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): 961 total — 5 pathogenic, 3 likely-pathogenic (top 3% of genes corpus-wide)
• Regional missense constraint (gnomAD): 1 of 3 regions constrained (≈1% of expected missense variation)
• GTEx eGene: eQTL in 11 tissues, sQTL in 0 (q < 0.05)
• Constraint (gnomAD): pLI 0.00 (LoF-tolerant), LOEUF 1.06 (unconstrained)
• MANE Select transcript: NM_152701
• Notable: 961 clinical variants but no curated precision-oncology (CIViC) evidence yet

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: 10 — 6 protein_coding, 2 nonsense_mediated_decay, 1 retained_intron, 1 protein_coding_CDS_not_defined

MANE Select: ENST00000435803

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

ENST00000435803, ENST00000411975, ENST00000417403, ENST00000435451, ENST00000453246, ENST00000484268, ENST00000544596, ENST00000611776, ENST00001110746, ENST00001142162

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.

Highest expression (Bgee): bronchial epithelial cell, bronchus, epithelium of nasopharynx, olfactory segment of nasal mucosa, mucosa of paranasal sinus.

Genetic regulation across tissues (GTEx eQTL / sQTL)

ABCA13 is an eGene in GTEx v10 — its expression is genetically regulated (eQTL) in 11 tissues and its splicing (sQTL) in 0 (q < 0.05). Strongest associations first; slope = normalized effect of the lead variant’s alternative allele.

11 significant tissue × QTL associations:

Tissue	QTL	q-value	Slope	Lead variant
Esophagus Mucosa	eqtl	8.8e-27	-0.50	7:48189576:C:T
Testis	eqtl	2.5e-11	+0.41	7:48192383:A:G
Thyroid	eqtl	1.6e-06	-0.19	7:48175967:G:A
Small Intestine Terminal Ileum	eqtl	2.6e-06	+0.35	7:48201539:C:G
Nerve Tibial	eqtl	4.1e-05	-0.10	7:48285300:C:A
Brain Nucleus accumbens basal ganglia	eqtl	1.0e-04	+1.45	7:48525793:G:A
Skin Not Sun Exposed Suprapubic	eqtl	2.0e-03	-0.21	7:48613032:C:T
Whole Blood	eqtl	4.0e-03	+0.12	7:48158439:A:C
Lung	eqtl	4.9e-03	+0.18	7:48279214:C:T
Skin Sun Exposed Lower leg	eqtl	6.9e-03	-0.23	7:48519062:G:A
Minor Salivary Gland	eqtl	1.3e-02	-0.40	7:48202451:G:T

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

showing 100 of 223 tissues 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
trigeminal ganglion	UBERON:0001675	55.75	gold quality
islet of Langerhans	UBERON:0000006	55.59	gold quality
lower lobe of lung	UBERON:0008949	55.54	silver quality
left testis	UBERON:0004533	55.36	gold quality
tonsil	UBERON:0002372	55.20	gold quality
minor salivary gland	UBERON:0001830	55.16	gold quality
metanephros cortex	UBERON:0010533	55.07	gold quality
adenohypophysis	UBERON:0002196	54.68	gold quality
mouth mucosa	UBERON:0003729	53.94	gold quality
gall bladder	UBERON:0002110	53.69	gold quality
lung	UBERON:0002048	51.70	gold quality
saliva-secreting gland	UBERON:0001044	51.68	gold quality
skin of abdomen	UBERON:0001416	51.13	gold quality
metanephros	UBERON:0000081	50.68	gold quality
upper lobe of lung	UBERON:0008948	50.62	gold quality
upper lobe of left lung	UBERON:0008952	50.26	gold quality
dorsal root ganglion	UBERON:0000044	49.70	gold quality
pituitary gland	UBERON:0000007	49.68	gold quality
zone of skin	UBERON:0000014	49.21	gold quality
vermiform appendix	UBERON:0001154	48.97	gold quality
right lobe of liver	UBERON:0001114	48.87	gold quality
cerebellar vermis	UBERON:0004720	48.63	gold quality
pancreas	UBERON:0001264	48.18	gold quality
gingiva	UBERON:0001828	47.65	silver quality
skin of leg	UBERON:0001511	47.48	gold quality
ventricular zone	UBERON:0003053	47.27	silver quality
caecum	UBERON:0001153	46.93	gold quality
liver	UBERON:0002107	46.91	gold quality
esophagus	UBERON:0001043	46.84	gold quality
nucleus accumbens	UBERON:0001882	46.81	gold quality
urinary bladder	UBERON:0001255	46.77	gold quality
granulocyte	CL:0000094	46.75	silver quality
endometrium	UBERON:0001295	46.55	gold quality
adult organism	UBERON:0007023	46.54	silver quality
spleen	UBERON:0002106	46.34	gold quality
rectum	UBERON:0001052	45.49	gold quality
duodenum	UBERON:0002114	44.96	gold quality
nipple	UBERON:0002030	44.63	gold quality
gingival epithelium	UBERON:0001949	44.57	silver quality
kidney	UBERON:0002113	44.31	gold quality
adult mammalian kidney	UBERON:0000082	44.25	gold quality
mammalian vulva	UBERON:0000997	44.24	silver quality
anatomical system	UBERON:0000467	43.95	gold quality
multicellular organism	UBERON:0000468	43.92	gold quality
adrenal tissue	UBERON:0018303	43.92	silver quality
material anatomical entity	UBERON:0000465	43.91	gold quality
body of pancreas	UBERON:0001150	43.61	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	43.37	gold quality
amniotic fluid	UBERON:0000173	43.04	gold quality
uterine cervix	UBERON:0000002	42.94	gold quality
thymus	UBERON:0002370	42.90	gold quality
vagina	UBERON:0000996	42.74	gold quality
secondary oocyte	CL:0000655	42.57	gold quality
endocervix	UBERON:0000458	42.46	gold quality
quadriceps femoris	UBERON:0001377	42.39	gold quality
cortex of kidney	UBERON:0001225	42.18	gold quality
esophagus squamous epithelium	UBERON:0006920	42.14	silver quality
hindlimb stylopod muscle	UBERON:0004252	42.05	gold quality
palpebral conjunctiva	UBERON:0001812	41.88	gold quality
germinal epithelium of ovary	UBERON:0001304	41.71	silver quality
cartilage tissue	UBERON:0002418	41.67	gold quality
small intestine	UBERON:0002108	41.54	gold quality
vastus lateralis	UBERON:0001379	41.41	gold quality
superficial temporal artery	UBERON:0001614	41.33	gold quality
uterus	UBERON:0000995	41.21	gold quality
skeletal muscle tissue	UBERON:0001134	41.15	gold quality
colonic epithelium	UBERON:0000397	40.99	gold quality
female reproductive system	UBERON:0000474	40.87	gold quality
muscle tissue	UBERON:0002385	40.74	gold quality
jejunal mucosa	UBERON:0000399	40.59	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

HPA expression

RNA tissue specificity: Tissue enriched

60 HPA tissues / cells by nTPM:

Tissue / cell	Axis	nTPM
Bone marrow	tissue	42.1
Cerebral cortex	tissue	5.9
Insular cortex	tissue	5.9
Putamen	tissue	5.7
Basal ganglia	tissue	5.6
Retrosplenial cortex	tissue	5.4
Motor cortex	tissue	5.2
Retrosplenial and cingulate cortex	tissue	5.1
Prefrontal cortex	tissue	4.8
Somatosensory cortex	tissue	4.8
Occipital cortex	tissue	4.8
Ventral forebrain	tissue	4.7
Cerebellum	tissue	4.6
Olfactory bulb	tissue	4.5
Hippocampal formation	tissue	4.4
Entorhinal cortex	tissue	4.4
Temporal cortex	tissue	4.4
Septum	tissue	4.0
Amygdala	tissue	3.7
Hypothalamus	tissue	3.6
Substantia nigra	tissue	3.3
Periaqueductal gray	tissue	3.2
Pons	tissue	3.1
Midbrain	tissue	3.1
Thalamus	tissue	3.0
Medulla oblongata	tissue	2.8
Superior colliculi	tissue	2.5
Corpus callosum	tissue	2.5
Spinal cord	tissue	2.3
Tonsil	tissue	1.6
Testis	tissue	1.5
Thyroid gland	tissue	1.3
Pituitary gland	tissue	1.2
Choroid plexus	tissue	1.1
Fallopian tube	tissue	1.1
Epididymis	tissue	1.0
Nucleus accumbens	tissue	1.0
Skin 1	tissue	0.9
Hippocampus	tissue	0.9
Esophagus	tissue	0.7
Breast	tissue	0.6
Pancreas	tissue	0.6
Lung	tissue	0.6
Kidney	tissue	0.5
Locus coeruleus	tissue	0.5
Thymus	tissue	0.5
Retina	tissue	0.4
Postcentral gyrus	tissue	0.4
Cervix	tissue	0.3
Gallbladder	tissue	0.3
Vagina	tissue	0.2
Seminal vesicle	tissue	0.2
Rectum	tissue	0.2
Colon	tissue	0.2
Duodenum	tissue	0.2
Lymph node	tissue	0.1
Urinary bladder	tissue	0.1
Endometrium 1	tissue	0.1
Small intestine	tissue	0.1
Appendix	tissue	0.1

Brain sub-regions (HPA Brain Atlas): detected in 188; highest nTPM — Dorsal hippocampus (4.2), Subiculum (4.2), Ventral hippocampus (4.1), White matter (2.5), Dorsal spinal cord (2.3).

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

Targeting ABCA13 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific).

showing 30 of 77 miRNAs:

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

Functional genomics

gnomAD constraint: pLI 3e-140, LOEUF 1.06, missense Z -0.0978 — population loss-of-function intolerance (pLI ≥ 0.9 = LoF-intolerant; lower LOEUF = more constrained). gnomAD

Regional missense constraint (gnomAD)

ENST00000435803 splits into 3 regions with different missense tolerance; 1 is missense-constrained (≈1% of the expected missense variation). Missense variants in a constrained region (low observed/expected) are more likely to be pathogenic. gnomAD

Region (GRCh38)	Missense obs / exp	o/e	Constrained
7:48,171,484–48,376,491	4423 / 4309.1	1.03	no
7:48,376,492–48,387,822	10 / 30.5	0.33	yes (p 2.0e-04)
7:48,387,823–48,645,509	1627 / 1571.0	1.04	no

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)

Mouse-model phenotypes

Observed phenotypes of the mouse ortholog (MGI:2388707) from MGI (Alliance of Genome Resources) — knockout/mutant phenotypes, ranked by annotation count. 7 distinct phenotype terms.

Mouse phenotype (MP)	Records
decreased prepulse inhibition	2
persistence of hyaloid vascular system	1
decreased circulating alkaline phosphatase level	1
abnormal neuron physiology	1
abnormal male genitalia morphology	1
abnormal retina blood vessel morphology	1
abnormal synaptic vesicle endocytosis	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
Mycobacterium tuberculosis CDC1551	P9WQL8	100.0%	Diamond
Mycobacterium tuberculosis H37Rv	P9WQL9	100.0%	Diamond
Burkholderia pseudomallei 1710b	Q3JSQ0	100.0%	Diamond
Burkholderia mallei ATCC 23344	Q62K72	100.0%	Diamond
Rhizobium leguminosarum bv. viciae	P08720	99.7%	Diamond
Rhizobium johnstonii 3841	Q1M7W6	99.7%	Diamond
Burkholderia pseudomallei K96243	Q63TX3	99.7%	Diamond
Bradyrhizobium diazoefficiens USDA 110	P26050	97.4%	Diamond
Bradyrhizobium sp. SNU001	Q9Z3I3	97.4%	Diamond
Burkholderia orbicola AU 1054	Q1BWI2	95.7%	Diamond
Burkholderia lata	Q39GT7	95.7%	Diamond
Sinorhizobium meliloti 1021	O52618	91.9%	Diamond
Sinorhizobium meliloti	Q8GNH6	91.9%	Diamond
Bos taurus	F1MWM0	89.4%	Diamond
Arabidopsis thaliana	Q8RWI9	86.1%	Diamond
Mesorhizobium japonicum MAFF 303099	P23703	82.5%	Diamond
Rhizobium sp. N33	P72335	82.5%	Diamond
Rhizobium etli CFN 42	Q8KLG1	80.0%	Diamond
Sinorhizobium fredii NGR234	P55476	77.5%	Diamond
Ralstonia pseudosolanacearum GMI1000	Q8XXY9	74.7%	Diamond
Neorhizobium galegae	P50332	74.6%	Diamond
Nostoc sp. PCC 7120 = FACHB-418	Q05067	63.4%	Diamond
Bacillus subtilis subsp. subtilis str. 168	C0SPB4	62.8%	Diamond
Alkalihalophilus pseudofirmus OF4	P26946	62.8%	Diamond
Streptomyces coeruleorubidus	P0DXU5	61.6%	Diamond
Dictyostelium discoideum	Q8T6J5	61.6%	Diamond
Levilactobacillus brevis ATCC 367	Q03SI5	60.1%	Diamond
Saccharomyces cerevisiae S288C	Q12298	55.3%	Diamond
Escherichia coli	P05529	42.0%	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
LINC03212	ncRNA	105375272
C7orf57	protein-coding	136288
SUN3	protein-coding	256979
UPP1	protein-coding	7378
LINC02838	ncRNA	105375273

Protein

Protein identifiers

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

All UniProt accessions (5): F5H7B7, Q86UQ4, 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)

• 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

Predicted structure (AlphaFold)

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

Human Protein Atlas

Protein class: Predicted membrane proteins

Protein evidence: Evidence at transcript level

Subcellular location (HPA, imaging): nucleoplasm; vesicles; basal body; centrosome; cytosol

Antibody reliability (HPA): IF approved

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)

Position	Role
3875–3882	ATP
4754–4761	ATP

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-6798695	Neutrophil degranulation	curated
R-HSA-168256	Immune System	—
R-HSA-168249	Innate 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

2 top-level categories:

Category	Pathways
Innate Immune System	1
Immune System	1

GO top-level categories

39 GO namespaces:

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
anion 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

Experimentally-supported GO annotations

GO terms backed by direct experimental evidence (ECO experimental codes) — 2 of 18 annotations. The rest are phylogenetic / computational / electronic (IEA).

2 experimentally-supported GO terms:

GO term	NS	Evidence
positive regulation of cholesterol transport	BP	direct assay
intracellular vesicle	CC	direct assay

Protein interactions and networks

STRING

showing 15 of 1,032 interactions by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ABCA13	ABCD4	O14678	587
ABCA13	PCLO	Q9Y6V0	570
ABCA13	PHETA1	Q8N4B1	552
ABCA13	CUX2	O14529	551
ABCA13	TSPEAR	Q8WU66	541
ABCA13	MUC16	Q8WXI7	520
ABCA13	OBSCN	Q5VST9	500
ABCA13	ABCF2	Q9UG63	497
ABCA13	DRD4	P21917	496
ABCA13	SNRNP70	P08621	490
ABCA13	ABCC9	O60706	479
ABCA13	LRP1B	Q9NZR2	473
ABCA13	ABCC6	P78420	471
ABCA13	SLCO3A1	Q9UIG8	454
ABCA13	DAOA	P59103	451

IntAct

BioGRID (29 interactions; top human partners by supporting records): CUL3 (Affinity Capture-MS; 2 records), APOA1 (Reconstituted Complex), APOA2 (Reconstituted Complex), CIAO1 (Proximity Label-MS), CLK1 (Biochemical Activity), DDA1 (Proximity Label-MS), ECT2 (Affinity Capture-MS), EFNA3 (Affinity Capture-MS), FANCD2 (Affinity Capture-MS), HAGH (Co-fractionation), HIST1H1C (Cross-Linking-MS (XL-MS)), HIST1H2BH (Cross-Linking-MS (XL-MS)), HSP90AB1 (Cross-Linking-MS (XL-MS)), KIF23 (Affinity Capture-MS), NEK4 (Affinity Capture-MS)

SIGNOR signaling

1 signaling interactions:

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

Disease & clinical

Genetic variants

Variant evidence for ABCA13: 961 ClinVar records (8 pathogenic / likely pathogenic); 6 GWAS associations. Per-variant detail is on Sugi Variant.

ClinVar

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

Classification	Count (floor)
Pathogenic	5
Likely pathogenic	3
Uncertain significance	737
Likely benign	114
Benign	38

Top pathogenic / likely-pathogenic (8)

Showing all 8 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
419105	NM_152701.5(ABCA13):c.4338dup (p.Pro1447fs)	Pathogenic	criteria provided, single submitter	1
210065	NM_152701.5(ABCA13):c.11473+2T>C	Likely pathogenic	criteria provided, single submitter	1
3024159	NM_152701.5(ABCA13):c.12064C>T (p.Arg4022Ter)	Likely pathogenic	criteria provided, single submitter	1
3024201	NM_152701.5(ABCA13):c.2510del (p.Leu837fs)	Likely pathogenic	criteria provided, single submitter	1
1527356	GRCh37/hg19 7p14.1-12.2(chr7:40778439-50228656)x1	Pathogenic	criteria provided, single submitter	1
145645	GRCh38/hg38 7p13-12.1(chr7:44571949-53699760)x1	Pathogenic	no assertion criteria provided	1
147754	GRCh38/hg38 7p14.1-12.1(chr7:40020598-50543500)x1	Pathogenic	no assertion criteria provided	1
441541	GRCh37/hg19 7p21.3-12.1(chr7:11048840-52863626)x3	Pathogenic	no assertion criteria provided	1

Per-variant reference — Sugi Variant

Explore ABCA13’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; 37 predictions of 6,344):

Position(s)	Effect	Δscore	Sites
7:48198235–48198236	acceptor_loss	1.0000	6
7:48198361–48198362	donor_loss	1.0000	5
7:48227260–48227261	acceptor_loss	1.0000	4
7:48240856	acceptor_gain	1.0000
7:48240865–48240866	acceptor_loss	1.0000	5
7:48241045	donor_gain	1.0000
7:48241067–48241068	donor_loss	1.0000	4
7:48244567	acceptor_gain	1.0000
7:48244574–48244575	acceptor_loss	1.0000	6
7:48244704–48244705	donor_loss	1.0000	4

AlphaMissense

3,184 missense substitutions predicted likely pathogenic (of 33,689 scored), across 1,132 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
D4881	8	0.914	0.960
D4888	8	0.907	0.950
F4750	8	0.890	0.971
F3524	8	0.882	0.975
F3464	8	0.856	0.962
F4764	8	0.845	0.962
M4887	8	0.837	0.939
F4525	8	0.813	0.964
H4914	8	0.807	0.921
N4535	8	0.805	0.954
D4507	8	0.803	0.863
F3719	8	0.786	0.935
F37	8	0.781	0.930
D4000	8	0.770	0.861
C3290	7	0.966	0.980
E4882	7	0.956	0.982
C3430	7	0.950	0.969
W3307	7	0.940	0.990
K4760	7	0.930	0.972
C4803	7	0.908	0.981

HPA cancer prognostics

RNA cancer specificity: Cancer enhanced (Lung Squamous Cell Carcinoma)

Disease associations

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

GenCC curated gene-disease

1 curated gene-disease records:

Disease	Classification	Inheritance	Records
schizophrenia	Limited	Unknown

Mondo (1): schizophrenia (MONDO:0005090)

Orphanet (1): NON RARE IN EUROPE: Schizophrenia (Orphanet:3140)

GWAS associations

6 associations:

Study	Trait	p-value
GCST003875_16	Gut microbiota (bacterial taxa)	4e-14
GCST004642_4	QT interval (ambient particulate matter interaction)	2e-6
GCST002685_13	Refractive astigmatism	4e-6
GCST002793_2	Vein graft stenosis in coronary artery bypass grafting	5e-6
GCST90093090_4	DHEAS levels	8e-6
GCST003134_24	Cerebrospinal fluid clusterin levels	9e-6

EFO canonical traits (from GWAS)

6 canonical traits:

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

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 — 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	increases abundance, increases palmitoylation, decreases expression, decreases reaction	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	affects binding, increases reaction	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	increases expression, affects cotreatment	1
NSC 689534	increases expression, affects binding	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)

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

showing 60 of 300 trials:

NCT	Phase	Status	Title
NCT00000374	Phase 4	COMPLETED	Treatment for First-Episode Schizophrenia
NCT00001656	Phase 4	COMPLETED	Comparison of Clozapine vs Olanzapine in Childhood-Onset Psychotic Disorders
NCT00007774	Phase 4	COMPLETED	To Determine if Olanzapine is More Cost Effective Than Haloperidol for the Treatment of Schizophrenia
NCT00014001	Phase 4	COMPLETED	CATIE- Schizophrenia Trial
NCT00018668	Phase 4	COMPLETED	Antipsychotic Response in Schizophrenia
NCT00034801	Phase 4	COMPLETED	Olanzapine Versus Active Comparator in the Treatment of Depression in Patients With Schizophrenia
NCT00034905	Phase 4	COMPLETED	A Comparison of Seroquel vs. Risperidone in Schizophrenia
NCT00036088	Phase 4	COMPLETED	Olanzapine Versus An Active Comparator in the Treatment of Schizophrenia
NCT00044187	Phase 4	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	Phase 4	COMPLETED	Switching Medication to Treat Schizophrenia
NCT00048828	Phase 4	COMPLETED	Treating Drug-Resistant Childhood Schizophrenia
NCT00053703	Phase 4	COMPLETED	Treatment of Early Onset Schizophrenia Spectrum Disorders (TEOSS)
NCT00056498	Phase 4	COMPLETED	Risperidone Treatment in Schizophrenia Patients Who Are Currently Taking Clozapine
NCT00061802	Phase 4	COMPLETED	Efficacy and Safety of Two Atypical Antipsychotics vs. Placebo in Patients With an Acute Exacerbation of Either Schizophrenia or Schizoaffective Disorder
NCT00080327	Phase 4	COMPLETED	Study of Three Doses of Aripiprazole in Patients With Acute Schizophrenia
NCT00088049	Phase 4	COMPLETED	Study of Olanzapine vs. Aripiprazole in the Treatment of Schizophrenia
NCT00090012	Phase 4	COMPLETED	Comparison of Continuing Olanzapine to Switching to Quetiapine in Overweight or Obese Patients With Schizophrenia and Schizoaffective Disorder
NCT00100776	Phase 4	COMPLETED	Efficacy of High Dose Olanzapine for the Treatment of Schizophrenia and Schizoaffective Disorder
NCT00103571	Phase 4	COMPLETED	Olanzapine Versus Aripiprazole in the Treatment of Acutely Ill Patients With Schizophrenia
NCT00108368	Phase 4	COMPLETED	The Effects of Risperidone and Olanzapine on Thinking
NCT00114595	Phase 4	COMPLETED	Ethyl-Eicosapentaenoic Acid and Tardive Dyskinesia
NCT00130923	Phase 4	COMPLETED	Risperidone Long-acting Versus Oral Risperidone in Patients With Schizophrenia and Alcohol Use Disorder
NCT00137020	Phase 4	COMPLETED	Clinical Effect Of Cross Titration Of Antipsychotics With Ziprasidone In Schizophrenia Or Schizoaffective Disorder
NCT00140166	Phase 4	COMPLETED	Treatment of Acute Schizophrenia With Vitamin Therapy
NCT00145847	Phase 4	COMPLETED	Naltrexone Treatment of Alcohol Abuse in Schizophrenia
NCT00148564	Phase 4	COMPLETED	Energy Homeostasis Under Treatment With Atypical Antipsychotics
NCT00156715	Phase 4	COMPLETED	Efficacy of Quetiapine in the Treatment of Patients With Schizophrenia and a Comorbid Substance Use Disorder
NCT00158223	Phase 4	COMPLETED	Effectiveness of Pimozide in Augmenting the Effects of Clozapine in the Treatment of Schizophrenia
NCT00159081	Phase 4	COMPLETED	One Year Drug Treatment in First-Episode Schizophrenia
NCT00159120	Phase 4	COMPLETED	Maintenance Treatment vs. Stepwise Drug Discontinuation in First-Episode Schizophrenia
NCT00159133	Phase 4	COMPLETED	Prodrome-Based Early Intervention With Antipsychotics vs. Benzodiazepines in First-Episode Schizophrenia
NCT00159757	Phase 4	TERMINATED	12 Week Open, Non-Comparative Switch Study Of Oral Ziprazidone In Previously Treated Schizophrenic Patients
NCT00167817	Phase 4	COMPLETED	Effect of Switch to Aripiprazole on Health and Smoking Parameters in Patients With Schizophrenia: A Pilot Study
NCT00169026	Phase 4	TERMINATED	Alcoholism and Schizophrenia: Effects of Clozapine
NCT00169039	Phase 4	TERMINATED	Clozapine Versus Chlorpromazine for Treatment-Unresponsive Schizophrenia
NCT00169065	Phase 4	COMPLETED	Effectiveness of Clozapine Versus Olanzapine for Treatment-resistant Schizophrenia
NCT00169091	Phase 4	TERMINATED	Clozapine Versus Haloperidol for Treating the First Episode of Schizophrenia
NCT00176423	Phase 4	COMPLETED	Efficacy Study of Galantamine for Cognitive Impairments in Schizophrenia
NCT00176436	Phase 4	COMPLETED	Atomoxetine for Treatment of Weight Gain in Olanzapine or Clozapine Patients
NCT00177008	Phase 4	COMPLETED	Aripiprazole for the Treatment of Schizophrenia With Co-Morbid Social Anxiety
NCT00177580	Phase 4	COMPLETED	Improving Symptoms of Schizophrenia and Schizoaffective Disorder by Supplementing Medications With Pravastatin
NCT00182442	Phase 4	COMPLETED	Cognition, Functioning and Quality of Life
NCT00182494	Phase 4	UNKNOWN	Diabetes Prevention Program in Schizophrenia [DPPS]
NCT00183625	Phase 4	COMPLETED	Supported Employment and Skills Training in Conjunction With Pharmacotherapy in Schizophrenia Patients
NCT00186771	Phase 4	UNKNOWN	Magnetic Stimulation as a Treatment for Auditory Hallucinations in Schizophrenia
NCT00190749	Phase 4	COMPLETED	Safety Study of Olanzapine and a Comparator in Patients With Schizophrenia and Schizoaffective Disorder
NCT00191555	Phase 4	COMPLETED	Efficacy Study of Switching Stabilized Schizophrenic Patients From Conventional to Atypical Antipsychotic Treatment
NCT00194025	Phase 4	COMPLETED	Valproate in Late Life Schizophrenia
NCT00199940	Phase 4	COMPLETED	Safety And Efficacy Study Of Ziprasidone In Pediatric Psychotic Illness
NCT00202306	Phase 4	COMPLETED	Indicated Prevention of Psychotic Disorders With Low-dose Lithium
NCT00203788	Phase 4	COMPLETED	Improving Work Outcome in People With Recent-onset Schizophrenia
NCT00204061	Phase 4	COMPLETED	Early Pharmacological and Psychological Intervention for Late Prodromal States of Psychosis
NCT00205660	Phase 4	COMPLETED	Changes in Adiposity, Metabolic Measures From Atypicals to Aripiprazole
NCT00206102	Phase 4	COMPLETED	A Study of the Cataractogenic Potential of Seroquel and Risperdal in the Treatment of Participants With Schizophrenia or Schizoaffective Disorder
NCT00208143	Phase 4	COMPLETED	Seroquel Therapy for Substance Use Disorders Comorbid With Schizophrenia
NCT00208169	Phase 4	COMPLETED	Abilify Therapy for Reducing Comorbid Substance Abuse
NCT00214578	Phase 4	COMPLETED	Seroquel on Glucose Metabolism
NCT00215579	Phase 4	COMPLETED	Determining the Effects of Risperdal Consta in Patients With Psychotic Disorders and Incomplete Adherence
NCT00216528	Phase 4	COMPLETED	A Study to Evaluate Symptomatic Remission in Schizophrenia With Long Acting Risperidone Microspheres
NCT00216632	Phase 4	COMPLETED	A Study of Treatment Success in Changing From Olanzapine to Long-acting Injectable Risperidone (RISPERDAL® CONSTA™)