SCUBE1

gene
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Summary

SCUBE1 (signal peptide, CUB domain and EGF like domain containing 1, HGNC:13441) is a protein-coding gene on chromosome 22q13.2, encoding Signal peptide, CUB and EGF-like domain-containing protein 1 (Q8IWY4). Could function as an adhesive molecule and its matrix bound and soluble fragments may play a critical role in vascular biology.

This gene encodes a cell surface glycoprotein that is a member of the SCUBE (signal peptide, CUB domain, EGF (epidermal growth factor)-like protein) family. Family members have an amino-terminal signal peptide, nine copies of EGF-like repeats and a CUB domain at the carboxyl terminus. This protein is expressed in platelets and endothelial cells and may play an important role in vascular biology.

Source: NCBI Gene 80274 — RefSeq curated summary.

At a glance

  • GWAS associations: 6
  • Clinical variants (ClinVar): 192 total
  • MANE Select transcript: NM_173050

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:13441
Approved symbolSCUBE1
Namesignal peptide, CUB domain and EGF like domain containing 1
Location22q13.2
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000159307
Ensembl biotypeprotein_coding
OMIM611746
Entrez80274

Gene structure

Transcript identifiers

Ensembl transcripts: 12 — 8 protein_coding, 4 protein_coding_CDS_not_defined

ENST00000290460, ENST00000360835, ENST00000449304, ENST00000461595, ENST00000470433, ENST00000477991, ENST00000480833, ENST00000911326, ENST00000911327, ENST00000911328, ENST00000911329, ENST00000954506

RefSeq mRNA: 1 — MANE Select: NM_173050 NM_173050

CCDS: CCDS14048

Canonical transcript exons

ENST00000360835 — 22 exons

ExonStartEnd
ENSE000010447544322263843222742
ENSE000010447774322737443227496
ENSE000013045774322309743223216
ENSE000013194194322117343221289
ENSE000018221224334317443343372
ENSE000019516514319728043204149
ENSE000022023224322045043220587
ENSE000022080474320753443207613
ENSE000022114924321825543218458
ENSE000022224954321004343210240
ENSE000022536584321409043214251
ENSE000022606284320807243208224
ENSE000023031404321242543212592
ENSE000024308694323883843238954
ENSE000024365514325821943258335
ENSE000024843914333910443339235
ENSE000024927384321092243211083
ENSE000025127744322907243229188
ENSE000025159074329104643291180
ENSE000025288284326272043262845
ENSE000025350974323175343231875
ENSE000036612894331993743320065

Expression profiles

Bgee: expression breadth ubiquitous, 188 present calls, max score 95.99.

FANTOM5 (CAGE): breadth broad, TPM avg 4.2371 / max 178.5057, expressed in 501 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
1945074.2371501

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
mucosa of stomachUBERON:000119995.99gold quality
tibiaUBERON:000097992.65gold quality
cortical plateUBERON:000534391.69gold quality
tibial nerveUBERON:000132389.00gold quality
kidney epitheliumUBERON:000481988.91gold quality
lower esophagus muscularis layerUBERON:003583387.19gold quality
lower esophagusUBERON:001347387.08gold quality
left ovaryUBERON:000211985.85gold quality
sural nerveUBERON:001548885.56gold quality
nasal cavity epitheliumUBERON:000538485.41gold quality
ganglionic eminenceUBERON:000402385.28gold quality
esophagogastric junction muscularis propriaUBERON:003584185.13gold quality
right ovaryUBERON:000211884.22gold quality
ventricular zoneUBERON:000305384.07gold quality
epithelial cell of pancreasCL:000008383.80silver quality
ovaryUBERON:000099281.81gold quality
left ventricle myocardiumUBERON:000656680.17gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099180.15gold quality
skeletal muscle tissue of rectus abdominisUBERON:000451179.90silver quality
skeletal muscle tissue of biceps brachiiUBERON:000450279.03gold quality
myocardiumUBERON:000234979.01gold quality
right lungUBERON:000216778.62gold quality
cardiac muscle of right atriumUBERON:000337978.26gold quality
descending thoracic aortaUBERON:000234578.01gold quality
vena cavaUBERON:000408776.70silver quality
left adrenal gland cortexUBERON:003582576.50gold quality
layer of synovial tissueUBERON:000761675.96gold quality
left adrenal glandUBERON:000123475.63gold quality
adrenal cortexUBERON:000123575.62gold quality
esophagusUBERON:000104375.04gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-MTAB-10137yes677.07
E-ANND-3no4.94

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

65 targeting SCUBE1, 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-190A-3P100.0080.355520
HSA-MIR-5011-5P100.0083.465820
HSA-MIR-6127100.0066.762188
HSA-MIR-4510100.0066.602050
HSA-MIR-6129100.0066.462080
HSA-MIR-6130100.0066.692012
HSA-MIR-6133100.0066.482064
HSA-MIR-4747-5P100.0067.902681
HSA-MIR-5196-5P100.0067.982761
HSA-MIR-23B-5P99.9866.07587
HSA-MIR-6780B-5P99.9669.602562
HSA-MIR-23A-5P99.9465.39468
HSA-MIR-449299.8768.253611
HSA-MIR-4728-5P99.8569.394718
HSA-MIR-473999.8465.251832
HSA-MIR-132199.8465.301811
HSA-MIR-4756-5P99.8464.981809
HSA-MIR-76599.8468.242442
HSA-MIR-6785-5P99.8268.684428
HSA-MIR-3121-3P99.8271.963630
HSA-MIR-3934-3P99.7665.511351
HSA-MIR-431999.7669.832586
HSA-MIR-11181-3P99.7566.382205
HSA-MIR-149-3P99.7268.223963
HSA-MIR-378G99.7164.901106
HSA-MIR-6883-5P99.6968.053785
HSA-MIR-320299.6667.702737
HSA-MIR-6887-3P99.6667.831778
HSA-MIR-1249-5P99.6166.552049
HSA-MIR-6797-5P99.6166.552084

Literature-anchored findings (GeneRIF, showing 21)

  • identification as secreted protein that is expressed in vascular endothelium and may play important roles in development, inflammation, and thrombosis (PMID:12270931)
  • SCUBE1 level, a potential acute ischemia marker, is elevated in hemodialysis patients with no clinical ischemic event. (PMID:22874483)
  • Primary prostatic cancer-associated fibroblasts (CAFs) were isolated and the expression of CAF markers, Dlk1 and SCUBE1 transcripts were characterised. (PMID:23136397)
  • SCUBE 1 levels in patients with gastric cancer were found higher compared to healthy subjects. (PMID:23220851)
  • SCUBE1 levels are a new biomarker that can be used in the differential diagnosis and monitoring of patients hospitalized with suspected CCHF. (PMID:23632301)
  • SCUBE1 may indicate hypercoagulability in patients with BC and thus help identify patients at greater risk of thrombosisSCUBE1 may indicate hypercoagulability in patients with breast cancer and thus help identify patients at greater risk of thrombosis (PMID:26438214)
  • describe novel mechanisms in targeting S1 to the plasma membrane and demonstrate that N-glycans are required for S1 functions during primitive haematopoiesis in zebrafish. (PMID:26699903)
  • SCUBE1 might be a novel prognostic biomarker after traumatic brain injury (PMID:26940951)
  • enhanced SCUBE1 concentrations are correlated with increasing severity and poor outcomes of aneurysmal subarachnoid hemorrhage patients, indicating SCUBE1 might have the potential to identify aneurysmal subarachnoid hemorrhage patients at risk of poor prognosis (PMID:27265525)
  • Increased serum SCUBE1 concentrations have close relation to increasing severity and poor prognosis of intracerebral hemorrhage (PMID:27496080)
  • The results of this pioneering study indicate that SCUBE protein family appears to have a probable role in the pathogenesis and angiogenesis development in psoriasis and SCUBE 1 and 3 may be novel markers of angiogenesis in psoriasis. (PMID:28238185)
  • Hemodialysis may contribute to cardiovascular events because of increased SCUBE1 levels after hemodialysis; however, no association was shown between SCUBE1 and electrocardiography/echocardiography findings. (PMID:30777551)
  • Evaluation of SCUBE-1 levels as a placental dysfunction marker at gestational diabetes mellitus. (PMID:31668102)
  • De Novo Damaging DNA Coding Mutations Are Associated With Obsessive-Compulsive Disorder and Overlap With Tourette’s Disorder and Autism. (PMID:31771860)
  • The relationship of serum SCUBE-1, -2 and -3 levels with clinical findings and ultrasonographic skin thickness in systemic sclerosis patients. (PMID:31991528)
  • Pericardial SCUBE1 levels may help predict postoperative results in patients operated on for coronary artery bypass graft surgery. (PMID:34292290)
  • SCUBE1 is associated with thrombotic complications, disease severity, and in-hospital mortality in COVID-19 patients. (PMID:36334396)
  • Predictive Value of Combined Plasma D-Dimer, SCUBE1, and Right Ventricular Tei Index for the Prognosis of Elderly Patients with Acute Pulmonary Thromboembolism. (PMID:36517978)
  • The diagnostic potential of plasma SCUBE-1 concentration for pulmonary embolism: A pilot study. (PMID:36748401)
  • Could SCUBE-1 be a marker for subclinical atherosclerosis other than carotid artery intima-media thickness in patients with psoriasis? (PMID:37198010)
  • SCUBE1 promotes pulmonary artery smooth muscle cell proliferation and migration in acute pulmonary embolism by modulating BMP7. (PMID:38259670)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_rerioscube1ENSDARG00000063097
mus_musculusScube1ENSMUSG00000016763
rattus_norvegicusScube1ENSRNOG00000010617

Paralogs (2): SCUBE3 (ENSG00000146197), SCUBE2 (ENSG00000175356)

Protein

Protein identifiers

Signal peptide, CUB and EGF-like domain-containing protein 1Q8IWY4 (reviewed: Q8IWY4)

All UniProt accessions (3): Q8IWY4, B1AH90, H0Y4Y9

UniProt curated annotations — full annotation on UniProt →

Function. Could function as an adhesive molecule and its matrix bound and soluble fragments may play a critical role in vascular biology.

Subunit / interactions. Forms homooligomers. Forms heterooligomers with SCUBE2. Forms heterooligomers with SCUBE3.

Subcellular location. Secreted. Cell membrane.

Tissue specificity. Detected in endothelial cells. Highly expressed in platelets. Stored in platelet alpha granules, and transferred to the cell surface upon activation and aggregation. A smaller form, probably produced by limited proteolysis, after being released from the storage granules, is associated with thrombus and localized with the subendothelial matrices in atherosclerotic plaques.

Post-translational modifications. N-glycosylated. Could be proteolytically cleaved to release a smaller active fragment.

Induction. Down-regulated by inflammatory cytokines.

RefSeq proteins (1): NP_766638* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000152EGF-type_Asp/Asn_hydroxyl_sitePTM
IPR000742EGFDomain
IPR000859CUB_domDomain
IPR001881EGF-like_Ca-bd_domDomain
IPR009030Growth_fac_rcpt_cys_sfHomologous_superfamily
IPR011641Tyr-kin_ephrin_A/B_rcpt-likeDomain
IPR018097EGF_Ca-bd_CSConserved_site
IPR024731NELL2-like_EGFDomain
IPR026823cEGFDomain
IPR035914Sperma_CUB_dom_sfHomologous_superfamily
IPR049883NOTCH1_EGF-likeDomain
IPR052071SCUB_EGF-like_domainFamily

Pfam: PF00431, PF07645, PF07699, PF12662, PF12947, PF14670

UniProt features (42 total): disulfide bond 19, domain 10, glycosylation site 6, sequence conflict 3, sequence variant 2, signal peptide 1, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q8IWY4-F177.690.14

Functional residue map

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

Disulfide bonds (19): 37–50, 44–59, 61–72, 78–91, 87–100, 102–115, 121–132, 128–141, 286–297, 293–306, 308–321, 327–337, 333–346, 348–360, 366–377, 373–386, 388–401, 798–824, 851–872

Glycosylation sites (6): 370, 466, 679, 750, 779, 789

Function

Pathways and Gene Ontology

Reactome pathways

2 pathways

IDPathway
R-HSA-1474228Degradation of the extracellular matrix
R-HSA-1474244Extracellular matrix organization

MSigDB gene sets: 91 (showing top): GOBP_EPITHELIUM_DEVELOPMENT, GOBP_INFLAMMATORY_RESPONSE, GOCC_CELL_SURFACE, HATADA_METHYLATED_IN_LUNG_CANCER_DN, GOBP_WOUND_HEALING, MARTINEZ_RB1_TARGETS_UP, GOBP_ENDOTHELIUM_DEVELOPMENT, GOBP_REGULATION_OF_SMOOTHENED_SIGNALING_PATHWAY, ZHAN_MULTIPLE_MYELOMA_LB_UP, GOBP_SMOOTHENED_SIGNALING_PATHWAY, GOBP_HEMOSTASIS, DBP_Q6, GOBP_ADULT_HEART_DEVELOPMENT, GATA4_Q3, GOBP_POSITIVE_REGULATION_OF_SMOOTHENED_SIGNALING_PATHWAY

GO Biological Process (7): inflammatory response (GO:0006954), signal transduction (GO:0007165), adult heart development (GO:0007512), blood coagulation (GO:0007596), post-embryonic development (GO:0009791), endothelial cell differentiation (GO:0045446), positive regulation of smoothened signaling pathway (GO:0045880)

GO Molecular Function (3): calcium ion binding (GO:0005509), identical protein binding (GO:0042802), protein binding (GO:0005515)

GO Cellular Component (6): obsolete extracellular space (GO:0005615), plasma membrane (GO:0005886), external side of plasma membrane (GO:0009897), cell surface (GO:0009986), extracellular region (GO:0005576), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-1 pathways:

CategoryPathways
Extracellular matrix organization1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure3
defense response1
cell communication1
cellular process1
signaling1
regulation of cellular process1
cellular response to stimulus1
heart development1
hemostasis1
wound healing1
coagulation1
multicellular organism development1
multicellular organismal process1
endothelium development1
epithelial cell differentiation1
smoothened signaling pathway1
regulation of smoothened signaling pathway1
positive regulation of signal transduction1
metal ion binding1
protein binding1
binding1
membrane1
cell periphery1
plasma membrane1
cell surface1
side of membrane1

Protein interactions and networks

STRING

1147 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
SCUBE1C1RP00736453
SCUBE1BMP2P12643446
SCUBE1C1SP09871440
SCUBE1GCC2Q8IWJ2390
SCUBE1BDNFP23560384
SCUBE1IL1BP01584361
SCUBE1CHRDQ9H2X0350
SCUBE1OR4D5Q8NGN0325
SCUBE1SEMA6AQ9H2E6324
SCUBE1LSMEM2Q8N112321
SCUBE1EGFP01133318
SCUBE1CADPS2Q86UW7317
SCUBE1IRX3P78415315
SCUBE1ICA1P78506314
SCUBE1XKR6Q5GH73310

IntAct

0 interactions, top by confidence:

ESM2 similar proteins: A0A096LNW5, B8JI71, D3ZHH1, G3I6Z6, O00548, O35516, O57409, P0DPK3, P0DPK4, P35442, P46531, P78504, P97677, Q01705, Q04721, Q05793, Q07008, Q08E66, Q2QI47, Q5G872, Q5ZQU0, Q61483, Q63722, Q66PY1, Q6DI48, Q6NZL8, Q70E20, Q7TQN3, Q7Z3S9, Q8IWY4, Q8IX30, Q8JZM4, Q8K3K1, Q8NFT8, Q8TER0, Q8TEU8, Q8UWJ4, Q8VHS2, Q90Y54, Q90Y57

Diamond homologs: A0A1D5NSM8, A2AVA0, D3YXF5, O02839, O19124, O35764, O43405, O62685, O62837, O70340, O76536, O95502, O96530, P00751, P04003, P04186, P06205, P06206, P06207, P06681, P07629, P08174, P08607, P0C6B8, P13944, P14151, P14650, P15529, P17690, P18337, P26022, P32018, P33703, P35419, P42201, P47970, P47971, P47972, P48199, P48759

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance163
Likely benign9
Benign7

Top pathogenic / likely-pathogenic (0)

SpliceAI

4732 predictions. Top by Δscore:

VariantEffectΔscore
22:43207528:A:ACdonor_gain1.0000
22:43207529:C:CCdonor_gain1.0000
22:43207529:CT:Cdonor_gain1.0000
22:43207529:CTCA:Cdonor_gain1.0000
22:43207531:CA:Cdonor_loss1.0000
22:43207532:A:ACdonor_gain1.0000
22:43207533:C:CCdonor_gain1.0000
22:43207533:C:CGdonor_loss1.0000
22:43207533:CT:Cdonor_gain1.0000
22:43207533:CTTT:Cdonor_gain1.0000
22:43207544:T:TAdonor_gain1.0000
22:43207627:C:CTacceptor_gain1.0000
22:43207628:A:Tacceptor_gain1.0000
22:43207630:C:CTacceptor_gain1.0000
22:43207631:A:Tacceptor_gain1.0000
22:43208065:ATCTT:Adonor_loss1.0000
22:43208066:TCTTA:Tdonor_loss1.0000
22:43208067:CTTA:Cdonor_loss1.0000
22:43208068:TTA:Tdonor_loss1.0000
22:43208069:TACC:Tdonor_loss1.0000
22:43208070:A:ACdonor_gain1.0000
22:43208070:A:Cdonor_loss1.0000
22:43208071:C:CCdonor_gain1.0000
22:43208071:C:CTdonor_loss1.0000
22:43208071:CCAT:Cdonor_gain1.0000
22:43208221:GAGG:Gacceptor_gain1.0000
22:43208223:GG:Gacceptor_gain1.0000
22:43208224:GC:Gacceptor_loss1.0000
22:43208225:C:CCacceptor_gain1.0000
22:43210039:ATACC:Adonor_loss1.0000

AlphaMissense

6560 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
22:43210114:A:GL837P1.000
22:43238842:G:CC280W1.000
22:43238843:C:GC280S1.000
22:43238843:C:TC280Y1.000
22:43238844:A:GC280R1.000
22:43238844:A:TC280S1.000
22:43238881:G:CC267W1.000
22:43238882:C:TC267Y1.000
22:43238883:A:GC267R1.000
22:43238888:C:GC265S1.000
22:43238889:A:GC265R1.000
22:43238889:A:TC265S1.000
22:43238914:G:CC256W1.000
22:43238915:C:GC256S1.000
22:43238915:C:TC256Y1.000
22:43238916:A:GC256R1.000
22:43238916:A:TC256S1.000
22:43238926:G:CC252W1.000
22:43238927:C:GC252S1.000
22:43238927:C:TC252Y1.000
22:43238928:A:GC252R1.000
22:43238928:A:TC252S1.000
22:43238947:G:CC245W1.000
22:43238948:C:TC245Y1.000
22:43238949:A:GC245R1.000
22:43258223:G:CC241W1.000
22:43258224:C:GC241S1.000
22:43258224:C:TC241Y1.000
22:43258225:A:GC241R1.000
22:43258225:A:TC241S1.000

dbSNP variants (sampled 300 via entrez): RS1000004043 (22:43223836 C>T), RS1000031673 (22:43229741 G>C), RS1000067867 (22:43223586 G>GT), RS1000080343 (22:43229345 C>T), RS1000093537 (22:43197339 T>C), RS1000100475 (22:43294637 C>T), RS1000133025 (22:43294898 T>C), RS1000158284 (22:43246845 C>T), RS1000170978 (22:43344179 G>A), RS1000209536 (22:43243765 GATC>G), RS1000220943 (22:43335772 A>G), RS1000221446 (22:43267318 G>A), RS1000234796 (22:43300022 C>G,T), RS1000259300 (22:43274914 G>A,C), RS1000294456 (22:43335589 C>G)

Disease associations

OMIM: gene MIM:611746 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

6 associations (top):

StudyTraitp-value
GCST001738_4Response to fenofibrate (adiponectin levels)2.000000e-06
GCST002114_5Molar-incisor hypomineralization4.000000e-07
GCST006585_252Blood protein levels4.000000e-14
GCST008161_32Waist circumference adjusted for body mass index1.000000e-06
GCST010732_11Sensory peripheral neuropathy in microtubule targeting agent-treated breast cancer3.000000e-06
GCST90000025_890Appendicular lean mass3.000000e-11

EFO canonical traits (4, from GWAS)

EFO IDTrait name
EFO:0005321molar-incisor hypomineralization
EFO:0007789BMI-adjusted waist circumference
EFO:0005260response to antimicrotubule agent
EFO:0004980appendicular lean mass

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

21 total (human), top 21 by PubMed support.

ChemicalActions (top 5)PubMed papers
Benzo(a)pyreneaffects methylation, increases methylation2
bisphenol Aincreases methylation1
tris(2-butoxyethyl) phosphateaffects expression1
sodium arseniteaffects methylation1
benzo(e)pyreneincreases methylation1
aflatoxin B2increases methylation1
bisphenol Sdecreases methylation1
Resveratrolaffects cotreatment, decreases expression1
Air Pollutantsincreases expression, increases abundance1
Copperaffects cotreatment, decreases expression1
Lucanthoneincreases expression1
Methapyrileneincreases methylation1
Oxygenincreases expression1
Ozoneincreases expression1
Silicon Dioxidedecreases methylation1
Smokeincreases expression1
Triclosandecreases expression1
Valproic Acidincreases methylation1
Aflatoxin B1affects methylation1
Cadmium Chlorideincreases expression1
Particulate Matterincreases abundance, increases expression1

Clinical trials (associated diseases)

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

  • Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): peripheral neuropathy