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CEPT1

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Summary

CEPT1 (choline/ethanolamine phosphotransferase 1, HGNC:24289) is a protein-coding gene on chromosome 1p13.3, encoding Choline/ethanolaminephosphotransferase 1 (Q9Y6K0). Catalyzes both phosphatidylcholine and phosphatidylethanolamine biosynthesis from CDP-choline and CDP-ethanolamine, respectively. It is a selective cancer dependency (DepMap: 22.9% of cell lines).

This gene codes for a choline/ethanolaminephosphotransferase, which functions in the synthesis of choline- or ethanolamine- containing phospholipids. Alternative splicing results in multiple transcript variants.

Source: NCBI Gene 10390 — RefSeq curated summary.

At a glance

  • GWAS associations: 4
  • Clinical variants (ClinVar): 47 total
  • Druggable target: yes
  • Cancer dependency (DepMap): dependent in 22.9% of screened cell lines
  • MANE Select transcript: NM_006090

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:24289
Approved symbolCEPT1
Namecholine/ethanolamine phosphotransferase 1
Location1p13.3
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000134255
Ensembl biotypeprotein_coding
OMIM616751
Entrez10390

Gene structure

Transcript identifiers

Ensembl transcripts: 25 — 15 protein_coding, 8 protein_coding_CDS_not_defined, 2 nonsense_mediated_decay

ENST00000357172, ENST00000460443, ENST00000467362, ENST00000473474, ENST00000476865, ENST00000478042, ENST00000480324, ENST00000483427, ENST00000498239, ENST00000545121, ENST00000700750, ENST00000700751, ENST00000700752, ENST00000874823, ENST00000874824, ENST00000874825, ENST00000874826, ENST00000874827, ENST00000874828, ENST00000874829, ENST00000874830, ENST00000938971, ENST00000942340, ENST00000942341, ENST00000942342

RefSeq mRNA: 4 — MANE Select: NM_006090 NM_001007794, NM_001330743, NM_001410844, NM_006090

CCDS: CCDS830, CCDS91024

Canonical transcript exons

ENST00000357172 — 9 exons

ExonStartEnd
ENSE00003501695111183462111183587
ENSE00003505918111161155111161296
ENSE00003527576111174879111174963
ENSE00003550489111147642111148053
ENSE00003593414111182799111182957
ENSE00003602100111182187111182318
ENSE00003628116111159380111159527
ENSE00003980728111184191111185104
ENSE00003980735111140223111140307

Expression profiles

Bgee: expression breadth ubiquitous, 282 present calls, max score 97.19.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 33.1991 / max 448.9475, expressed in 1818 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter IDTPM avgSamples expressed
460029.61901812
45971.8085858
45981.2197608
45990.4436180
2016120.108431

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
buccal mucosa cellCL:000233697.19gold quality
spleenUBERON:000210695.78gold quality
lymph nodeUBERON:000002995.36gold quality
monocyteCL:000057694.21gold quality
calcaneal tendonUBERON:000370194.07gold quality
leukocyteCL:000073893.87gold quality
right uterine tubeUBERON:000130293.86gold quality
mononuclear cellCL:000084293.85gold quality
granulocyteCL:000009493.80gold quality
esophagus squamous epitheliumUBERON:000692093.10gold quality
secondary oocyteCL:000065593.00gold quality
rectumUBERON:000105292.87gold quality
small intestine Peyer’s patchUBERON:000345492.71gold quality
adrenal tissueUBERON:001830392.47gold quality
vermiform appendixUBERON:000115492.31gold quality
tonsilUBERON:000237292.17gold quality
epithelium of esophagusUBERON:000197691.90gold quality
gall bladderUBERON:000211091.87gold quality
choroid plexus epitheliumUBERON:000391191.52gold quality
cartilage tissueUBERON:000241891.46gold quality
small intestineUBERON:000210891.30gold quality
minor salivary glandUBERON:000183091.25gold quality
adipose tissueUBERON:000101390.98gold quality
right adrenal glandUBERON:000123390.88gold quality
islet of LangerhansUBERON:000000690.87gold quality
right adrenal gland cortexUBERON:003582790.85gold quality
connective tissueUBERON:000238490.78gold quality
subcutaneous adipose tissueUBERON:000219090.69gold quality
right lobe of liverUBERON:000111490.60gold quality
left adrenal glandUBERON:000123490.58gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 2.

ExperimentMarker?Max mean expression
E-MTAB-9543yes14.33
E-ANND-3yes5.13
E-MTAB-6386no460.63

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

71 targeting CEPT1, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-LET-7A-3P100.0074.033932
HSA-LET-7B-3P100.0074.083913
HSA-LET-7F-1-3P100.0074.023928
HSA-MIR-98-3P100.0074.083907
HSA-MIR-340-5P100.0072.504437
HSA-MIR-4795-3P100.0074.624024
HSA-MIR-126-5P100.0072.713180
HSA-MIR-186-5P99.9970.833707
HSA-MIR-513B-5P99.9969.962150
HSA-MIR-428299.9975.366408
HSA-MIR-27A-3P99.9872.132955
HSA-MIR-27B-3P99.9872.132955
HSA-MIR-998599.9872.112939
HSA-MIR-4666A-3P99.9671.713434
HSA-MIR-548AT-5P99.9670.832666
HSA-MIR-381-3P99.9371.872854
HSA-MIR-314399.9371.963104
HSA-MIR-30099.9271.762856
HSA-MIR-311999.9271.342390
HSA-MIR-6768-5P99.9267.361942
HSA-MIR-449699.8868.892236
HSA-MIR-5582-3P99.8672.484221
HSA-MIR-548AR-3P99.8571.263889
HSA-MIR-548AZ-3P99.8270.563549
HSA-MIR-548BC99.8270.613524
HSA-MIR-548E-3P99.8270.593514
HSA-MIR-548F-3P99.8270.593540
HSA-MIR-313399.8170.923506
HSA-MIR-548A-3P99.7670.583524
HSA-MIR-6885-3P99.7570.363187

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 22.9% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 7)

  • A yeast expression system devoid of endogenous cholinephosphotransferase and ethanolaminephosphotransferase activities to assess the diradylglycerol specificity of CEPT1 (PMID:12216837)
  • Association of the -629C>A (rs1800775) CETP Polymorphism with the Development of Essential Hypertension in Mexican Population. (PMID:32551884)
  • Locations and contributions of the phosphotransferases EPT1 and CEPT1 to the biosynthesis of ethanolamine phospholipids. (PMID:32576654)
  • CEPT1-Mediated Phospholipogenesis Regulates Endothelial Cell Function and Ischemia-Induced Angiogenesis Through PPARalpha. (PMID:33214136)
  • Differential contributions of choline phosphotransferases CPT1 and CEPT1 to the biosynthesis of choline phospholipids. (PMID:34331935)
  • Structural basis for catalysis of human choline/ethanolamine phosphotransferase 1. (PMID:37137909)
  • Proteomic analysis of ferroptosis pathways reveals a role of CEPT1 in suppressing ferroptosis. (PMID:38430542)

Cross-species orthologs

7 orthologs

OrganismSymbolGene ID
danio_reriocept1bENSDARG00000021177
danio_reriocept1aENSDARG00000058716
mus_musculusCept1ENSMUSG00000040774
rattus_norvegicusCept1ENSRNOG00000017723
drosophila_melanogasterbbcFBGN0033844
caenorhabditis_elegansWBGENE00009057
caenorhabditis_elegansWBGENE00013024

Paralogs (2): CHPT1 (ENSG00000111666), SELENOI (ENSG00000138018)

Protein

Protein identifiers

Choline/ethanolaminephosphotransferase 1 — Q9Y6K0 (reviewed: Q9Y6K0)

Alternative names: 1-alkenyl-2-acylglycerol choline phosphotransferase

All UniProt accessions (4): A0A8V8TQ23, A0A8V8TQL1, A0A8V8TRF3, Q9Y6K0

UniProt curated annotations — full annotation on UniProt →

Function. Catalyzes both phosphatidylcholine and phosphatidylethanolamine biosynthesis from CDP-choline and CDP-ethanolamine, respectively. Involved in protein-dependent process of phospholipid transport to distribute phosphatidyl choline to the lumenal surface. Has a higher cholinephosphotransferase activity than ethanolaminephosphotransferase activity.

Subunit / interactions. Homodimer.

Subcellular location. Endoplasmic reticulum membrane. Nucleus membrane.

Tissue specificity. Ubiquitously expressed.

Pathway. Phospholipid metabolism; phosphatidylethanolamine biosynthesis; phosphatidylethanolamine from ethanolamine: step 3/3. Phospholipid metabolism; phosphatidylcholine biosynthesis; phosphatidylcholine from phosphocholine: step 2/2.

Similarity. Belongs to the CDP-alcohol phosphatidyltransferase class-I family.

RefSeq proteins (4): NP_001007795, NP_001317672, NP_001397773, NP_006081* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000462CDP-OH_P_transFamily
IPR014472CHOPTFamily
IPR043130CDP-OH_PTrfase_TM_domHomologous_superfamily
IPR048254CDP_ALCOHOL_P_TRANSF_CSConserved_site

Pfam: PF01066

Enzyme classification (BRENDA):

  • EC 2.7.8.1 — ethanolaminephosphotransferase (BRENDA: 17 organisms, 70 substrates, 58 inhibitors, 34 Km, 0 kcat entries)
  • EC 2.7.8.2 — diacylglycerol cholinephosphotransferase (BRENDA: 34 organisms, 101 substrates, 94 inhibitors, 36 Km, 0 kcat entries)

Substrate kinetics (BRENDA)

34 substrates with measured Km, best-characterized 15. Km ranges are aggregated across organisms/conditions.

SubstrateKm (mM)Measurements
CDP-ETHANOLAMINE0.0006–180015
CDP-CHOLINE0.0166–0.538
CDP-CHOLINE0.036–10.74
1,2-DIOLEOYLGLYCEROL0.0118–0.1472
CMP0.04–0.142
1,2-DIOLEOYL-SN-GLYCEROL0.0509–0.122
CDP-ETHANOLAMINE0.098–0.1012
1-ALKYL-2-ACYL-SN-GLYCEROL1.91
1-ARACHIDOYL-2-OCTADECENOYLGLYCEROL0.1821
1-DODECANOYL-2-OCTADECENOYLGLYCEROL0.1111
1-HEPTADECANOYL-2-OCTADECENOYLGLYCEROL0.121
1-NONADECANOYL-2-OCTADECENOYLGLYCEROL0.1281
1-OCTADECANOYL-2-OCTADECENOYLGLYCEROL0.1671
1-PENTADECANOYL-2-OCTADECENOYLGLYCEROL0.1141
DIACYLGLYCEROL0.0631

Catalyzed reactions (Rhea), 12 shown:

  • CDP-choline + a 1,2-diacyl-sn-glycerol = a 1,2-diacyl-sn-glycero-3-phosphocholine + CMP + H(+) (RHEA:32939)
  • CDP-ethanolamine + a 1,2-diacyl-sn-glycerol = a 1,2-diacyl-sn-glycero-3-phosphoethanolamine + CMP + H(+) (RHEA:32943)
  • 1-O-alkyl-2-acyl-sn-glycerol + CDP-choline = a 1-O-alkyl-2-acyl-sn-glycero-3-phosphocholine + CMP + H(+) (RHEA:36179)
  • a 1-O-(1Z-alkenyl)-2-acyl-sn-glycerol + CDP-choline = a 1-O-(1Z-alkenyl)-2-acyl-sn-glycero-3-phosphocholine + CMP + H(+) (RHEA:36227)
  • 1,2-dioctanoyl-sn-glycerol + CDP-choline = 1,2-dioctanoyl-sn-glycero-3-phosphocholine + CMP + H(+) (RHEA:54232)
  • 1,2-didecanoyl-sn-glycerol + CDP-choline = 1,2-didecanoyl-sn-glycero-3-phosphocholine + CMP + H(+) (RHEA:54236)
  • CDP-choline + 1,2-di-(9Z-octadecenoyl)-sn-glycerol = 1,2-di-(9Z-octadecenoyl)-sn-glycero-3-phosphocholine + CMP + H(+) (RHEA:54240)
  • 1-hexadecanoyl-2-(9Z-octadecenoyl)-sn-glycerol + CDP-choline = 1-hexadecanoyl-2-(9Z-octadecenoyl)-sn-glycero-3-phosphocholine + CMP + H(+) (RHEA:54244)
  • CDP-ethanolamine + 1,2-di-(9Z-octadecenoyl)-sn-glycerol = 1,2-di-(9Z-octadecenoyl)-sn-glycero-3-phosphoethanolamine + CMP + H(+) (RHEA:54248)
  • 1-hexadecanoyl-2-(9Z-octadecenoyl)-sn-glycerol + CDP-ethanolamine = 1-hexadecanoyl-2-(9Z-octadecenoyl)-sn-glycero-3-phosphoethanolamine + CMP + H(+) (RHEA:54252)
  • 1-hexadecanoyl-2-(4Z,7Z,10Z,13Z,16Z,19Z-docosahexaenoyl)-sn-glycerol + CDP-choline = 1-hexadecanoyl-2-(4Z,7Z,10Z,13Z,16Z,19Z-docosahexaenoyl)-sn-glycero-3-phosphocholine + CMP + H(+) (RHEA:54332)
  • 1,2-di-(9Z-hexadecenoyl)-sn-glycerol + CDP-choline = 1,2-di-(9Z-hexadecenoyl)-sn-glycero-3-phosphocholine + CMP + H(+) (RHEA:54336)

UniProt features (47 total): mutagenesis site 23, transmembrane region 10, binding site 7, modified residue 2, chain 1, region of interest 1, active site 1, site 1, glycosylation site 1

Structure

Experimental structures (PDB)

2 structures.

PDBMethodResolution (Å)
8GYXELECTRON MICROSCOPY3.7
8GYWELECTRON MICROSCOPY3.9

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9Y6K0-F189.270.84

Functional residue map

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

Catalytic / active sites (2): 155 (proton acceptor); 151 (increases basicity of active site his)

Ligand- & substrate-binding residues (7): 86; 133; 133; 151; 154; 154; 158

Post-translational modifications (2): 18, 40

Glycosylation sites (1): 144

Mutagenesis-validated functional residues (23):

PositionPhenotype
86strongly decreased cholinephosphotransferase activity.
136decreased cholinephosphotransferase activity.
138induces a reduction in both cholinephosphotransferase and ethanolaminephosphotransferase activities.
144no effect.
146no effect.
151strongly decreased cholinephosphotransferase activity.
154abolished cholinephosphotransferase activity.
156induces a reduction in cholinephosphotransferase activity and abolishes ethanolaminephosphotransferase activity.
158decreased cholinephosphotransferase activity.
162decreased cholinephosphotransferase activity.
169decreased cholinephosphotransferase activity.
196decreased cholinephosphotransferase activity.
212decreased cholinephosphotransferase activity.
214alters the profile of diacylglycerol utilization and results in modest reduction in enzyme activity.
215induces a strong reduction in enzyme activity without altering diacylglycerol specificity.
215induces a strong reduction in enzyme activity and alters diacylglycerol specificity.
216alters the profile of diacylglycerol utilization and results in modest reduction in enzyme activity.
217decreased cholinephosphotransferase activity.
221alters the profile of diacylglycerol utilization and results in modest reduction in enzyme activity.
226does not affect either the enzyme activity or the diacylglycerol specificity.
228does not affect either the enzyme activity or the diacylglycerol specificity.
261decreased cholinephosphotransferase activity.
265decreased cholinephosphotransferase activity.

Function

Pathways and Gene Ontology

Reactome pathways

6 pathways

IDPathway
R-HSA-1483191Synthesis of PC
R-HSA-1483213Synthesis of PE
R-HSA-1430728Metabolism
R-HSA-1483206Glycerophospholipid biosynthesis
R-HSA-1483257Phospholipid metabolism
R-HSA-556833Metabolism of lipids

MSigDB gene sets: 189 (showing top): GOBP_PHOSPHOLIPID_METABOLIC_PROCESS, TAATAAT_MIR126, GOBP_PHOSPHATIDYLCHOLINE_METABOLIC_PROCESS, GOBP_PHOSPHATIDYLCHOLINE_BIOSYNTHETIC_PROCESS, GOBP_ORGANOPHOSPHATE_METABOLIC_PROCESS, GOBP_ORGANOPHOSPHATE_BIOSYNTHETIC_PROCESS, CEBPB_01, GOBP_PHOSPHOLIPID_BIOSYNTHETIC_PROCESS, GOBP_GLYCEROLIPID_METABOLIC_PROCESS, KYNG_ENVIRONMENTAL_STRESS_RESPONSE_NOT_BY_GAMMA_IN_WS, GOBP_GLYCEROLIPID_BIOSYNTHETIC_PROCESS, TGANTCA_AP1_C, GOBP_GLYCEROPHOSPHOLIPID_METABOLIC_PROCESS, GOBP_LIPID_METABOLIC_PROCESS, AACTTT_UNKNOWN

GO Biological Process (5): lipid metabolic process (GO:0006629), phosphatidylethanolamine biosynthetic process (GO:0006646), phosphatidylcholine biosynthetic process (GO:0006656), CDP-choline pathway (GO:0006657), phospholipid biosynthetic process (GO:0008654)

GO Molecular Function (7): diacylglycerol cholinephosphotransferase activity (GO:0004142), ethanolaminephosphotransferase activity (GO:0004307), metal ion binding (GO:0046872), 1-alkenyl-2-acylglycerol choline phosphotransferase activity (GO:0047359), protein binding (GO:0005515), transferase activity (GO:0016740), phosphotransferase activity, for other substituted phosphate groups (GO:0016780)

GO Cellular Component (8): endoplasmic reticulum membrane (GO:0005789), Golgi apparatus (GO:0005794), membrane (GO:0016020), nuclear membrane (GO:0031965), nucleus (GO:0005634), cytoplasm (GO:0005737), endoplasmic reticulum (GO:0005783), endomembrane system (GO:0012505)

Reactome top-level categories

Rollup of top-4 pathways:

CategoryPathways
Glycerophospholipid biosynthesis2
Phospholipid metabolism1
Metabolism of lipids1
Metabolism1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
intracellular membrane-bounded organelle3
cellular anatomical structure3
glycerophospholipid biosynthetic process2
CDP-alcohol phosphatidyltransferase activity2
organelle membrane2
cytoplasm2
endomembrane system2
primary metabolic process1
phosphatidylethanolamine metabolic process1
phosphatidylcholine metabolic process1
choline kinase activity1
diacylglycerol cholinephosphotransferase activity1
phosphatidylcholine biosynthetic process1
phospholipid metabolic process1
lipid biosynthetic process1
organophosphate biosynthetic process1
cation binding1
phosphotransferase activity, for other substituted phosphate groups1
binding1
catalytic activity1
transferase activity, transferring phosphorus-containing groups1
nuclear outer membrane-endoplasmic reticulum membrane network1
endoplasmic reticulum subcompartment1
nucleus1
nuclear envelope1
intracellular anatomical structure1
vacuole1
plasma membrane1

Protein interactions and networks

STRING

1624 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
CEPT1CDIPTO14735791
CEPT1PCYT1AP49585789
CEPT1PCYT2Q99447772
CEPT1PCYT1BQ9Y5K3770
CEPT1CHKAP35790744
CEPT1PEMTQ9UBM1733
CEPT1PISDQ9UG56715
CEPT1ETNK2Q9NVF9645
CEPT1PTDSS2Q9BVG9628
CEPT1CHKBQ9Y259625
CEPT1RAB10P61026615
CEPT1ETNK1Q9HBU6606
CEPT1LPCAT2Q7L5N7540
CEPT1GPCPD1Q9NPB8514
CEPT1PTDSS1P48651513

IntAct

84 interactions, top by confidence:

ABTypeScore
KIF22KPNA4psi-mi:“MI:0914”(association)0.730
CFTRESYT2psi-mi:“MI:0914”(association)0.710
OAZ1AZIN1psi-mi:“MI:0914”(association)0.640
CEPT1TMEM14Bpsi-mi:“MI:0915”(physical association)0.560
SPG21CEPT1psi-mi:“MI:0915”(physical association)0.560
TMEM14BCEPT1psi-mi:“MI:0915”(physical association)0.560
CEPT1RBM6psi-mi:“MI:0914”(association)0.530
CEPT1TMEM263psi-mi:“MI:0915”(physical association)0.400
Tor1aip1PEX10psi-mi:“MI:0914”(association)0.350
Kifc5bKPNA3psi-mi:“MI:0914”(association)0.350
CDC42BBXpsi-mi:“MI:0914”(association)0.350
CSNK2A2WDR46psi-mi:“MI:0914”(association)0.350
Cdc26psi-mi:“MI:0914”(association)0.350
SMC6IFT88psi-mi:“MI:0914”(association)0.350
MYH14psi-mi:“MI:0914”(association)0.350
Mtx2NRDCpsi-mi:“MI:0914”(association)0.350
TOMM40NOS1APpsi-mi:“MI:0914”(association)0.350
Chmp4cSF1psi-mi:“MI:0914”(association)0.350
Prmt6LAMA1psi-mi:“MI:0914”(association)0.350
VAPApsi-mi:“MI:0914”(association)0.350
PSMC1ZNF561psi-mi:“MI:0914”(association)0.350
CHST15SLC43A3psi-mi:“MI:0914”(association)0.350
Rock1psi-mi:“MI:0914”(association)0.350
WDR62MAPKBP1psi-mi:“MI:0914”(association)0.350
YIPF5SSR3psi-mi:“MI:0914”(association)0.350
QSOX2NAP1L1psi-mi:“MI:0914”(association)0.350
UGGT1SF3B1psi-mi:“MI:0914”(association)0.350

BioGRID (87): CEPT1 (Affinity Capture-MS), CEPT1 (Affinity Capture-MS), CEPT1 (Affinity Capture-MS), CEPT1 (Affinity Capture-MS), CEPT1 (Affinity Capture-MS), CEPT1 (Affinity Capture-MS), CEPT1 (Affinity Capture-MS), CEPT1 (Affinity Capture-MS), CEPT1 (Affinity Capture-MS), CEPT1 (Affinity Capture-MS), CEPT1 (Affinity Capture-MS), CEPT1 (Affinity Capture-MS), CEPT1 (Affinity Capture-MS), CEPT1 (Affinity Capture-MS), CEPT1 (Affinity Capture-MS)

ESM2 similar proteins: A0JNC1, A2VE61, A7XZ53, B1H3H9, D3ZEH5, F4HXY7, O35052, O95674, P48651, P98191, Q00576, Q01685, Q0JR55, Q0VCK9, Q28CY9, Q28H54, Q2KHY9, Q5EA65, Q5N8Q3, Q5R7B1, Q5U239, Q5ZKD1, Q5ZKJ0, Q5ZM65, Q6AXM5, Q6DD44, Q6DED0, Q6I628, Q7ZYQ3, Q803C9, Q8BGS7, Q8BXA5, Q8CIF6, Q8NBJ9, Q91XU8, Q91ZQ0, Q92903, Q96KA5, Q99KU0, Q99L43

Diamond homologs: O13901, O82567, O82568, P17898, P22140, Q1LZE6, Q28H54, Q4KLV1, Q54XM0, Q550W1, Q5NV96, Q5ZHQ5, Q5ZKD1, Q66H21, Q6AXM5, Q7ZW02, Q7ZYQ3, Q80TA1, Q8BGS7, Q8C025, Q8T2Q6, Q8WUD6, Q95ZE2, Q9C0D9, Q9Y6K0, Q55AQ3, Q17QM4

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance29
Likely benign0
Benign1

Top pathogenic / likely-pathogenic (0)

SpliceAI

1963 predictions. Top by Δscore:

VariantEffectΔscore
1:111159374:TCACA:Tacceptor_loss1.0000
1:111159375:CACAG:Cacceptor_loss1.0000
1:111159376:ACAGG:Aacceptor_loss1.0000
1:111159377:CAGG:Cacceptor_loss1.0000
1:111159378:A:ACacceptor_loss1.0000
1:111159523:AACAG:Adonor_loss1.0000
1:111159525:CAGG:Cdonor_loss1.0000
1:111159526:AGGTA:Adonor_loss1.0000
1:111161230:C:CAacceptor_gain1.0000
1:111161231:G:Aacceptor_gain1.0000
1:111182176:A:AGacceptor_gain1.0000
1:111182180:A:AGacceptor_gain1.0000
1:111182184:A:Gacceptor_gain1.0000
1:111182186:G:GCacceptor_loss1.0000
1:111182314:TAGCA:Tdonor_gain1.0000
1:111182315:AGCA:Adonor_gain1.0000
1:111182316:GCA:Gdonor_gain1.0000
1:111182316:GCAG:Gdonor_gain1.0000
1:111182317:CA:Cdonor_gain1.0000
1:111182317:CAG:Cdonor_loss1.0000
1:111182318:AG:Adonor_loss1.0000
1:111182319:G:GGdonor_gain1.0000
1:111182320:TAA:Tdonor_loss1.0000
1:111182321:AA:Adonor_loss1.0000
1:111183454:A:AGacceptor_gain1.0000
1:111183457:CATA:Cacceptor_loss1.0000
1:111183459:TA:Tacceptor_loss1.0000
1:111183460:A:AGacceptor_gain1.0000
1:111183460:A:Cacceptor_loss1.0000
1:111183460:AG:Aacceptor_gain1.0000

AlphaMissense

2730 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
1:111159447:A:TD136V1.000
1:111159501:A:CD154A1.000
1:111159501:A:TD154V1.000
1:111159502:T:AD154E1.000
1:111159502:T:GD154E1.000
1:111159504:A:CH155P1.000
1:111159505:T:AH155Q1.000
1:111159505:T:GH155Q1.000
1:111159513:A:CD158A1.000
1:111159513:A:GD158G1.000
1:111159513:A:TD158V1.000
1:111159514:T:AD158E1.000
1:111159514:T:GD158E1.000
1:111147968:C:AP85Q0.999
1:111147972:T:AN86K0.999
1:111147972:T:GN86K0.999
1:111147980:C:TT89I0.999
1:111147989:G:AG92E0.999
1:111147992:T:CL93P0.999
1:111159438:A:CD133A0.999
1:111159438:A:GD133G0.999
1:111159438:A:TD133V0.999
1:111159439:T:AD133E0.999
1:111159439:T:GD133E0.999
1:111159446:G:CD136H0.999
1:111159446:G:TD136Y0.999
1:111159447:A:CD136A0.999
1:111159447:A:GD136G0.999
1:111159448:T:AD136E0.999
1:111159448:T:GD136E0.999

dbSNP variants (sampled 300 via entrez): RS1000062678 (1:111147376 A>G), RS1000086073 (1:111168735 A>G), RS1000218858 (1:111166822 A>G,T), RS1000283980 (1:111153211 T>G), RS1000290777 (1:111169029 A>G), RS1000378365 (1:111162104 A>C), RS1000432859 (1:111155766 G>A,T), RS1000457805 (1:111150681 T>C), RS1000467615 (1:111174036 G>C), RS1000573719 (1:111151052 C>T), RS1000604537 (1:111174466 A>T), RS1000707370 (1:111163677 A>G), RS1000825995 (1:111157040 C>G,T), RS1000886941 (1:111155605 T>G), RS1000917354 (1:111143358 T>C)

Disease associations

OMIM: gene MIM:616751 | 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):

StudyTraitp-value
GCST001277_9Liver enzyme levels (gamma-glutamyl transferase)7.000000e-09
GCST005752_169Systemic lupus erythematosus8.000000e-07
GCST90002398_489Neutrophil count1.000000e-14
GCST90013407_131Liver enzyme levels (gamma-glutamyl transferase)2.000000e-20

EFO canonical traits (2, from GWAS)

EFO IDTrait name
EFO:0004532serum gamma-glutamyl transferase measurement
EFO:0004833neutrophil count

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL4105740 (SINGLE PROTEIN)

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

ChEMBL bioactivities

41 potent at pChembl≥5 of 45 total, top 41 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChemblTypeValueUnitMolecule
8.40Kd3.969nMCHEMBL3752910
8.40ED503.969nMCHEMBL3752910
7.55IC5028nMCHEMBL593709
7.51IC5031nMCHEMBL596491
7.36IC5044nMCHEMBL595357
7.34IC5046nMCHEMBL595352
7.24IC5058nMCHEMBL596476
7.23IC5059nMCHEMBL596490
7.22IC5060nMCHEMBL596130
7.21IC5062nMCHEMBL606349
7.10IC5080nMCHEMBL594868
7.07IC5086nMCHEMBL595359
7.03IC5094nMCHEMBL593247
6.96IC50110nMCHEMBL606696
6.89IC50130nMCHEMBL260546
6.80IC50160nMCHEMBL592998
6.70IC50200nMCHEMBL594183
6.68IC50210nMCHEMBL593246
6.68IC50210nMCHEMBL595358
6.57IC50270nMCHEMBL594978
6.42IC50380nMCHEMBL593007
6.39IC50410nMCHEMBL596131
6.36IC50440nMCHEMBL593966
6.29IC50510nMCHEMBL606983
6.24IC50570nMCHEMBL407147
6.08IC50840nMCHEMBL411258
6.04IC50910nMCHEMBL594182
6.03IC50940nMCHEMBL261273
5.96IC501100nMCHEMBL261275
5.89IC501300nMCHEMBL261496
5.89IC501300nMCHEMBL263126
5.72IC501900nMCHEMBL260010
5.72IC501900nMCHEMBL603211
5.70IC502000nMCHEMBL260011
5.70IC502000nMCHEMBL594285
5.55IC502800nMCHEMBL594980
5.54IC502900nMCHEMBL595921
5.50IC503200nMCHEMBL258586
5.47IC503400nMCHEMBL594778
5.28IC505200nMCHEMBL596438
5.12IC507500nMCHEMBL260591

PubChem BioAssay actives

40 with measured affinity, of 67 total; 40 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

CompoundAssayTypeValueUnit
4-methyl-3-[(1-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide2148061: Binding affinity to human CEPT1 incubated for 45 mins by Kinobead based pull down assaykd0.0040uM
N-[4-[5-cyano-7-(2-hydroxypropan-2-yl)-1,3-benzoxazol-2-yl]phenyl]-2-(2-methylphenoxy)acetamide455256: inhibition of human CEPT assessed as cholesteryl ester transfer by fluorescence transfer assayic500.0280uM
N-[4-[5-cyano-7-(2-hydroxybutan-2-yl)-1,3-benzoxazol-2-yl]phenyl]-2-(2-methylphenoxy)acetamide455256: inhibition of human CEPT assessed as cholesteryl ester transfer by fluorescence transfer assayic500.0310uM
N-[4-[5-bromo-7-(2-hydroxypropan-2-yl)-1,3-benzoxazol-2-yl]phenyl]-2-(2-methylphenoxy)acetamide455256: inhibition of human CEPT assessed as cholesteryl ester transfer by fluorescence transfer assayic500.0440uM
N-[4-[5-cyano-7-(1-hydroxyethyl)-1,3-benzoxazol-2-yl]phenyl]-2-(2-methylphenoxy)acetamide455256: inhibition of human CEPT assessed as cholesteryl ester transfer by fluorescence transfer assayic500.0460uM
N-[4-[5-cyano-7-(2-hydroxypentan-2-yl)-1,3-benzoxazol-2-yl]phenyl]-2-(2-methylphenoxy)acetamide455256: inhibition of human CEPT assessed as cholesteryl ester transfer by fluorescence transfer assayic500.0580uM
N-[4-[5-bromo-7-(1-hydroxyethyl)-1,3-benzoxazol-2-yl]phenyl]-2-(2-methylphenoxy)acetamide455256: inhibition of human CEPT assessed as cholesteryl ester transfer by fluorescence transfer assayic500.0590uM
N-[4-(5-cyano-7-methyl-1,3-benzoxazol-2-yl)phenyl]-2-(2-methylphenoxy)acetamide455256: inhibition of human CEPT assessed as cholesteryl ester transfer by fluorescence transfer assayic500.0600uM
N-[4-(5-cyano-7-fluoro-1,3-benzoxazol-2-yl)phenyl]-2-(2-methylphenoxy)acetamide455256: inhibition of human CEPT assessed as cholesteryl ester transfer by fluorescence transfer assayic500.0620uM
N-[4-[5-cyano-7-(2-hydroxy-3-methylbutan-2-yl)-1,3-benzoxazol-2-yl]phenyl]-2-(2-methylphenoxy)acetamide455256: inhibition of human CEPT assessed as cholesteryl ester transfer by fluorescence transfer assayic500.0800uM
N-[4-(7-acetyl-5-cyano-1,3-benzoxazol-2-yl)phenyl]-2-(2-methylphenoxy)acetamide455256: inhibition of human CEPT assessed as cholesteryl ester transfer by fluorescence transfer assayic500.0860uM
N-[4-[5-bromo-7-(2-hydroxybut-3-yn-2-yl)-1,3-benzoxazol-2-yl]phenyl]-2-(2-methylphenoxy)acetamide455256: inhibition of human CEPT assessed as cholesteryl ester transfer by fluorescence transfer assayic500.0940uM
N-[4-[5-bromo-7-(2-hydroxybutan-2-yl)-1,3-benzoxazol-2-yl]phenyl]-2-(2-methylphenoxy)acetamide455256: inhibition of human CEPT assessed as cholesteryl ester transfer by fluorescence transfer assayic500.1100uM
N-[4-(5-cyano-1,3-benzoxazol-2-yl)phenyl]-2-(2-methylphenoxy)acetamide455256: inhibition of human CEPT assessed as cholesteryl ester transfer by fluorescence transfer assayic500.1300uM
N-[4-[5-cyano-7-(2-hydroxypent-3-yn-2-yl)-1,3-benzoxazol-2-yl]phenyl]-2-(2-methylphenoxy)acetamide455256: inhibition of human CEPT assessed as cholesteryl ester transfer by fluorescence transfer assayic500.1600uM
N-[4-[5-bromo-7-(2-hydroxypentan-2-yl)-1,3-benzoxazol-2-yl]phenyl]-2-(2-methylphenoxy)acetamide455256: inhibition of human CEPT assessed as cholesteryl ester transfer by fluorescence transfer assayic500.2000uM
N-[4-[5-bromo-7-(2-hydroxy-3-methylbutan-2-yl)-1,3-benzoxazol-2-yl]phenyl]-2-(2-methylphenoxy)acetamide455256: inhibition of human CEPT assessed as cholesteryl ester transfer by fluorescence transfer assayic500.2100uM
N-[4-[5-bromo-7-(2-hydroxypent-3-yn-2-yl)-1,3-benzoxazol-2-yl]phenyl]-2-(2-methylphenoxy)acetamide455256: inhibition of human CEPT assessed as cholesteryl ester transfer by fluorescence transfer assayic500.2100uM
N-[4-(5,7-dicyano-1,3-benzoxazol-2-yl)phenyl]-2-(2-methylphenoxy)acetamide455256: inhibition of human CEPT assessed as cholesteryl ester transfer by fluorescence transfer assayic500.2700uM
N-[4-(7-acetyl-5-bromo-1,3-benzoxazol-2-yl)phenyl]-2-(2-methylphenoxy)acetamide455256: inhibition of human CEPT assessed as cholesteryl ester transfer by fluorescence transfer assayic500.3800uM
N-[4-(6-cyano-1,3-benzoxazol-2-yl)phenyl]-2-(2-methylphenoxy)acetamide455256: inhibition of human CEPT assessed as cholesteryl ester transfer by fluorescence transfer assayic500.4100uM
N-[4-[7-(2-hydroxypropan-2-yl)-1,3-benzoxazol-2-yl]phenyl]-2-(2-methylphenoxy)acetamide455256: inhibition of human CEPT assessed as cholesteryl ester transfer by fluorescence transfer assayic500.4400uM
N-[4-(5-bromo-7-methyl-1,3-benzoxazol-2-yl)phenyl]-2-(2-methylphenoxy)acetamide455256: inhibition of human CEPT assessed as cholesteryl ester transfer by fluorescence transfer assayic500.5100uM
N-[4-(5-chloro-7-nitro-1,3-benzoxazol-2-yl)phenyl]-2-(2-methylphenoxy)acetamide455256: inhibition of human CEPT assessed as cholesteryl ester transfer by fluorescence transfer assayic500.5700uM
N-[4-(5-methoxy-1,3-benzoxazol-2-yl)phenyl]-2-(2-methylphenoxy)acetamide455256: inhibition of human CEPT assessed as cholesteryl ester transfer by fluorescence transfer assayic500.8400uM
N-[4-(5-bromo-7-fluoro-1,3-benzoxazol-2-yl)phenyl]-2-(2-methylphenoxy)acetamide455256: inhibition of human CEPT assessed as cholesteryl ester transfer by fluorescence transfer assayic500.9100uM
2-(2-methylphenoxy)-N-[4-(5-nitro-1,3-benzoxazol-2-yl)phenyl]acetamide455256: inhibition of human CEPT assessed as cholesteryl ester transfer by fluorescence transfer assayic500.9400uM
N-[4-(5-chloro-1,3-benzoxazol-2-yl)phenyl]-2-(2-methylphenoxy)acetamide455256: inhibition of human CEPT assessed as cholesteryl ester transfer by fluorescence transfer assayic501.1000uM
N-[4-(5-bromo-1,3-benzoxazol-2-yl)phenyl]-2-(2-methylphenoxy)acetamide455256: inhibition of human CEPT assessed as cholesteryl ester transfer by fluorescence transfer assayic501.3000uM
N-[4-(5-acetyl-1,3-benzoxazol-2-yl)phenyl]-2-(2-methylphenoxy)acetamide455256: inhibition of human CEPT assessed as cholesteryl ester transfer by fluorescence transfer assayic501.3000uM
N-[4-(5-fluoro-1,3-benzoxazol-2-yl)phenyl]-2-(2-methylphenoxy)acetamide455256: inhibition of human CEPT assessed as cholesteryl ester transfer by fluorescence transfer assayic501.9000uM
N-[4-(5-cyano-6-methyl-1,3-benzoxazol-2-yl)phenyl]-2-(2-methylphenoxy)acetamide455256: inhibition of human CEPT assessed as cholesteryl ester transfer by fluorescence transfer assayic501.9000uM
N-[4-(5-methyl-1,3-benzoxazol-2-yl)phenyl]-2-(2-methylphenoxy)acetamide455256: inhibition of human CEPT assessed as cholesteryl ester transfer by fluorescence transfer assayic502.0000uM
N-[4-(5-ethynyl-1,3-benzoxazol-2-yl)phenyl]-2-(2-methylphenoxy)acetamide455256: inhibition of human CEPT assessed as cholesteryl ester transfer by fluorescence transfer assayic502.0000uM
N-[4-(5-ethenyl-1,3-benzoxazol-2-yl)phenyl]-2-(2-methylphenoxy)acetamide455256: inhibition of human CEPT assessed as cholesteryl ester transfer by fluorescence transfer assayic502.8000uM
2-(2-methylphenoxy)-N-[4-(5-methylsulfanyl-1,3-benzoxazol-2-yl)phenyl]acetamide455256: inhibition of human CEPT assessed as cholesteryl ester transfer by fluorescence transfer assayic502.9000uM
2-(2-methylphenoxy)-N-[4-(6-nitro-1,3-benzoxazol-2-yl)phenyl]acetamide455256: inhibition of human CEPT assessed as cholesteryl ester transfer by fluorescence transfer assayic503.2000uM
N-[4-[5-(1-hydroxyethyl)-1,3-benzoxazol-2-yl]phenyl]-2-(2-methylphenoxy)acetamide455256: inhibition of human CEPT assessed as cholesteryl ester transfer by fluorescence transfer assayic503.4000uM
N-[4-(7-cyano-1,3-benzoxazol-2-yl)phenyl]-2-(2-methylphenoxy)acetamide455256: inhibition of human CEPT assessed as cholesteryl ester transfer by fluorescence transfer assayic505.2000uM
N-[4-(6-fluoro-1,3-benzoxazol-2-yl)phenyl]-2-(2-methylphenoxy)acetamide455256: inhibition of human CEPT assessed as cholesteryl ester transfer by fluorescence transfer assayic507.5000uM

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Cadmium Chloridedecreases expression, increases expression3
methacrylaldehydedecreases expression, increases abundance, affects cotreatment, affects expression2
Acroleinaffects cotreatment, affects expression, decreases expression, increases abundance2
Ozonedecreases expression, increases abundance, affects cotreatment, affects expression2
aristolochic acid Idecreases expression1
TAK-243decreases sumoylation1
dicrotophosdecreases expression1
urushiolincreases expression1
methylmercuric chloridedecreases expression1
triphenyl phosphateaffects expression1
alpha-pineneincreases abundance, affects cotreatment, affects expression1
bisphenol Aincreases expression1
trichostatin Aincreases expression1
beta-lapachoneincreases expression1
sodium arsenitedecreases expression1
potassium chromate(VI)affects cotreatment, decreases expression1
nickel sulfatedecreases expression1
beta-methylcholineaffects expression1
epigallocatechin gallateaffects cotreatment, decreases expression1
bisphenol Bincreases expression1
abrineincreases expression1
bisphenol Sincreases expression1
Sunitinibincreases expression1
Zoledronic Acidincreases expression1
Air Pollutantsaffects cotreatment, affects expression, increases abundance1
Carbamazepineaffects expression1
Succimeraffects cotreatment, increases expression1
Gasolineaffects cotreatment, decreases expression, increases abundance1
Hydrogen Peroxideaffects cotreatment, increases expression1
Oxygendecreases expression1

ChEMBL screening assays

3 unique, capped per target: 3 binding

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL1070006Bindinginhibition of human CEPT assessed as cholesteryl ester transfer by fluorescence transfer assay2-Arylbenzoxazoles as CETP inhibitors: Substitution of the benzoxazole moiety. — Bioorg Med Chem Lett

Cellosaurus cell lines

2 cell lines: 2 transformed cell line

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

CellosaurusNameCategorySex
CVCL_D7G7Ubigene HEK293T CEPT1 KOTransformed cell lineFemale
CVCL_D9BVUbigene HEK293 CEPT1 KOTransformed cell lineFemale

Clinical trials (associated diseases)

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

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.

About this page

Generated deterministically by Sugi Atlas from primary biomedical databases via BioBTree. Every record on this page traces to a primary source.

Generated
Atlas version
v1.1.4
BioBTree
v2.0.2

Sources 78

This page pulls from 78 datasets indexed by BioBTree:

alphafoldalphamissenseantibodybgeebgee_evidencebindingdbbiogrid_interactionbrendabrenda_kineticsccdscellosauruschembl_activitychembl_assaychembl_documentchembl_moleculechembl_targetciviccivic_evidenceclingen_dosageclingen_gene_validityclinical_trialsclinvarcollectrictd_gene_interactiondbsnpdepmapdiamond_similarityefoensemblentrezesm2_similarityexonfantom5_genefantom5_promotergenccgenerifgogoparentgtopdbgwasgwas_studyhgnchpointactinterprointogenjasparmeshmimmirdbmondomsigdborphanetorthologparalogpdbpfampharmgkb_clinicalpharmgkb_genepharmgkb_guidelinepharmgkb_variantpubchempubchem_activitypubchem_assaypubmedreactomereactomeparentrefseqrhearnacentralscxa_expressionscxa_gene_experimentsignorspliceaistring_interactiontranscriptufeatureuniprot