EBPL

Summary

EBPL (EBP like, HGNC:18061) is a protein-coding gene on chromosome 13q14.2, encoding Emopamil-binding protein-like (Q9BY08). Does not possess sterol isomerase activity and does not bind sigma ligands.

Predicted to enable cholestenol delta-isomerase activity. Predicted to be involved in sterol metabolic process. Located in endoplasmic reticulum.

Source: NCBI Gene 84650 — RefSeq curated summary.

At a glance

• GWAS associations: 4
• Clinical variants (ClinVar): 41 total
• Druggable target: yes — 2 molecules with ChEMBL bioactivity
• MANE Select transcript: NM_032565

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:18061
Approved symbol	EBPL
Name	EBP like
Location	13q14.2
Locus type	gene with protein product
Status	Approved
Aliases	EBRP
Ensembl gene	ENSG00000123179
Ensembl biotype	protein_coding
OMIM	617335
Entrez	84650

Gene structure

Transcript identifiers

Ensembl transcripts: 9 — 7 protein_coding, 2 protein_coding_CDS_not_defined

ENST00000242827, ENST00000378268, ENST00000378270, ENST00000378272, ENST00000378284, ENST00000473576, ENST00000495963, ENST00000900209, ENST00000900210

RefSeq mRNA: 2 — MANE Select: NM_032565 NM_001278636, NM_032565

CCDS: CCDS61334, CCDS9420

Canonical transcript exons

ENST00000242827 — 4 exons

Exon	Start	End
ENSE00001816161	49660674	49661208
ENSE00001827833	49691254	49691486
ENSE00003502877	49669777	49669846
ENSE00003673328	49663057	49663195

Expression profiles

Bgee: expression breadth ubiquitous, 137 present calls, max score 97.05.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 73.7289 / max 1101.6147, expressed in 1815 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
137325	73.7289	1815

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right lobe of liver	UBERON:0001114	97.05	gold quality
left adrenal gland cortex	UBERON:0035825	96.25	gold quality
left adrenal gland	UBERON:0001234	96.02	gold quality
esophagus mucosa	UBERON:0002469	95.98	gold quality
right adrenal gland	UBERON:0001233	95.86	gold quality
right adrenal gland cortex	UBERON:0035827	95.65	gold quality
body of pancreas	UBERON:0001150	95.55	gold quality
vagina	UBERON:0000996	95.45	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	95.24	gold quality
liver	UBERON:0002107	95.11	gold quality
lower esophagus mucosa	UBERON:0035834	94.88	gold quality
adrenal gland	UBERON:0002369	94.59	gold quality
ectocervix	UBERON:0012249	94.47	gold quality
skin of abdomen	UBERON:0001416	94.24	gold quality
mucosa of transverse colon	UBERON:0004991	94.13	gold quality
left ovary	UBERON:0002119	93.97	gold quality
pancreas	UBERON:0001264	93.78	gold quality
ovary	UBERON:0000992	93.75	gold quality
zone of skin	UBERON:0000014	93.57	gold quality
endocervix	UBERON:0000458	93.39	gold quality
right ovary	UBERON:0002118	93.34	gold quality
skin of leg	UBERON:0001511	93.17	gold quality
body of stomach	UBERON:0001161	92.72	gold quality
esophagus	UBERON:0001043	92.71	gold quality
uterine cervix	UBERON:0000002	92.51	gold quality
fallopian tube	UBERON:0003889	92.27	gold quality
left uterine tube	UBERON:0001303	92.08	gold quality
fundus of stomach	UBERON:0001160	92.05	gold quality
endometrium	UBERON:0001295	91.99	gold quality
minor salivary gland	UBERON:0001830	91.84	gold quality

Single-cell (SCXA)

Detected in 12 experiment(s), a significant marker in 9.

Experiment	Marker?	Max mean expression
E-MTAB-5061	yes	402.54
E-HCAD-4	yes	85.30
E-CURD-114	yes	61.81
E-GEOD-125970	yes	45.81
E-MTAB-10042	yes	13.76
E-HCAD-1	yes	13.13
E-MTAB-6701	yes	11.70
E-CURD-112	yes	8.61
E-HCAD-6	no	30.13
E-GEOD-81608	no	8.15
E-ENAD-27	no	4.27
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

34 targeting EBPL, 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-126-5P	100.00	72.71	3180
HSA-MIR-4795-3P	100.00	74.62	4024
HSA-MIR-568	99.98	69.86	2084
HSA-MIR-548AA	99.96	70.64	3753
HSA-MIR-548AP-3P	99.96	70.64	3753
HSA-MIR-548T-3P	99.96	70.64	3753
HSA-MIR-1-3P	99.93	72.35	1914
HSA-MIR-206	99.93	72.50	1893
HSA-MIR-613	99.91	71.50	1710
HSA-MIR-4753-3P	99.90	71.03	3786
HSA-MIR-4446-5P	99.72	69.19	2544
HSA-MIR-7154-5P	99.69	70.52	1900
HSA-MIR-7156-5P	99.64	68.81	1369
HSA-MIR-510-3P	99.54	70.06	2965
HSA-MIR-6833-5P	99.50	68.93	1161
HSA-MIR-4273	99.45	67.93	1206
HSA-MIR-1206	99.30	69.32	1016
HSA-MIR-6739-3P	99.22	68.84	1843
HSA-MIR-10399-5P	99.17	69.87	2610
HSA-MIR-6504-3P	99.17	69.31	2891
HSA-MIR-3926	98.95	69.26	1438
HSA-MIR-8060	98.61	66.93	1187
HSA-MIR-4463	98.56	66.05	1071
HSA-MIR-548S	98.50	67.17	1213
HSA-MIR-2117	98.48	67.97	1307
HSA-MIR-6883-3P	97.97	67.35	643
HSA-MIR-3190-3P	97.61	66.95	1406
HSA-MIR-4670-3P	97.37	68.35	1378
HSA-MIR-3194-5P	96.80	64.90	1027
HSA-MIR-4491	96.53	66.20	935

Literature-anchored findings (GeneRIF, showing 1)

• encoded by four exons on human chromosome 13q14.2 covering 30.7 kb, and a partially processed EBPL pseudogene was found on 16q21; expressed ubiquitously and most abundant in liver, lung and kidney (PMID:12760743)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	ebpl	ENSDARG00000036636
mus_musculus	Ebpl	ENSMUSG00000021928
rattus_norvegicus	Ebpl	ENSRNOG00000014659

Paralogs (1): EBP (ENSG00000147155)

Protein

Protein identifiers

Emopamil-binding protein-like — Q9BY08 (reviewed: Q9BY08)

Alternative names: Emopamil-binding-related protein

All UniProt accessions (2): A0A0A0MRV2, Q9BY08

UniProt curated annotations — full annotation on UniProt →

Function. Does not possess sterol isomerase activity and does not bind sigma ligands.

Subunit / interactions. Homodimer.

Subcellular location. Endoplasmic reticulum membrane.

Tissue specificity. Widely expressed with highest levels in liver, lung and kidney.

Similarity. Belongs to the EBP family.

Isoforms (5)

UniProt ID	Names	Canonical?
Q9BY08-1	1	yes
Q9BY08-2	2
Q9BY08-3	3
Q9BY08-4	4
Q9BY08-5	5

RefSeq proteins (2): NP_001265565, NP_115954* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR007905	EBP	Family
IPR033118	EXPERA	Domain

Pfam: PF05241

UniProt features (16 total): splice variant 9, transmembrane region 4, chain 1, sequence conflict 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9BY08-F1	94.06	0.92

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 122 (showing top): HORIUCHI_WTAP_TARGETS_DN, CHIANG_LIVER_CANCER_SUBCLASS_UNANNOTATED_DN, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GOBP_LIPID_METABOLIC_PROCESS, JAATINEN_HEMATOPOIETIC_STEM_CELL_UP, CHIANG_LIVER_CANCER_SUBCLASS_CTNNB1_UP, KONDO_PROSTATE_CANCER_HCP_WITH_H3K27ME3, GOBP_STEROID_METABOLIC_PROCESS, chr13q14, OSMAN_BLADDER_CANCER_DN, GOCC_NUCLEAR_OUTER_MEMBRANE_ENDOPLASMIC_RETICULUM_MEMBRANE_NETWORK, GOCC_ORGANELLE_SUBCOMPARTMENT, GOMF_INTRAMOLECULAR_OXIDOREDUCTASE_ACTIVITY_TRANSPOSING_C_C_BONDS, GOMF_INTRAMOLECULAR_OXIDOREDUCTASE_ACTIVITY, GOMF_ISOMERASE_ACTIVITY

GO Biological Process (1): sterol metabolic process (GO:0016125)

GO Molecular Function (1): cholestenol delta-isomerase activity (GO:0047750)

GO Cellular Component (3): endoplasmic reticulum (GO:0005783), endoplasmic reticulum membrane (GO:0005789), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
steroid metabolic process	1
intramolecular oxidoreductase activity, transposing C=C bonds	1
cytoplasm	1
endomembrane system	1
intracellular membrane-bounded organelle	1
organelle membrane	1
nuclear outer membrane-endoplasmic reticulum membrane network	1
endoplasmic reticulum subcompartment	1
cellular anatomical structure	1

Protein interactions and networks

STRING

660 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
EBPL	SPRYD7	Q5W111	505
EBPL	WDR13	Q9H1Z4	492
EBPL	TSR3	Q9UJK0	484
EBPL	DLEU7	Q6UYE1	466
EBPL	DHCR24	Q15392	465
EBPL	TBC1D25	Q3MII6	458
EBPL	FTSJ1	Q9UET6	458
EBPL	TMEM158	Q8WZ71	455
EBPL	TM6SF1	Q9BZW5	438
EBPL	DHDDS	Q86SQ9	429
EBPL	ARL11	Q969Q4	419
EBPL	CCDC117	Q8IWD4	414
EBPL	ITM2B	Q9Y287	405
EBPL	DHCR7	Q9UBM7	402
EBPL	RCBTB1	Q8NDN9	399

IntAct

3 interactions, top by confidence:

A	B	Type	Score
EBPL	HNRNPU	psi-mi:“MI:0915”(physical association)	0.400
EBPL	DEPDC1B	psi-mi:“MI:0915”(physical association)	0.370

BioGRID (3): EBPL (Two-hybrid), EBPL (Proximity Label-MS), EBPL (Two-hybrid)

ESM2 similar proteins: E9Q6C8, F1NZP5, O35052, P27544, P27545, P98191, Q01685, Q15035, Q15629, Q17QQ5, Q32PG7, Q3ZBF8, Q49LS8, Q5E9R6, Q5GH57, Q5GH73, Q5ND56, Q5R7Z3, Q5U2T1, Q5XI41, Q5XIY2, Q5ZKZ9, Q6DED0, Q6EUN0, Q71RH2, Q7RTS5, Q7TNV1, Q80ZE4, Q8IU99, Q8N5B7, Q8TBR7, Q8TCT7, Q8TD43, Q8W4Y5, Q91V04, Q924Z4, Q924Z5, Q92903, Q96CP7, Q96G23

Diamond homologs: A0A067DFU5, A0A067E3D8, A0A9Y1LNE1, A0A9Y1LQX3, O48962, P0DXH1, P70245, Q15125, Q9BY08, Q9D0P0, Q9FTZ2, Q9JJ46, Q60490

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	30
Likely benign	3
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

553 predictions. Top by Δscore:

Variant	Effect	Δscore
13:49691249:CTTA:C	donor_loss	1.0000
13:49691250:TTACC:T	donor_loss	1.0000
13:49691251:TACC:T	donor_loss	1.0000
13:49691252:A:AC	donor_gain	1.0000
13:49691252:AC:A	donor_gain	1.0000
13:49691252:ACCAG:A	donor_gain	1.0000
13:49691253:C:CA	donor_gain	1.0000
13:49691253:CC:C	donor_gain	1.0000
13:49691253:CCA:C	donor_gain	1.0000
13:49691253:CCAG:C	donor_gain	1.0000
13:49691253:CCAGC:C	donor_gain	1.0000
13:49661206:TGC:T	acceptor_gain	0.9900
13:49661207:GC:G	acceptor_gain	0.9900
13:49661207:GCC:G	acceptor_loss	0.9900
13:49661208:CC:C	acceptor_gain	0.9900
13:49661208:CCTG:C	acceptor_loss	0.9900
13:49661209:C:CC	acceptor_gain	0.9900
13:49663050:CACCT:C	donor_loss	0.9900
13:49663051:ACCT:A	donor_loss	0.9900
13:49663052:CCTA:C	donor_loss	0.9900
13:49663053:CTACC:C	donor_loss	0.9900
13:49663054:TAC:T	donor_loss	0.9900
13:49663055:A:AC	donor_gain	0.9900
13:49663056:C:A	donor_loss	0.9900
13:49663056:C:CC	donor_gain	0.9900
13:49663193:TCC:T	acceptor_gain	0.9900
13:49663194:CC:C	acceptor_gain	0.9900
13:49663194:CCC:C	acceptor_gain	0.9900
13:49663195:CC:C	acceptor_gain	0.9900
13:49663195:CCTAA:C	acceptor_loss	0.9900

AlphaMissense

1309 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
13:49669835:A:C	F61L	0.938
13:49669835:A:T	F61L	0.938
13:49669837:A:G	F61L	0.938
13:49661151:G:C	F146L	0.899
13:49661151:G:T	F146L	0.899
13:49661153:A:G	F146L	0.899
13:49691289:A:G	W46R	0.899
13:49691289:A:T	W46R	0.899
13:49663166:A:G	W91R	0.867
13:49663166:A:T	W91R	0.867
13:49669777:A:G	W81R	0.859
13:49669777:A:T	W81R	0.859
13:49663164:C:A	W91C	0.858
13:49663164:C:G	W91C	0.858
13:49663057:C:G	R127P	0.855
13:49669844:T:A	E58D	0.854
13:49669844:T:G	E58D	0.854
13:49661184:G:C	C135W	0.845
13:49661186:A:G	C135R	0.836
13:49669833:A:T	V62D	0.836
13:49661196:C:A	Q131H	0.833
13:49661196:C:G	Q131H	0.833
13:49691283:A:G	C48R	0.830
13:49691352:C:G	G25R	0.822
13:49663173:A:C	D88E	0.821
13:49663173:A:T	D88E	0.821
13:49663174:T:A	D88V	0.819
13:49663167:T:A	R90S	0.818
13:49663167:T:G	R90S	0.818
13:49663168:C:G	R90T	0.811

dbSNP variants (sampled 300 via entrez): RS1000127469 (13:49672919 G>C), RS1000182295 (13:49677310 C>T), RS1000297670 (13:49677765 T>C), RS1000309778 (13:49672059 G>C), RS1000357460 (13:49682441 C>T), RS1000612231 (13:49660880 C>G,T), RS1000639057 (13:49673336 A>G), RS1000916588 (13:49687123 G>A,C,T), RS1000975199 (13:49687383 G>A), RS1001073291 (13:49671037 G>A), RS1001160958 (13:49693056 A>C), RS1001229534 (13:49664383 G>A), RS1001508887 (13:49692619 C>T), RS1001529899 (13:49692817 C>A), RS1001607733 (13:49686858 T>C)

Disease associations

OMIM: gene MIM:617335 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

4 associations (top):

Study	Trait	p-value
GCST007052_4	Lipoprotein (a) levels	1.000000e-06
GCST010002_186	Refractive error	1.000000e-36
GCST012227_482	Hip circumference adjusted for BMI	2.000000e-12
GCST90020028_1175	Hip circumference adjusted for BMI	1.000000e-14

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0006925	lipoprotein A measurement
EFO:0008039	BMI-adjusted hip circumference

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL2311238 (SINGLE PROTEIN)

Molecules with ChEMBL bioactivity

2 molecules (phase ≥1), by development phase (incl. off-target/promiscuous compounds). Patent mentions across the top 20 by phase: 191,679 (via chembl_molecule»patent_compound — counts attach to the compound, not the gene–compound relationship, so off-target/promiscuous molecules can dominate).

Molecule	Name	Phase	Patents
CHEMBL422	TRIFLUOPERAZINE	4	20,044
CHEMBL83	TAMOXIFEN	4	171,635

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

ChEMBL bioactivities

4 potent at pChembl≥5 of 4 total, top 4 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChembl	Type	Value	Unit	Molecule
8.76	Ki	1.72	nM	CHEMBL2314420
8.55	Ki	2.8	nM	TAMOXIFEN
8.41	Ki	3.9	nM	TRIFLUOPERAZINE
5.85	Ki	1400	nM	[18F]FLUSPIDINE

PubChem BioAssay actives

4 with measured affinity, of 4 total; 4 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

Compound	Assay	Type	Value	Unit
1-[2-(3-hydroperoxy-4-methoxyphenyl)ethyl]-4-(3-phenylpropyl)piperazine	723649: Binding affinity to emopamil binding protein (unknown origin)	ki	0.0017	uM
Tamoxifen	723649: Binding affinity to emopamil binding protein (unknown origin)	ki	0.0028	uM
Trifluoperazine	723649: Binding affinity to emopamil binding protein (unknown origin)	ki	0.0039	uM
1’-benzyl-1-(2-(17F)fluoroethyl)spiro[1H-2-benzofuran-3,4’-piperidine]	723649: Binding affinity to emopamil binding protein (unknown origin)	ki	1.4000	uM

CTD chemical–gene interactions

25 total (human), top 25 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	increases abundance, increases expression, decreases expression, affects cotreatment	3
Air Pollutants	decreases expression, increases abundance	2
Arsenic	affects cotreatment, increases abundance, increases expression	2
Benzo(a)pyrene	decreases expression, decreases methylation	2
Particulate Matter	decreases expression, increases abundance	2
aristolochic acid I	decreases expression	1
triphenyl phosphate	affects expression	1
CGP 52608	affects binding, increases reaction	1
entinostat	increases expression	1
K 7174	decreases expression	1
abrine	decreases expression	1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic acid	increases expression	1
Temozolomide	increases expression	1
Acetaminophen	decreases expression	1
Cisplatin	decreases expression	1
Estradiol	affects cotreatment, decreases expression	1
Formaldehyde	decreases expression	1
Gallic Acid	decreases expression	1
Methyl Methanesulfonate	decreases expression	1
Thiram	decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
Tretinoin	decreases expression	1
Urethane	decreases expression	1
Valproic Acid	decreases expression	1
Sodium Selenite	increases expression	1

ChEMBL screening assays

1 unique, capped per target: 1 binding

Representative assays (with source publication via chembl_document):

Assay ID	Type	Description	Source paper
CHEMBL2320419	Binding	Binding affinity to emopamil binding protein (unknown origin)	Synthesis and biological evaluation of ¹⁸F labeled fluoro-oligo-ethoxylated 4-benzylpiperazine derivatives for sigma-1 receptor imaging. — Bioorg Med Chem

Clinical trials (associated diseases)

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