APOD

Summary

APOD (apolipoprotein D, HGNC:612) is a protein-coding gene on chromosome 3q29, encoding Apolipoprotein D (P05090). APOD occurs in the macromolecular complex with lecithin-cholesterol acyltransferase.

This gene encodes a component of high density lipoprotein that has no marked similarity to other apolipoprotein sequences. It has a high degree of homology to plasma retinol-binding protein and other members of the alpha 2 microglobulin protein superfamily of carrier proteins, also known as lipocalins. This glycoprotein is closely associated with the enzyme lecithin:cholesterol acyltransferase - an enzyme involved in lipoprotein metabolism.

Source: NCBI Gene 347 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 46 total
• MANE Select transcript: NM_001647

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:612
Approved symbol	APOD
Name	apolipoprotein D
Location	3q29
Locus type	gene with protein product
Status	Approved
Aliases	Apo-D
Ensembl gene	ENSG00000189058
Ensembl biotype	protein_coding
OMIM	107740
Entrez	347

Gene structure

Transcript identifiers

Ensembl transcripts: 10 — 8 protein_coding, 1 nonsense_mediated_decay, 1 retained_intron

ENST00000343267, ENST00000421243, ENST00000453131, ENST00000458447, ENST00000463719, ENST00000852526, ENST00000852527, ENST00000852528, ENST00000852529, ENST00000953531

RefSeq mRNA: 1 — MANE Select: NM_001647 NM_001647

CCDS: CCDS33925

Canonical transcript exons

ENST00000343267 — 5 exons

Exon	Start	End
ENSE00001373102	195568705	195569135
ENSE00001702388	195583878	195583940
ENSE00003560706	195579339	195579495
ENSE00003620908	195573850	195573971
ENSE00003673484	195571277	195571365

Expression profiles

Bgee: expression breadth ubiquitous, 276 present calls, max score 100.00.

FANTOM5 (CAGE): breadth broad, TPM avg 181.2274 / max 20840.1805, expressed in 853 samples.

FANTOM5 promoters (10 alternative TSS)

Promoter ID	TPM avg	Samples expressed
46295	162.5054	762
46296	14.2277	652
46290	1.5744	332
46286	1.1359	283
46293	0.8122	41
46287	0.3578	149
46291	0.3570	146
46292	0.1988	96
46294	0.0401	25
203074	0.0182	14

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
dorsal root ganglion	UBERON:0000044	100.00	gold quality
olfactory bulb	UBERON:0002264	100.00	gold quality
tibial nerve	UBERON:0001323	99.98	gold quality
trigeminal ganglion	UBERON:0001675	99.98	gold quality
mucosa of stomach	UBERON:0001199	99.87	gold quality
right coronary artery	UBERON:0001625	99.83	gold quality
right lobe of thyroid gland	UBERON:0001119	99.82	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	99.82	gold quality
inferior vagus X ganglion	UBERON:0005363	99.81	gold quality
right lung	UBERON:0002167	99.80	gold quality
spinal cord	UBERON:0002240	99.79	gold quality
middle frontal gyrus	UBERON:0002702	99.77	gold quality
medial globus pallidus	UBERON:0002477	99.76	gold quality
left uterine tube	UBERON:0001303	99.75	gold quality
omental fat pad	UBERON:0010414	99.75	gold quality
coronary artery	UBERON:0001621	99.74	gold quality
left coronary artery	UBERON:0001626	99.74	gold quality
adipose tissue of abdominal region	UBERON:0007808	99.73	gold quality
peritoneum	UBERON:0002358	99.72	gold quality
skin of leg	UBERON:0001511	99.71	gold quality
globus pallidus	UBERON:0001875	99.71	gold quality
minor salivary gland	UBERON:0001830	99.70	gold quality
corpus callosum	UBERON:0002336	99.70	gold quality
endocervix	UBERON:0000458	99.69	gold quality
mammary duct	UBERON:0001765	99.69	gold quality
saliva-secreting gland	UBERON:0001044	99.67	gold quality
pericardium	UBERON:0002407	99.65	gold quality
left ventricle myocardium	UBERON:0006566	99.65	gold quality
skin of abdomen	UBERON:0001416	99.63	gold quality
trachea	UBERON:0003126	99.63	gold quality

Single-cell (SCXA)

Detected in 22 experiment(s), a significant marker in 22.

Experiment	Marker?	Max mean expression
E-GEOD-84465	yes	26049.48
E-CURD-126	yes	13871.64
E-MTAB-10885	yes	10496.99
E-MTAB-9841	yes	9991.44
E-GEOD-135922	yes	6851.69
E-MTAB-6701	yes	6108.04
E-HCAD-24	yes	4767.16
E-MTAB-10287	yes	4425.50
E-HCAD-23	yes	2635.39
E-HCAD-11	yes	2057.58
E-MTAB-9435	yes	782.19
E-MTAB-8142	yes	102.17
E-HCAD-1	yes	75.98
E-HCAD-25	yes	54.67
E-GEOD-134144	yes	32.27

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): APEX1, CTNNB1, ESR1, IFI16, NOTCH3, PARP1, TP53, TP63, TP73

miRNA regulators (miRDB)

12 targeting APOD, 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-545-3P	99.95	70.74	2783
HSA-MIR-298	99.63	67.56	1916
HSA-MIR-4666A-5P	99.41	69.72	1887
HSA-MIR-511-5P	98.97	70.94	2268
HSA-MIR-11399	98.71	65.69	869
HSA-MIR-1301-3P	98.64	68.27	1071
HSA-MIR-5047	98.64	68.62	1035
HSA-MIR-509-3P	98.12	67.25	612
HSA-MIR-5087	98.01	69.09	965
HSA-MIR-6783-5P	97.67	67.21	1528
HSA-MIR-621	96.76	66.89	371
HSA-MIR-4440	90.29	63.67	61

Literature-anchored findings (GeneRIF, showing 40)

• Altered levels of apoD may help to understand the nature and possible mechanism of phospholipid membrane pathology in schizophrenia. (PMID:12363390)
• Data suggest that the risk of Alzheimer disease among African-Americans may be modified by genetic variation in APOD. (PMID:12497622)
• APOD is a senescence-associated gene in normal human oral keratinocytes. (PMID:12837283)
• Apolipoprotein D levels are elevated in prefrontal cortex of subjects with Alzheimer’s disease, suggesting that it may be related to the cognitive decline observed in AD patients. (PMID:12873803)
• ApoD selectively modulates the proliferative response of vascular smooth muscle cells to growth factors by a mechanism related to nuclear translocation of ERK1/2. (PMID:14551159)
• In a study comparing brains from Alzheimer’s patients and controls, it was found that hippocampal apolipoprotein D level depends on Braak stage and APOE genotype. (PMID:14596852)
• ApoD can be expressed or taken up by SMCs and can regulate their motility in response to growth factors. (PMID:15192024)
• The -352G allele was associated with a significant 3-fold increase in the risk of early-onset Alzheimer’s disease (OR: 2.7; 95% CI: 1.1-6.5). The -352G containing haplotypes were more common for early-onset Alzheimer’s disease cases. (PMID:15316799)
• Elevated apoD in AD brain may influence Abeta aggregation, or facilitate phagocytosis and transport of Abeta fibrils from plaques to cerebral vasculature. (PMID:15916898)
• study of the presence of apo D in the substantia nigra of control and Parkinson disease (PD) subjects; dopaminergic neurons were not immunoreactive for apo D but surrounding glial cells showed immunostaining for apo D and signal increases in PD cases (PMID:16437381)
• Apo D differentiates superficial acral fibromyxoma from dermatofibrosarcoma protuberans. (PMID:17885669)
• ApoD positive tumors had both a significantly shorter relapse-free survival (all locations) and a decreased breast cancer-specific survival. (PMID:18330697)
• These observations, together with its transcriptional up-regulation in the brain upon oxidative insult, identify ApoD as an acute response protein with a protective and therefore beneficial function mediated by the control of peroxidated lipids. (PMID:18419796)
• ApoD and its orthologs play an evolutionarily conserved role in response to stress, possibly managing or preventing lipid peroxidation. (PMID:18458334)
• Logistic analysis revealed that both APOD rs5952 C and rs1568566 T alleles increase the risk of sporadic Alzheimer’s disease. The rs5952T-rs1568566C haplotype showed lower risk. (PMID:18671953)
• Role for apoD in regulation of inflammation. It may protect from HCoV-OC43-induced encephalitis, most likely through phospholipase A2 signaling pathways. (PMID:18842892)
• study demonstrated that Apo D was highly expressed in the mRNA and protein levels in human failing hearts compared with non-failing hearts (PMID:18979643)
• Variations in the levels and/or sites of apoD expression influence the lipid and glucose metabolism, consolidating apoD as a target for insulin-resistance-related disorders. (PMID:19176353)
• Apolipoprotein D (APOD) and two further transcripts were significantly upregulated by dihydrotestosterone (DHT) in scrotum fibroblasts (PMID:19330472)
• apoD expression is increased throughout life in the human prefrontal cortex (PMID:19519777)
• The decrease in plasma ApoD concentration during pregnancy is an adaptive response aimed at maintaining fetal lipid homeostasis. (PMID:19723339)
• A strong relationship with gestational diabetes and APOD in the placenta that may reflect its suggested function in defense mechanisms against oxidative stress. (PMID:19944460)
• Importance of Parp-1, APEX-1 and ERK1/2 catalytic activities in the growth arrest-induced apoD gene expression. (PMID:20493910)
• Our findings show that Apo D expression is influenced by age, Braak stage, and sex. (PMID:21429623)
• increased JNK1 activation in the apocrine cells from axillary osmidrosis contributes to the increased ApoD expression (PMID:21526344)
• Endothelial cells downregulate apolipoprotein D expression in mural cells through paracrine secretion and Notch3 signaling. (PMID:21705670)
• Molecular dynamics analysis of apolipoprotein-D-lipid hydroperoxide interactions show the mechanism for selective oxidation of Met-93 (PMID:22479522)
• ApoD is marker of initial stages of colorectal cancer progression. (PMID:23296401)
• Rs7659, 3’ UTR polymorphism of the APOD gene was associated with early onset Alzheimer disease in APOEepsilon4 (-) subgroup. Our results suggest that the variation of the APOD gene modifies the risk for Alzheimer disease. (PMID:23690001)
• ApoE is located in the nucleus and on the ApoD promoter in human hepatic and glioblastoma cells lines. (PMID:23715769)
• Data suggest that ApoD binds various lyophilic ligands: retinoic acid, retinol, fatty acids, sphingomyelin, and anandamide. ApoD successfully delivers retinoic acid to immature neuronal cell line resulting in neurogenesis (i.e., neurite formation). (PMID:23777559)
• ApoD mRNA expression is seen in whole endometrium, stromal and epithelial cells in the secretory phase, as well as after hormonal stimulation in vitro. (PMID:23895740)
• We propose that strong brainstem expression of Apo D throughout adult life contributes to resistance against neurodegenerative disease and age-related degeneration, possibly by preventing oxidative stress and ensuing lipid peroxidation. (PMID:24167586)
• The SNP rs7659 within the APOD gene might be related to risk and severity of ischemic stroke in patients. (PMID:25261976)
• apoD mediates binding of high density lipoprotein to low density lipoprotein and to growing T24 carcinomas, thereby highlighting the importance of apoD in lipid metabolism. (PMID:25513803)
• The internalization of apoD is mediated by basigin. (PMID:25918162)
• The data suggest that the presence of Apo D in the nucleus, which some authors related with a specific transport, is a consequence of structural and functional alterations during oxidative stress (PMID:25953740)
• hepatic steatosis observed in apoD Tg mice is a consequence of increased PPARgamma transcriptional activity by AA leading to increased fatty acid uptake by the liver (PMID:26083030)
• Our results provide a viable solution to the production of recombinant ApoD protein in lieu of previous obstacles in generating soluble and functional ApoD protein (PMID:26826316)
• apoD protein levels are variable across different brain regions. (PMID:26829325)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	apodb	ENSDARG00000057437
danio_rerio	apoda.1	ENSDARG00000060345
mus_musculus	Apod	ENSMUSG00000022548
rattus_norvegicus	Apod	ENSRNOG00000048273

Protein

Protein identifiers

Apolipoprotein D — P05090 (reviewed: P05090)

All UniProt accessions (4): C9JF17, C9JX71, F8WBT9, P05090

UniProt curated annotations — full annotation on UniProt →

Function. APOD occurs in the macromolecular complex with lecithin-cholesterol acyltransferase. It is probably involved in the transport and binding of bilin. Appears to be able to transport a variety of ligands in a number of different contexts.

Subunit / interactions. Homodimer. In plasma, also exists as a disulfide-linked heterodimer with APOA2.

Subcellular location. Secreted.

Tissue specificity. Expressed in liver, intestine, pancreas, kidney, placenta, adrenal, spleen, fetal brain tissue and tears.

Post-translational modifications. N-glycosylated. N-glycan heterogeneity at Asn-65: Hex5HexNAc4 (major) and Hex6HexNAc5 (minor); at Asn-98: Hex5HexNAc4 (minor), dHex1Hex5HexNAc4 (major), dHex1Hex6HexNAc5 (minor) and dHex1Hex7HexNAc6 (minor).

Miscellaneous. APOD is primarily localized in HDL (60-65%), with most of the remainder in VHDL and only trace amounts in VLDL and LDL.

Similarity. Belongs to the calycin superfamily. Lipocalin family.

RefSeq proteins (1): NP_001638* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000566	Lipocln_cytosolic_FA-bd_dom	Domain
IPR002969	ApolipopD	Family
IPR012674	Calycin	Homologous_superfamily
IPR022271	Lipocalin_ApoD	Family
IPR022272	Lipocalin_CS	Conserved_site
IPR026222	ApoD_vertbrte	Family

Pfam: PF08212

UniProt features (23 total): strand 10, sequence variant 3, disulfide bond 3, helix 2, glycosylation site 2, signal peptide 1, chain 1, modified residue 1

Structure

Experimental structures (PDB)

2 structures.

PDB	Method	Resolution (Å)
2HZQ	X-RAY DIFFRACTION	1.8
2HZR	X-RAY DIFFRACTION	1.8

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P05090-F1	90.57	0.76

Functional residue map

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

Post-translational modifications (1): 21

Disulfide bonds (3): 28–134, 61–185, 136

Glycosylation sites (2): 65, 98

Function

Pathways and Gene Ontology

Reactome pathways

8 pathways

ID	Pathway
R-HSA-804914	Transport of fatty acids
R-HSA-9029569	NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux
R-HSA-162582	Signal Transduction
R-HSA-382551	Transport of small molecules
R-HSA-425397	Transport of vitamins, nucleosides, and related molecules
R-HSA-425407	SLC-mediated transmembrane transport
R-HSA-9006931	Signaling by Nuclear Receptors
R-HSA-9024446	NR1H2 and NR1H3-mediated signaling

MSigDB gene sets: 351 (showing top): GOBP_PLATELET_DERIVED_GROWTH_FACTOR_RECEPTOR_SIGNALING_PATHWAY, GOBP_LIPID_MODIFICATION, GOBP_NEGATIVE_REGULATION_OF_SMOOTH_MUSCLE_CELL_PROLIFERATION, GOBP_INTRACELLULAR_PROTEIN_TRANSPORT, GOBP_INFLAMMATORY_RESPONSE, GOBP_LIPOPROTEIN_METABOLIC_PROCESS, GOBP_NEGATIVE_REGULATION_OF_LIPID_METABOLIC_PROCESS, GOZGIT_ESR1_TARGETS_DN, GOBP_FOCAL_ADHESION_ASSEMBLY, ASTON_MAJOR_DEPRESSIVE_DISORDER_DN, GOBP_GROWTH, MCBRYAN_PUBERTAL_TGFB1_TARGETS_DN, DARWICHE_SKIN_TUMOR_PROMOTER_UP, GOBP_REGENERATION, DARWICHE_PAPILLOMA_RISK_LOW_DN

GO Biological Process (19): response to reactive oxygen species (GO:0000302), angiogenesis (GO:0001525), glucose metabolic process (GO:0006006), lipid metabolic process (GO:0006629), brain development (GO:0007420), negative regulation of platelet-derived growth factor receptor signaling pathway (GO:0010642), peripheral nervous system axon regeneration (GO:0014012), tissue regeneration (GO:0042246), negative regulation of protein import into nucleus (GO:0042308), negative regulation of smooth muscle cell proliferation (GO:0048662), response to axon injury (GO:0048678), negative regulation of focal adhesion assembly (GO:0051895), negative regulation of lipoprotein lipid oxidation (GO:0060588), negative regulation of monocyte chemotactic protein-1 production (GO:0071638), negative regulation of cytokine production involved in inflammatory response (GO:1900016), negative regulation of smooth muscle cell-matrix adhesion (GO:2000098), negative regulation of T cell migration (GO:2000405), lipid transport (GO:0006869), response to stress (GO:0006950)

GO Molecular Function (5): lipid carrier activity (GO:0005319), cholesterol binding (GO:0015485), protein binding (GO:0005515), lipid binding (GO:0008289), pigment binding (GO:0031409)

GO Cellular Component (9): extracellular region (GO:0005576), obsolete extracellular space (GO:0005615), cytoplasm (GO:0005737), cytosolic ribosome (GO:0022626), dendrite (GO:0030425), neuronal cell body (GO:0043025), perinuclear region of cytoplasm (GO:0048471), extracellular exosome (GO:0070062), endoplasmic reticulum (GO:0005783)

Reactome top-level categories

Rollup of top-6 pathways:

Category	Pathways
Transport of vitamins, nucleosides, and related molecules	1
NR1H2 and NR1H3-mediated signaling	1
SLC-mediated transmembrane transport	1
Transport of small molecules	1
Signal Transduction	1
Signaling by Nuclear Receptors	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	3
cellular anatomical structure	3
negative regulation of cell-matrix adhesion	2
cytoplasm	2
response to oxidative stress	1
response to oxygen-containing compound	1
blood vessel morphogenesis	1
anatomical structure formation involved in morphogenesis	1
hexose metabolic process	1
primary metabolic process	1
central nervous system development	1
animal organ development	1
head development	1
negative regulation of signal transduction	1
regulation of platelet-derived growth factor receptor signaling pathway	1
platelet-derived growth factor receptor signaling pathway	1
axon regeneration	1
regeneration	1
developmental growth	1
protein import into nucleus	1
regulation of protein import into nucleus	1
negative regulation of nucleocytoplasmic transport	1
negative regulation of intracellular protein transport	1
negative regulation of protein localization to nucleus	1
negative regulation of cell population proliferation	1
smooth muscle cell proliferation	1
regulation of smooth muscle cell proliferation	1
response to wounding	1
focal adhesion assembly	1
regulation of focal adhesion assembly	1
negative regulation of cell-substrate junction organization	1
negative regulation of cell junction assembly	1
lipoprotein lipid oxidation	1
negative regulation of lipoprotein oxidation	1
negative regulation of lipid metabolic process	1
regulation of lipoprotein lipid oxidation	1
negative regulation of chemokine production	1
monocyte chemotactic protein-1 production	1
regulation of monocyte chemotactic protein-1 production	1
negative regulation of cytokine production	1

Protein interactions and networks

STRING

2648 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
APOD	APOA2	P02652	986
APOD	APOA1	P02647	946
APOD	CLU	P10909	935
APOD	APOE	P02649	932
APOD	APOA4	P06727	864
APOD	APOB	P04114	859
APOD	LCAT	P04180	856
APOD	LCN1	P31025	851
APOD	APOC1	P02654	843
APOD	APOF	Q13790	805
APOD	APOH	P02749	800
APOD	APOM	O95445	785
APOD	CSTB	P04080	781
APOD	C1QB	P02746	778
APOD	APOC3	P02656	768

IntAct

293 interactions, top by confidence:

A	B	Type	Score
ESR1	ESR1	psi-mi:“MI:0914”(association)	0.870
APOD	VAPA	psi-mi:“MI:0915”(physical association)	0.720
APOD	CREB3	psi-mi:“MI:0915”(physical association)	0.670
SINHCAF	TNRC18	psi-mi:“MI:0914”(association)	0.640
MAZ	APOD	psi-mi:“MI:0915”(physical association)	0.590
SLC35C1	APOD	psi-mi:“MI:0915”(physical association)	0.590
	APOD	psi-mi:“MI:0915”(physical association)	0.560
APOD		psi-mi:“MI:0915”(physical association)	0.560
APOD	TEX29	psi-mi:“MI:0915”(physical association)	0.560
APOD	MTERF2	psi-mi:“MI:0915”(physical association)	0.560
APOD	MTIF3	psi-mi:“MI:0915”(physical association)	0.560
APOD	GJA8	psi-mi:“MI:0915”(physical association)	0.560
APOD	FPR2	psi-mi:“MI:0915”(physical association)	0.560
APOD	MFF	psi-mi:“MI:0915”(physical association)	0.560
APOD	TMEM79	psi-mi:“MI:0915”(physical association)	0.560
APOD	GDAP1	psi-mi:“MI:0915”(physical association)	0.560
APOD	BIK	psi-mi:“MI:0915”(physical association)	0.560
APOD	CLEC10A	psi-mi:“MI:0915”(physical association)	0.560
APOD	TMEM237	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (209): VAPA (Two-hybrid), APOD (Affinity Capture-MS), APOD (Affinity Capture-MS), APOD (Affinity Capture-MS), APOD (Affinity Capture-MS), APOD (Affinity Capture-MS), APOD (Two-hybrid), APOD (Affinity Capture-MS), CREB3 (Two-hybrid), VAPA (Two-hybrid), APOD (Affinity Capture-MS), APOD (Affinity Capture-MS), APOD (Affinity Capture-MS), APOD (Affinity Capture-MS), ALCAM (Affinity Capture-MS)

ESM2 similar proteins: A5A6I6, A6QP57, B0FHH8, O02380, O93429, O94183, O97763, P02787, P02789, P05090, P08071, P09571, P0CP28, P0CP29, P12346, P17900, P19134, P23593, P27425, P31729, P49278, P51910, P61916, P61917, P61918, P79345, P79815, P79819, P80384, P80426, P80429, Q08188, Q25481, Q28895, Q29290, Q29443, Q336T5, Q4X136, Q52FS9, Q60648

Diamond homologs: M5AXY1, P02753, P04916, P05090, P06172, P06912, P08938, P18902, P24774, P24775, P27485, P41263, P51909, P61641, Q00724, Q28369, P00305, P09464, P37153, P49291, Q00630, Q32KY0, Q5ECE3, Q8SPI0, P0A901, P0A902, P23593, P51910, Q46036, Q5URA7, Q9FGT8, Q08790, Q29487, P80007, Q9STS7

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	27
Likely benign	7
Benign	5

Top pathogenic / likely-pathogenic (0)

SpliceAI

692 predictions. Top by Δscore:

Variant	Effect	Δscore
3:195569131:CATAA:C	acceptor_gain	1.0000
3:195569132:ATAAC:A	acceptor_loss	1.0000
3:195569133:TAA:T	acceptor_gain	1.0000
3:195569133:TAAC:T	acceptor_loss	1.0000
3:195569135:AC:A	acceptor_loss	1.0000
3:195569136:C:CA	acceptor_loss	1.0000
3:195569136:C:CC	acceptor_gain	1.0000
3:195569137:T:A	acceptor_loss	1.0000
3:195569159:T:TC	acceptor_gain	1.0000
3:195571275:A:AC	donor_gain	1.0000
3:195571275:ACAC:A	donor_gain	1.0000
3:195571276:C:CC	donor_gain	1.0000
3:195571276:CA:C	donor_gain	1.0000
3:195571276:CACC:C	donor_gain	1.0000
3:195571276:CACCA:C	donor_gain	1.0000
3:195571291:A:C	donor_gain	1.0000
3:195571294:T:TA	donor_gain	1.0000
3:195571361:CAGCT:C	acceptor_gain	1.0000
3:195571363:GCT:G	acceptor_gain	1.0000
3:195571364:CT:C	acceptor_gain	1.0000
3:195571364:CTC:C	acceptor_gain	1.0000
3:195571365:TCT:T	acceptor_gain	1.0000
3:195571366:C:CC	acceptor_gain	1.0000
3:195571376:T:C	acceptor_gain	1.0000
3:195571376:T:TC	acceptor_gain	1.0000
3:195573845:CTCA:C	donor_loss	1.0000
3:195573846:TCACC:T	donor_loss	1.0000
3:195573847:CACCT:C	donor_loss	1.0000
3:195573848:A:C	donor_loss	1.0000
3:195573849:C:A	donor_loss	1.0000

AlphaMissense

1237 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
3:195573957:C:A	W46C	0.998
3:195573957:C:G	W46C	0.998
3:195573913:C:G	C61S	0.997
3:195573914:A:T	C61S	0.997
3:195573959:A:G	W46R	0.997
3:195573959:A:T	W46R	0.997
3:195573914:A:G	C61R	0.995
3:195569085:C:G	A129P	0.994
3:195569073:A:G	S133P	0.993
3:195571284:A:C	F109L	0.993
3:195571284:A:T	F109L	0.993
3:195571285:A:C	F109C	0.993
3:195571286:A:G	F109L	0.993
3:195571297:A:G	L105P	0.993
3:195569017:T:A	R151S	0.992
3:195569017:T:G	R151S	0.992
3:195579379:C:G	C28S	0.992
3:195579380:A:T	C28S	0.992
3:195568916:C:G	C185S	0.991
3:195568917:A:T	C185S	0.991
3:195569081:A:G	L130P	0.991
3:195573927:A:C	F56L	0.991
3:195573927:A:T	F56L	0.991
3:195573929:A:G	F56L	0.991
3:195573958:C:G	W46S	0.991
3:195568982:A:G	L163P	0.990
3:195569069:C:T	C134Y	0.990
3:195571331:C:G	A94P	0.990
3:195579380:A:G	C28R	0.990
3:195569029:C:A	W147C	0.989

dbSNP variants (sampled 300 via entrez): RS1000148184 (3:195575300 T>A,C), RS1000535219 (3:195573758 G>A,T), RS1000589318 (3:195579978 G>T), RS1000750771 (3:195585781 C>A), RS1000897275 (3:195570415 A>G,T), RS1000977615 (3:195582932 C>A), RS1001485279 (3:195569924 T>C), RS1001538963 (3:195575900 A>T), RS1001718991 (3:195582087 G>A,T), RS1002308544 (3:195584154 G>A), RS1002544912 (3:195577357 A>G), RS1002672886 (3:195568569 ACTCCCGGC>A), RS1002805451 (3:195574277 T>A), RS1003151527 (3:195583194 C>T), RS1003455828 (3:195585207 T>A)

Disease associations

OMIM: gene MIM:107740 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST010242_106	HDL cholesterol levels	2.000000e-08

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004612	high density lipoprotein cholesterol measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Estradiol	affects cotreatment, decreases expression, increases expression, decreases reaction	6
Paraquat	decreases response to substance, affects cotreatment, increases expression, affects localization, increases uptake (+1 more)	4
Progesterone	affects cotreatment, increases expression	3
bisphenol A	decreases expression, increases expression, decreases reaction, increases abundance	2
Fulvestrant	affects cotreatment, decreases expression, decreases reaction, increases expression	2
Benzo(a)pyrene	increases methylation, affects methylation	2
Tobacco Smoke Pollution	affects expression	2
Tretinoin	affects binding, increases expression	2
Aflatoxin B1	increases methylation	2
Raloxifene Hydrochloride	increases expression, decreases expression, decreases reaction	2
ginger extract	decreases reaction, increases abundance, increases expression	1
4-oxoretinoic acid	increases expression	1
propionaldehyde	increases expression	1
methylselenic acid	affects expression	1
trichostatin A	affects cotreatment, affects expression	1
afimoxifene	increases expression	1
3-methyladenine	affects localization	1
benzo(e)pyrene	increases methylation	1
1-anilino-8-naphthalenesulfonate	affects binding	1
aflatoxin B2	decreases methylation	1
11-(dansylamino)undecanoic acid	affects binding	1
Ospemifene	decreases expression, decreases reaction	1
pyrazolanthrone	decreases reaction, increases expression	1
nutlin 3	affects cotreatment, increases expression	1
2,3-bis(4-hydroxyphenyl)-propionitrile	decreases expression	1
4,4’,4’’-(4-propyl-((1)H)-pyrazole-1,3,5-triyl) tris-phenol	decreases expression	1
abrine	decreases expression	1
jinfukang	affects cotreatment, increases expression	1
incobotulinumtoxinA	increases expression	1
bisphenol AF	increases expression	1

Cellosaurus cell lines

3 cell lines: 2 cancer cell line, 1 transformed cell line

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

Cellosaurus	Name	Category	Sex
CVCL_D7K9	Ubigene A-549 APOD KO	Cancer cell line	Male
CVCL_D8ZA	Ubigene HEK293 APOD KO	Transformed cell line	Female
CVCL_F1UU	HyCyte U-87MG KO-hAPOD	Cancer cell line	Male

Clinical trials (associated diseases)

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