ABCA10

Summary

ABCA10 (ATP binding cassette subfamily A member 10, HGNC:30) is a protein-coding gene on chromosome 17q24.3, encoding ATP-binding cassette sub-family A member 10 (Q8WWZ4). Probable transporter which may play a role in macrophage lipid transport and homeostasis.

The membrane-associated protein encoded by this gene is a member of the superfamily of ATP-binding cassette (ABC) transporters. ABC proteins transport various molecules across extra- and intracellular membranes. ABC genes are divided into seven distinct subfamilies (ABC1, MDR/TAP, MRP, ALD, OABP, GCN20, and White). This encoded protein is a member of the ABC1 subfamily. Members of the ABC1 subfamily comprise the only major ABC subfamily found exclusively in multicellular eukaryotes. This gene is clustered among 4 other ABC1 family members on 17q24, but neither the substrate nor the function of this gene is known.

Source: NCBI Gene 10349 — RefSeq curated summary.

At a glance

• GWAS associations: 7
• Clinical variants (ClinVar): 230 total — 2 pathogenic
• MANE Select transcript: NM_001377321

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:30
Approved symbol	ABCA10
Name	ATP binding cassette subfamily A member 10
Location	17q24.3
Locus type	gene with protein product
Status	Approved
Aliases	EST698739
Ensembl gene	ENSG00000154263
Ensembl biotype	protein_coding
OMIM	612508
Entrez	10349

Gene structure

Transcript identifiers

Ensembl transcripts: 13 — 5 nonsense_mediated_decay, 4 protein_coding, 2 protein_coding_CDS_not_defined, 2 retained_intron

ENST00000269081, ENST00000518929, ENST00000519732, ENST00000521526, ENST00000521538, ENST00000522406, ENST00000522787, ENST00000523419, ENST00000523512, ENST00000524231, ENST00000524273, ENST00000588514, ENST00000690296

RefSeq mRNA: 2 — MANE Select: NM_001377321 NM_001377321, NM_080282

CCDS: CCDS11684

Canonical transcript exons

ENST00000690296 — 39 exons

Exon	Start	End
ENSE00001014916	69201500	69201668
ENSE00001105057	69221792	69221895
ENSE00001372518	69227145	69227285
ENSE00003346005	69222533	69222697
ENSE00003467871	69153471	69153546
ENSE00003470019	69152043	69152183
ENSE00003473607	69197064	69197122
ENSE00003476231	69215815	69216000
ENSE00003478898	69174281	69174394
ENSE00003498536	69175406	69175513
ENSE00003503855	69225325	69225529
ENSE00003506184	69193110	69193248
ENSE00003512568	69149984	69150063
ENSE00003516561	69216217	69216358
ENSE00003538588	69193814	69193989
ENSE00003538790	69219545	69219771
ENSE00003542006	69155805	69155925
ENSE00003544102	69187681	69187879
ENSE00003546928	69185477	69185643
ENSE00003547375	69149033	69149088
ENSE00003557395	69182675	69182808
ENSE00003558556	69191176	69191315
ENSE00003560184	69153831	69154009
ENSE00003560839	69152362	69152481
ENSE00003562941	69214704	69214851
ENSE00003578362	69193493	69193612
ENSE00003586261	69155019	69155136
ENSE00003592115	69148007	69148925
ENSE00003601797	69156832	69156923
ENSE00003603676	69154235	69154326
ENSE00003619697	69192563	69192653
ENSE00003635211	69153305	69153399
ENSE00003641662	69164964	69165083
ENSE00003648384	69164074	69164154
ENSE00003648603	69190358	69190477
ENSE00003649214	69182153	69182290
ENSE00003661242	69194385	69194495
ENSE00003688714	69174607	69174777
ENSE00003926592	69228581	69228824

Expression profiles

Bgee: expression breadth ubiquitous, 137 present calls, max score 97.11.

FANTOM5 (CAGE): breadth broad, TPM avg 1.1133 / max 108.5102, expressed in 201 samples.

FANTOM5 promoters (8 alternative TSS)

Promoter ID	TPM avg	Samples expressed
167790	0.3607	114
167791	0.2755	94
167788	0.1632	69
167784	0.1118	24
167789	0.0935	55
167785	0.0521	13
167787	0.0430	24
167786	0.0136	6

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
tibial nerve	UBERON:0001323	97.11	gold quality
sural nerve	UBERON:0015488	96.35	gold quality
left ovary	UBERON:0002119	95.87	gold quality
right ovary	UBERON:0002118	95.11	gold quality
ovary	UBERON:0000992	94.86	gold quality
calcaneal tendon	UBERON:0003701	93.30	gold quality
right uterine tube	UBERON:0001302	92.68	gold quality
thoracic mammary gland	UBERON:0005200	92.37	gold quality
omental fat pad	UBERON:0010414	91.27	gold quality
adipose tissue	UBERON:0001013	90.70	gold quality
subcutaneous adipose tissue	UBERON:0002190	90.48	gold quality
mucosa of stomach	UBERON:0001199	90.43	gold quality
left uterine tube	UBERON:0001303	90.31	gold quality
apex of heart	UBERON:0002098	89.24	gold quality
fallopian tube	UBERON:0003889	88.98	gold quality
hindlimb stylopod muscle	UBERON:0004252	87.25	gold quality
right atrium auricular region	UBERON:0006631	86.95	gold quality
gastrocnemius	UBERON:0001388	86.86	gold quality
minor salivary gland	UBERON:0001830	86.84	gold quality
muscle of leg	UBERON:0001383	86.56	gold quality
skeletal muscle organ	UBERON:0014892	86.52	gold quality
saliva-secreting gland	UBERON:0001044	86.31	gold quality
right coronary artery	UBERON:0001625	85.90	gold quality
skeletal muscle tissue	UBERON:0001134	85.45	gold quality
right lung	UBERON:0002167	85.36	gold quality
thyroid gland	UBERON:0002046	85.26	gold quality
heart	UBERON:0000948	84.94	gold quality
right lobe of thyroid gland	UBERON:0001119	84.85	gold quality
fundus of stomach	UBERON:0001160	84.80	gold quality
heart left ventricle	UBERON:0002084	84.72	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-MTAB-11268	yes	1721.77
E-CURD-119	yes	48.84
E-ANND-3	yes	25.55

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

58 targeting ABCA10, 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-3646	100.00	73.56	5283
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-3688-3P	99.97	72.02	2834
HSA-MIR-302E	99.96	70.74	2669
HSA-MIR-23A-3P	99.95	74.24	3163
HSA-MIR-23B-3P	99.95	74.24	3163
HSA-MIR-23C	99.95	73.92	3192
HSA-MIR-106A-5P	99.90	73.94	2683
HSA-MIR-17-5P	99.89	73.83	2665
HSA-MIR-302A-3P	99.89	71.23	1777
HSA-MIR-302B-3P	99.89	71.23	1777
HSA-MIR-302C-3P	99.89	71.20	1778
HSA-MIR-302D-3P	99.89	71.25	1777
HSA-MIR-4496	99.88	68.89	2236
HSA-MIR-106B-5P	99.88	74.72	2795
HSA-MIR-20A-5P	99.88	74.76	2769
HSA-MIR-20B-5P	99.88	74.01	2621
HSA-MIR-519D-3P	99.88	73.97	2607
HSA-MIR-526B-3P	99.88	74.06	2587
HSA-MIR-93-5P	99.88	73.98	2606
HSA-MIR-4503	99.85	71.45	1869
HSA-MIR-373-3P	99.84	70.68	1668
HSA-MIR-520E-3P	99.84	70.55	1698
HSA-MIR-372-3P	99.83	70.58	1691
HSA-MIR-520A-3P	99.83	70.59	1687
HSA-MIR-520B-3P	99.83	70.56	1699
HSA-MIR-520C-3P	99.83	70.56	1699
HSA-MIR-520D-3P	99.83	70.78	1676
HSA-MIR-12129	99.72	67.45	1311

Literature-anchored findings (GeneRIF, showing 3)

• ABCA10 is a novel member of the group of ABCA6-like transporters involved in macrophage lipid homeostasis (PMID:12821155)
• Results suggest a possible role for multidrug resistance genes ABCA10 and ABCA6 in follicular lymphoma survival and add to the evidence that genetic variation in CD46 and IL8 may have prognostic implications follicular lymphoma. (PMID:25294155)
• A 4-gene signature predicts prognosis of uterine serous carcinoma. (PMID:33579221)

Cross-species orthologs

14 orthologs

Organism	Symbol	Gene ID
danio_rerio	abca5	ENSDARG00000074041
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), ABCA5 (ENSG00000154265), ABCA1 (ENSG00000165029), ABCA3 (ENSG00000167972), ABCA13 (ENSG00000179869), ABCA4 (ENSG00000198691)

Protein

Protein identifiers

ATP-binding cassette sub-family A member 10 — Q8WWZ4 (reviewed: Q8WWZ4)

All UniProt accessions (6): Q8WWZ4, E5RFN6, E5RFP5, H0YBL8, K7EMH5, K7ERP5

UniProt curated annotations — full annotation on UniProt →

Function. Probable transporter which may play a role in macrophage lipid transport and homeostasis.

Subcellular location. Membrane.

Tissue specificity. Widely expressed. Highly expressed in skeletal muscle, heart, brain and gastrointestinal tract.

Induction. Down-regulated by cholesterol loading of macrophages.

Similarity. Belongs to the ABC transporter superfamily. ABCA family.

Isoforms (5)

UniProt ID	Names	Canonical?
Q8WWZ4-1	1	yes
Q8WWZ4-2	2, ABCA10delta+82
Q8WWZ4-3	3, ABCA10delta-104
Q8WWZ4-4	4, ABCA10delta-176
Q8WWZ4-5	5

RefSeq proteins (2): NP_001364250, NP_525021 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR003439	ABC_transporter-like_ATP-bd	Domain
IPR003593	AAA+_ATPase	Domain
IPR013525	ABC2_TM	Domain
IPR017871	ABC_transporter-like_CS	Conserved_site
IPR026082	ABCA	Family
IPR027417	P-loop_NTPase	Homologous_superfamily
IPR056264	R2_ABCA1-4-like	Domain

Pfam: PF00005, PF12698, PF23321

UniProt features (40 total): transmembrane region 15, splice variant 7, sequence conflict 6, sequence variant 4, domain 2, compositionally biased region 2, binding site 2, chain 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8WWZ4-F1	75.70	0.11

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): 427–434; 1239–1246

Function

Pathways and Gene Ontology

Reactome pathways

3 pathways

ID	Pathway
R-HSA-1369062	ABC transporters in lipid homeostasis
R-HSA-382551	Transport of small molecules
R-HSA-382556	ABC-family protein mediated transport

MSigDB gene sets: 44 (showing top): KEGG_ABC_TRANSPORTERS, AACTTT_UNKNOWN, GOBP_LIPID_LOCALIZATION, NIKOLSKY_BREAST_CANCER_17Q21_Q25_AMPLICON, GOBP_TRANSMEMBRANE_TRANSPORT, GOMF_LIPID_TRANSPORTER_ACTIVITY, GOMF_HYDROLASE_ACTIVITY_ACTING_ON_ACID_ANHYDRIDES, GOMF_ACTIVE_TRANSMEMBRANE_TRANSPORTER_ACTIVITY, GOMF_ATP_HYDROLYSIS_ACTIVITY, GOMF_ADENYL_NUCLEOTIDE_BINDING, GOMF_TRANSPORTER_ACTIVITY, GOMF_PRIMARY_ACTIVE_TRANSMEMBRANE_TRANSPORTER_ACTIVITY, REACTOME_TRANSPORT_OF_SMALL_MOLECULES, HES2_TARGET_GENES, HMGA1_TARGET_GENES

GO Biological Process (2): lipid transport (GO:0006869), 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 (2): plasma membrane (GO:0005886), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-2 pathways:

Category	Pathways
ABC-family protein mediated transport	1
Transport of small molecules	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
transport	2
ATP-dependent activity	2
lipid localization	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
cellular anatomical structure	1

Protein interactions and networks

STRING

656 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ABCA10	MAP2K6	P52564	642
ABCA10	FAM187B	Q17R55	566
ABCA10	OR7G3	Q8NG95	542
ABCA10	ABCF3	Q9NUQ8	528
ABCA10	SLC22A24	Q8N4F4	501
ABCA10	MSLNL	Q96KJ4	489
ABCA10	ABCC9	O60706	471
ABCA10	CBY2	Q8NA61	457
ABCA10	ABCC11	Q96J66	444
ABCA10	ZNF80	P51504	427
ABCA10	IQANK1	A8MXQ7	425
ABCA10	CCHCR1	Q8TD31	416
ABCA10	SLC22A10	Q63ZE4	396
ABCA10	SLC27A6	Q9Y2P4	394
ABCA10	MAGEB16	A2A368	390

IntAct

5 interactions, top by confidence:

A	B	Type	Score
CUL4A	HAX1	psi-mi:“MI:0914”(association)	0.350
COPS5	FBLL1	psi-mi:“MI:0914”(association)	0.350
ABCA10	POTEF	psi-mi:“MI:0914”(association)	0.350
ABCA6	STX6	psi-mi:“MI:0914”(association)	0.350

BioGRID (8): ABCA10 (Affinity Capture-MS), POTEF (Affinity Capture-MS), ABCA9 (Affinity Capture-MS), ABCA10 (Affinity Capture-MS), ABCA10 (Cross-Linking-MS (XL-MS)), ABCA10 (Proximity Label-MS), ABCA10 (Affinity Capture-MS), ABCA10 (Affinity Capture-MS)

ESM2 similar proteins: A0A0G2K1Q8, B2RX12, E9PU17, E9PX95, F1MWM0, O00329, O15438, O35600, O75899, O88563, O88871, O94911, O95477, P41233, P55205, P58428, P78363, Q09427, Q09428, Q09429, Q2NKY8, Q5BJS0, Q5R607, Q5ZI74, Q6TL19, Q7L2E3, Q7TNJ2, Q80T41, Q84M24, Q8CF82, Q8IUA7, Q8K440, Q8K441, Q8K442, Q8K448, Q8K449, Q8LPK0, Q8N139, Q8NCL4, Q8R420

Diamond homologs: A0A0M3R8G1, A0A0M4FLW6, A0A1L9WQK0, A0A2H1A768, A0A481WQK1, A9YWR6, B8ALI0, B9G5Y5, D3GE74, F1MWM0, H9BZ66, O34814, O65934, O69063, O80946, O94911, P08720, P0C086, P0C087, P10090, P16532, P32568, P33302, P40550, P43071, P58428, P78363, P94440, P9WQK0, P9WQK1, Q02785, Q02MI4, Q05360, Q17320, Q1I7I9, Q1LQB5, Q1M7W6, Q2JLH7, Q3E9B8, Q4L8L7

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	2
Likely pathogenic	0
Uncertain significance	193
Likely benign	18
Benign	2

Top pathogenic / likely-pathogenic (2)

Variant ID	HGVS	Classification
395646	GRCh37/hg19 17q21.31-25.3(chr17:42580684-81085615)x3	Pathogenic
59609	GRCh38/hg38 17q24.2-24.3(chr17:67833866-70085854)x1	Pathogenic

SpliceAI

6188 predictions. Top by Δscore:

Variant	Effect	Δscore
17:69149085:TTCA:T	acceptor_gain	1.0000
17:69149086:TCA:T	acceptor_gain	1.0000
17:69149087:CA:C	acceptor_gain	1.0000
17:69149087:CAC:C	acceptor_gain	1.0000
17:69149089:C:CC	acceptor_gain	1.0000
17:69149093:A:C	acceptor_gain	1.0000
17:69149982:A:AC	donor_gain	1.0000
17:69149983:C:CA	donor_gain	1.0000
17:69149983:CT:C	donor_gain	1.0000
17:69149983:CTCG:C	donor_gain	1.0000
17:69150064:C:CC	acceptor_gain	1.0000
17:69152046:T:A	donor_gain	1.0000
17:69153298:T:A	donor_gain	1.0000
17:69153299:CCTTA:C	donor_loss	1.0000
17:69153300:CTTA:C	donor_loss	1.0000
17:69153301:TTA:T	donor_loss	1.0000
17:69153302:TA:T	donor_loss	1.0000
17:69153303:A:AC	donor_gain	1.0000
17:69153303:A:C	donor_loss	1.0000
17:69153304:C:CC	donor_gain	1.0000
17:69153304:CCA:C	donor_gain	1.0000
17:69153304:CCACA:C	donor_gain	1.0000
17:69153397:CAG:C	acceptor_gain	1.0000
17:69153795:T:TA	donor_gain	1.0000
17:69153820:T:TA	donor_gain	1.0000
17:69154234:CCA:C	donor_gain	1.0000
17:69155016:AACCT:A	donor_loss	1.0000
17:69155017:ACCT:A	donor_loss	1.0000
17:69155136:CCTG:C	acceptor_loss	1.0000
17:69155137:C:CC	acceptor_gain	1.0000

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000030091 (17:69154394 T>A,C), RS1000041945 (17:69224487 A>G,T), RS1000064407 (17:69230787 T>C), RS1000081898 (17:69154151 T>A), RS1000098070 (17:69208692 A>G,T), RS1000156681 (17:69195973 C>A,T), RS1000184207 (17:69163203 T>C,G), RS1000247229 (17:69191310 T>C,G), RS1000272370 (17:69232894 T>C), RS1000272967 (17:69244688 A>T), RS1000310168 (17:69147802 C>A,T), RS1000312128 (17:69224756 A>G), RS1000399354 (17:69225916 T>A,C), RS1000410609 (17:69225596 C>A), RS1000412489 (17:69211348 T>C,G)

Disease associations

OMIM: gene MIM:612508 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

7 associations (top):

Study	Trait	p-value
GCST003031_2	MGMT methylation in smokers	2.000000e-07
GCST005352_7	Paclitaxel disposition in epithelial ovarian cancer	7.000000e-06
GCST009996_8	HDL cholesterol levels	9.000000e-07
GCST010243_31	Apolipoprotein B levels	3.000000e-19
GCST010245_143	LDL cholesterol levels	5.000000e-21
GCST011390_11	Corneal resistance factor	4.000000e-43
GCST011391_9	Corneal hysteresis	7.000000e-35

EFO canonical traits (6, from GWAS)

EFO ID	Trait name
EFO:0006959	gene methylation measurement
EFO:0007805	HDL cholesterol change measurement
EFO:0004615	apolipoprotein B measurement
EFO:0004611	low density lipoprotein cholesterol measurement
EFO:0010067	corneal resistance factor
EFO:0010066	corneal hysteresis

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

15 total (human), top 15 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	decreases expression, increases methylation	2
bisphenol A	increases expression	1
2,5,2’,5’-tetrachlorobiphenyl	decreases expression	1
sodium arsenite	affects expression	1
CGP 52608	affects binding, increases reaction	1
licochalcone B	increases expression	1
(+)-JQ1 compound	decreases expression	1
Docetaxel	increases expression, decreases response to substance	1
Arbutin	decreases expression	1
Dichlorodiphenyl Dichloroethylene	decreases expression	1
N-Nitrosopyrrolidine	decreases expression	1
Oxygen	increases expression	1
Testosterone	decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
Aflatoxin B1	decreases expression	1

Clinical trials (associated diseases)

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