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Atlas / Gene / SCPEP1

SCPEP1

gene
On this page

Also known as RISC

Summary

SCPEP1 (serine carboxypeptidase 1, HGNC:29507) is a protein-coding gene on chromosome 17q22, encoding Retinoid-inducible serine carboxypeptidase (Q9HB40). May be involved in vascular wall and kidney homeostasis.

Predicted to enable serine-type carboxypeptidase activity. Predicted to be involved in negative regulation of blood pressure and retinoic acid metabolic process. Predicted to act upstream of or within blood vessel diameter maintenance. Located in extracellular exosome.

Source: NCBI Gene 59342 — RefSeq curated summary.

At a glance

  • Clinical variants (ClinVar): 91 total
  • Druggable target: yes
  • MANE Select transcript: NM_021626

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:29507
Approved symbolSCPEP1
Nameserine carboxypeptidase 1
Location17q22
Locus typegene with protein product
StatusApproved
AliasesRISC
Ensembl geneENSG00000121064
Ensembl biotypeprotein_coding
OMIM619723
Entrez59342

Gene structure

Transcript identifiers

Ensembl transcripts: 22 — 11 protein_coding, 5 retained_intron, 3 protein_coding_CDS_not_defined, 3 nonsense_mediated_decay

ENST00000262288, ENST00000570479, ENST00000570480, ENST00000570505, ENST00000570589, ENST00000571345, ENST00000571898, ENST00000572591, ENST00000572710, ENST00000573239, ENST00000573789, ENST00000573823, ENST00000575395, ENST00000575423, ENST00000576154, ENST00000631024, ENST00000858469, ENST00000858470, ENST00000858471, ENST00000914327, ENST00000914328, ENST00000951949

RefSeq mRNA: 1 — MANE Select: NM_021626 NM_021626

CCDS: CCDS11593

Canonical transcript exons

ENST00000262288 — 13 exons

ExonStartEnd
ENSE000026422375700617357006768
ENSE000034738385700085557000992
ENSE000034993765699550756995635
ENSE000035115075698108256981230
ENSE000035132975700201857002181
ENSE000035681385699696256997055
ENSE000035705365699498156995018
ENSE000035868205699838556998498
ENSE000035899115698821656988290
ENSE000035935805698769556987850
ENSE000035973065698537856985467
ENSE000036214585697813156978235
ENSE000037908435699109956991171

Expression profiles

Bgee: expression breadth ubiquitous, 290 present calls, max score 99.26.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 56.4624 / max 560.9933, expressed in 1819 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
16182356.46241819

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
right adrenal gland cortexUBERON:003582799.26gold quality
monocyteCL:000057699.15gold quality
right adrenal glandUBERON:000123399.13gold quality
adrenal tissueUBERON:001830398.96gold quality
left adrenal gland cortexUBERON:003582598.96gold quality
left adrenal glandUBERON:000123498.94gold quality
mononuclear cellCL:000084298.92gold quality
adrenal cortexUBERON:000123598.92gold quality
leukocyteCL:000073898.81gold quality
olfactory segment of nasal mucosaUBERON:000538698.69gold quality
left lobe of thyroid glandUBERON:000112098.68gold quality
adrenal glandUBERON:000236998.66gold quality
right lobe of thyroid glandUBERON:000111998.48gold quality
thyroid glandUBERON:000204698.46gold quality
descending thoracic aortaUBERON:000234598.37gold quality
gall bladderUBERON:000211098.09gold quality
thoracic aortaUBERON:000151598.07gold quality
ascending aortaUBERON:000149698.03gold quality
mucosa of stomachUBERON:000119997.96gold quality
right coronary arteryUBERON:000162597.96gold quality
minor salivary glandUBERON:000183097.88gold quality
right lungUBERON:000216797.81gold quality
esophagogastric junction muscularis propriaUBERON:003584197.80gold quality
lower esophagusUBERON:001347397.68gold quality
lower esophagus muscularis layerUBERON:003583397.68gold quality
saliva-secreting glandUBERON:000104497.63gold quality
muscle layer of sigmoid colonUBERON:003580597.58gold quality
epithelium of bronchusUBERON:000203197.57gold quality
skin of abdomenUBERON:000141697.56gold quality
left coronary arteryUBERON:000162697.53gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-HCAD-1yes645.00
E-MTAB-10553yes4.99
E-ANND-3no0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

34 targeting SCPEP1, 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-MIR-5011-5P100.0083.465820
HSA-MIR-190A-3P100.0080.355520
HSA-MIR-1277-5P100.0073.955056
HSA-MIR-3924100.0072.092394
HSA-MIR-5692A100.0074.406850
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-196A-1-3P99.9972.152772
HSA-MIR-365899.9673.874379
HSA-MIR-1250-3P99.9670.044038
HSA-MIR-7-1-3P99.9171.534384
HSA-MIR-7-2-3P99.9171.404394
HSA-MIR-153-5P99.8973.866317
HSA-MIR-579-3P99.8671.663628
HSA-MIR-664B-3P99.8471.653590
HSA-MIR-489-3P99.8066.46839
HSA-MIR-472999.6972.184233
HSA-MIR-3942-3P99.5769.032854
HSA-MIR-103A-1-5P99.3967.781545
HSA-MIR-103A-2-5P99.3967.721577
HSA-MIR-568399.3668.592083
HSA-MIR-580-5P99.2870.941776
HSA-MIR-329-5P99.2768.111597
HSA-MIR-664A-3P99.2271.082696
HSA-MIR-125399.1267.081688
HSA-MIR-314698.8566.77601
HSA-MIR-2276-3P98.7667.751384
HSA-MIR-990398.4766.70748
HSA-MIR-397798.0068.171500
HSA-MIR-6787-3P97.7566.171233
HSA-MIR-6836-3P97.0864.99712

Literature-anchored findings (GeneRIF, showing 2)

  • RACK1 binds to KH-type splicing regulatory protein (KSRP), a member of the Dicer complex, and is required for the recruitment of mature miRNAs to the RNA-induced silencing complex (RISC). (PMID:21935400)
  • The structures of active lysosomal serine carboxypeptidase cathepsin A and the inactive precursor are very similar. (PMID:24530914)

Cross-species orthologs

9 orthologs

OrganismSymbolGene ID
danio_rerioscpep1ENSDARG00000040072
mus_musculusScpep1ENSMUSG00000000278
rattus_norvegicusScpep1ENSRNOG00000002358
drosophila_melanogasterhiroFBGN0035154
drosophila_melanogasterCG31821FBGN0051821
drosophila_melanogasterCG31823FBGN0051823
drosophila_melanogasterCG32483FBGN0052483
caenorhabditis_elegansWBGENE00009058
caenorhabditis_elegansWBGENE00012530

Paralogs (2): CTSA (ENSG00000064601), CPVL (ENSG00000106066)

Protein

Protein identifiers

Retinoid-inducible serine carboxypeptidase — Q9HB40 (reviewed: Q9HB40)

Alternative names: Serine carboxypeptidase 1

All UniProt accessions (6): Q9HB40, I3L195, I3L2N6, I3L4Z3, I3L4Z9, I3L506

UniProt curated annotations — full annotation on UniProt →

Function. May be involved in vascular wall and kidney homeostasis.

Subcellular location. Secreted.

Miscellaneous. May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay.

Similarity. Belongs to the peptidase S10 family.

Isoforms (2)

UniProt IDNamesCanonical?
Q9HB40-11yes
Q9HB40-22

RefSeq proteins (1): NP_067639* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001563Peptidase_S10Family
IPR018202Ser_caboxypep_ser_ASActive_site
IPR029058AB_hydrolase_foldHomologous_superfamily

Pfam: PF00450

UniProt features (12 total): active site 3, glycosylation site 3, sequence variant 2, splice variant 2, signal peptide 1, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9HB40-F190.200.83

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 (3): 167; 371; 431

Glycosylation sites (3): 64, 126, 362

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 205 (showing top): GOBP_REGULATION_OF_BLOOD_PRESSURE, GOBP_CIRCULATORY_SYSTEM_PROCESS, GOZGIT_ESR1_TARGETS_DN, MODULE_511, GOBP_REGULATION_OF_HORMONE_LEVELS, SARRIO_EPITHELIAL_MESENCHYMAL_TRANSITION_DN, GOBP_MONOCARBOXYLIC_ACID_METABOLIC_PROCESS, GOLDRATH_ANTIGEN_RESPONSE, GOBP_REGULATION_OF_ANATOMICAL_STRUCTURE_SIZE, ROSS_LEUKEMIA_WITH_MLL_FUSIONS, GOBP_RETINOIC_ACID_METABOLIC_PROCESS, GOBP_LIPID_METABOLIC_PROCESS, GOBP_ORGANIC_ACID_METABOLIC_PROCESS, GOBP_NEGATIVE_REGULATION_OF_BLOOD_PRESSURE, CHARAFE_BREAST_CANCER_LUMINAL_VS_BASAL_DN

GO Biological Process (5): proteolysis (GO:0006508), retinoic acid metabolic process (GO:0042573), negative regulation of blood pressure (GO:0045776), blood vessel diameter maintenance (GO:0097746), regulation of biological quality (GO:0065008)

GO Molecular Function (4): serine-type carboxypeptidase activity (GO:0004185), carboxypeptidase activity (GO:0004180), peptidase activity (GO:0008233), hydrolase activity (GO:0016787)

GO Cellular Component (2): extracellular exosome (GO:0070062), extracellular region (GO:0005576)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
protein metabolic process1
retinoid metabolic process1
monocarboxylic acid metabolic process1
hormone metabolic process1
regulation of blood pressure1
vascular process in circulatory system1
blood circulation1
regulation of tube diameter1
biological regulation1
carboxypeptidase activity1
serine-type exopeptidase activity1
exopeptidase activity1
hydrolase activity1
catalytic activity, acting on a protein1
catalytic activity1
extracellular vesicle1
cellular anatomical structure1

Protein interactions and networks

STRING

1533 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
SCPEP1PTTG1IPP53801498
SCPEP1RASL10BQ96S79476
SCPEP1AHDC1Q5TGY3420
SCPEP1ABHD10Q9NUJ1416
SCPEP1C17orf67Q0P5P2414
SCPEP1SMTNL2Q2TAL5414
SCPEP1ANKFN1Q8N957411
SCPEP1UTS2RQ9UKP6408
SCPEP1JAKMIP2Q96AA8399
SCPEP1ABHD14BQ96IU4376
SCPEP1GRIP2Q9C0E4376
SCPEP1FAM151BQ6UXP7361
SCPEP1AKAP1Q92667358
SCPEP1LYPLA2O95372355
SCPEP1APPP05067349

IntAct

27 interactions, top by confidence:

ABTypeScore
ADAMTS4MANBApsi-mi:“MI:0914”(association)0.530
LPAR1TMEM223psi-mi:“MI:0914”(association)0.530
ZSCAN21LRP4psi-mi:“MI:0914”(association)0.530
HSCBRBP5psi-mi:“MI:0914”(association)0.350
TANKCNOT1psi-mi:“MI:0914”(association)0.350
TEX101PSMD12psi-mi:“MI:0914”(association)0.350
TEX101NDUFA4psi-mi:“MI:0914”(association)0.350
CANXHLA-Apsi-mi:“MI:0914”(association)0.350
SCPEP1CCDC85Cpsi-mi:“MI:0914”(association)0.350
BRICD5TMEM131Lpsi-mi:“MI:0914”(association)0.350
NCR3POTEFpsi-mi:“MI:0914”(association)0.350
SH2D3AA2ML1psi-mi:“MI:0914”(association)0.350
PCP4A2ML1psi-mi:“MI:0914”(association)0.350
NT5C1AA2ML1psi-mi:“MI:0914”(association)0.350
KLK15APAF1psi-mi:“MI:0914”(association)0.350
EMP3NDUFS4psi-mi:“MI:0914”(association)0.350
ATP6AP2KLK10psi-mi:“MI:0914”(association)0.350
ZNF460TOMM40psi-mi:“MI:0914”(association)0.350
IGF2RMANBApsi-mi:“MI:0914”(association)0.350
BRICD5PODXLpsi-mi:“MI:0914”(association)0.350
C1orf54QSOX1psi-mi:“MI:0914”(association)0.350
C1QTNF9BDNASE2psi-mi:“MI:0914”(association)0.350
HPNDDX39Apsi-mi:“MI:0914”(association)0.350
LCN6HIGD1Cpsi-mi:“MI:0914”(association)0.350
SCPEP1CLGNpsi-mi:“MI:0914”(association)0.350
TMEM25ATE1psi-mi:“MI:0914”(association)0.350

BioGRID (88): CD2AP (Co-fractionation), PRDX6 (Co-fractionation), SCPEP1 (Co-fractionation), SCPEP1 (Co-fractionation), SCPEP1 (Co-fractionation), ZNF507 (Affinity Capture-MS), SCPEP1 (Affinity Capture-MS), SCPEP1 (Affinity Capture-MS), SCPEP1 (Affinity Capture-MS), SCPEP1 (Two-hybrid), SCPEP1 (Proximity Label-MS), SCPEP1 (Affinity Capture-MS), NCR3LG1 (Affinity Capture-MS), GMCL1 (Affinity Capture-MS), NAT14 (Affinity Capture-MS)

ESM2 similar proteins: A5D6U8, A6H730, J3SDX8, O16956, O35409, O61866, O75795, P04068, P04634, P07098, P07099, P07687, P08430, P0DTE5, P11515, P19224, P21529, P36510, P37891, P38571, P49614, P70627, P70691, P79381, P80035, Q28611, Q29458, Q38924, Q3U4B4, Q3YBN2, Q41005, Q4R4S5, Q5VXI9, Q5VXJ0, Q5VYY2, Q5W064, Q64194, Q64435, Q64550, Q67ZU1

Diamond homologs: A5YCB8, A7UKV5, B2AWD5, B6HPP6, B6V867, B8NXS9, C4JNM2, C5FGX1, C5FW30, D4AIF1, D4AP52, D4AQ54, D4AZ71, D4AZG9, D4B0Q6, D4DD24, D4DLI1, O04084, O64811, P32825, P34946, P52708, P52714, P52716, P52719, Q2H9G6, Q2TYA1, Q2V465, Q4QR71, Q5J6J1, Q5J6J2, Q67Y83, Q8H780, Q8RUW5, Q8RWJ6, Q9CAU0, Q9CAU1, Q9CAU2, Q9CAU3, Q9CAU4

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance67
Likely benign3
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1920 predictions. Top by Δscore:

VariantEffectΔscore
17:56978232:GCAG:Gdonor_gain1.0000
17:56978234:AGG:Adonor_loss1.0000
17:56978235:GGTA:Gdonor_loss1.0000
17:56978236:GT:Gdonor_loss1.0000
17:56978237:T:Adonor_loss1.0000
17:56981226:TTCAG:Tdonor_loss1.0000
17:56981227:TCAG:Tdonor_loss1.0000
17:56981228:CAG:Cdonor_loss1.0000
17:56981229:AGG:Adonor_loss1.0000
17:56981230:GGT:Gdonor_loss1.0000
17:56981231:GT:Gdonor_loss1.0000
17:56981232:T:Adonor_loss1.0000
17:56985473:G:GGdonor_gain1.0000
17:56985490:C:Gdonor_gain1.0000
17:56987685:T:TAacceptor_gain1.0000
17:56987847:CCAGG:Cdonor_loss1.0000
17:56987849:AGGT:Adonor_loss1.0000
17:56987851:G:Tdonor_loss1.0000
17:56987852:T:Adonor_loss1.0000
17:56988214:A:AGacceptor_gain1.0000
17:56988215:G:GGacceptor_gain1.0000
17:56988215:GAC:Gacceptor_gain1.0000
17:56988215:GACA:Gacceptor_gain1.0000
17:56988286:ATAAG:Adonor_loss1.0000
17:56988287:TAAGG:Tdonor_loss1.0000
17:56988288:AAGG:Adonor_loss1.0000
17:56988289:AGGTA:Adonor_loss1.0000
17:56988290:G:GAdonor_loss1.0000
17:56988291:G:Tdonor_loss1.0000
17:56988292:T:Adonor_loss1.0000

AlphaMissense

2968 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
17:56981222:T:AW73R0.998
17:56981222:T:CW73R0.998
17:56985413:C:AN87K0.997
17:56985413:C:GN87K0.997
17:56985465:T:AW105R0.997
17:56985465:T:CW105R0.997
17:56987746:A:CS123R0.996
17:56987748:T:AS123R0.996
17:56987748:T:GS123R0.996
17:56988243:T:CS167P0.996
17:56981159:T:CF52L0.995
17:56981161:C:AF52L0.995
17:56981161:C:GF52L0.995
17:56985396:A:CS82R0.995
17:56985398:C:AS82R0.995
17:56985398:C:GS82R0.995
17:56987722:G:CD115H0.995
17:56985427:G:AG92E0.994
17:56987740:G:TG121W0.994
17:57000972:A:TD371V0.994
17:56987741:G:AG121E0.993
17:56988283:T:CL180P0.993
17:57000971:G:CD371H0.993
17:57000972:A:CD371A0.993
17:57000973:T:AD371E0.993
17:57000973:T:GD371E0.993
17:57002029:T:AW382R0.993
17:57002029:T:CW382R0.993
17:56981224:G:CW73C0.992
17:56981224:G:TW73C0.992

dbSNP variants (sampled 300 via entrez): RS1000028895 (17:56996506 C>T), RS1000049789 (17:57006853 A>G), RS1000059903 (17:56996370 A>G), RS1000573656 (17:56981986 G>A), RS1000871268 (17:56984034 G>A), RS1001151254 (17:56977547 A>G), RS1001216679 (17:57000293 T>C), RS1001390362 (17:56990806 G>C), RS1001443701 (17:56998464 G>C), RS1001694132 (17:56982567 T>C), RS1001703788 (17:56997150 A>G), RS1001787297 (17:56982350 G>A), RS1001855809 (17:57000654 G>C), RS1001983101 (17:57001680 T>G), RS1002065338 (17:56978034 G>C)

Disease associations

OMIM: gene MIM:619723 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL2189131 (SINGLE PROTEIN)

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

GtoPdb / IUPHAR curated pharmacology

(IUPHAR/BPS Guide to Pharmacology — expert-curated)

Target class: enzyme — S10: Carboxypeptidase Y

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects cotreatment, increases expression, affects expression8
bisphenol Aaffects expression, increases expression2
sodium arsenitedecreases expression2
cobaltous chlorideincreases expression2
Vorinostatdecreases expression, increases expression2
Cisplatinincreases expression, affects cotreatment2
Tretinoinincreases expression2
testosterone enanthateaffects expression1
methylmercuric chloridedecreases expression1
triphenyl phosphateaffects expression1
glycidyl methacrylatedecreases expression1
trichostatin Aaffects expression1
beta-methylcholineaffects expression1
di-n-butylphosphoric acidaffects expression1
entinostatincreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, increases expression1
dorsomorphinaffects cotreatment, increases expression1
jinfukangaffects cotreatment, increases expression1
bisphenol AFincreases expression1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic aciddecreases expression1
Bortezomibincreases expression1
Resveratrolaffects cotreatment, increases expression1
Arsenic Trioxideincreases expression1
Acetaminophenincreases expression1
Air Pollutantsaffects expression, increases abundance1
Benzo(a)pyreneincreases methylation1
Calcitriolincreases expression1
Doxorubicinincreases expression1
Ethyl Methanesulfonateincreases expression1
Formaldehydeincreases expression1

ChEMBL screening assays

1 unique, capped per target: 1 binding

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL2209090BindingInhibition of SCPEP1 binding to FP-biotin in [12C][14N]-lysine, arginine and [13C6][15N2]-lysine, arginine labeled HEK293T cells at 20 uM after 1 hr by isotopic activity-based protein profiling-MudPIT assayDiscovery and optimization of sulfonyl acrylonitriles as selective, covalent inhibitors of protein phosphatase methylesterase-1. — J Med Chem

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
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BioBTree
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Sources 78

This page pulls from 78 datasets indexed by BioBTree:

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