weight Gain in Olanzapine or Clozapine Patients
NCT00177008	PHASE4	COMPLETED	Aripiprazole for the Treatment of Schizophrenia With Co-Morbid Social Anxiety