CST1

gene
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Summary

CST1 (cystatin SN, HGNC:2473) is a protein-coding gene on chromosome 20p11.21, encoding Cystatin-SN (P01037). Human saliva appears to contain several cysteine proteinase inhibitors that are immunologically related to cystatin S but that differ in their specificity due to amino acid sequence differences.

The cystatin superfamily encompasses proteins that contain multiple cystatin-like sequences. Some of the members are active cysteine protease inhibitors, while others have lost or perhaps never acquired this inhibitory activity. There are three inhibitory families in the superfamily, including the type 1 cystatins (stefins), type 2 cystatins and the kininogens. The type 2 cystatin proteins are a class of cysteine proteinase inhibitors found in a variety of human fluids and secretions, where they appear to provide protective functions. The cystatin locus on chromosome 20 contains the majority of the type 2 cystatin genes and pseudogenes. This gene is located in the cystatin locus and encodes a cysteine proteinase inhibitor found in saliva, tears, urine, and seminal fluid.

Source: NCBI Gene 1469 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): male infertility with azoospermia or oligozoospermia due to single gene mutation (Limited, GenCC)
  • GWAS associations: 1
  • Clinical variants (ClinVar): 49 total
  • MANE Select transcript: NM_001898

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:2473
Approved symbolCST1
Namecystatin SN
Location20p11.21
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000170373
Ensembl biotypeprotein_coding
OMIM123855
Entrez1469

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000304749, ENST00000398402

RefSeq mRNA: 1 — MANE Select: NM_001898 NM_001898

CCDS: CCDS13160

Canonical transcript exons

ENST00000304749 — 3 exons

ExonStartEnd
ENSE000016049362374901623749129
ENSE000016942432375063923750935
ENSE000018340682374756223747899

Expression profiles

Bgee: expression breadth ubiquitous, 106 present calls, max score 97.33.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 1.1758 / max 1873.1436, expressed in 36 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
1867381.148636
1867390.02721

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
gall bladderUBERON:000211097.33gold quality
parotid glandUBERON:000183183.81gold quality
olfactory segment of nasal mucosaUBERON:000538680.41gold quality
tibial nerveUBERON:000132363.52gold quality
skeletal muscle tissue of biceps brachiiUBERON:000450263.31silver quality
pancreatic ductal cellCL:000207962.96silver quality
prostate glandUBERON:000236762.11gold quality
tonsilUBERON:000237261.81gold quality
gluteal muscleUBERON:000200061.74gold quality
triceps brachiiUBERON:000150961.72gold quality
nasal cavity mucosaUBERON:000182659.93gold quality
endometriumUBERON:000129558.20gold quality
vermiform appendixUBERON:000115458.17gold quality
caecumUBERON:000115356.23gold quality
right uterine tubeUBERON:000130255.85gold quality
cartilage tissueUBERON:000241854.99gold quality
adult organismUBERON:000702353.99gold quality
mucosa of paranasal sinusUBERON:000503053.71gold quality
islet of LangerhansUBERON:000000653.30gold quality
thymusUBERON:000237052.89silver quality
hair follicleUBERON:000207352.43gold quality
quadriceps femorisUBERON:000137752.06gold quality
epithelial cell of pancreasCL:000008351.71gold quality
deltoidUBERON:000147651.47gold quality
vastus lateralisUBERON:000137951.02gold quality
seminal vesicleUBERON:000099850.93silver quality
urinary bladderUBERON:000125550.90gold quality
Brodmann (1909) area 46UBERON:000648350.20gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099149.63silver quality
myocardiumUBERON:000234949.60gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-MTAB-7008yes9938.22
E-ANND-3yes6.42

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

14 targeting CST1, 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-6888-3P99.9765.951170
HSA-MIR-444799.8567.812900
HSA-MIR-473999.8465.251832
HSA-MIR-6756-5P99.8267.972466
HSA-MIR-6766-5P99.6867.702325
HSA-MIR-452-5P99.6569.631762
HSA-MIR-4676-3P99.6569.311733
HSA-MIR-892C-3P99.6569.381745
HSA-MIR-466399.6265.33957
HSA-MIR-4685-5P99.2565.991563
HSA-MIR-6837-5P99.2565.471632
HSA-MIR-4722-5P98.4666.341611
HSA-MIR-302F98.4469.021776
HSA-MIR-6753-5P94.7064.08470

Literature-anchored findings (GeneRIF, showing 28)

  • Murine monoclonal antibodies were made which can distinguish between CST1 and CST2. (PMID:15829315)
  • CST1 might be highly involved in gastric tumorigenesis and regulate the proteolytic activity of cysteine proteases. (PMID:19463800)
  • Identification of Cystatin SN as a novel tumor marker for colorectal cancer. (PMID:19513549)
  • CST1 expression at both the messenger RNA and protein levels was barely detected in control cells, which included early passage proliferating, quiescent, or immortal human fibroblasts (PMID:21636832)
  • CST1 may contribute to inactivation of protease allergens and help re-establish homeostasis of the nasal membranes. (PMID:23950865)
  • In conclusion, our data suggest that CST1 might contribute to the proliferation of pancreatic cancer cells and could be a potential biomarker for the early detection of pancreatic cancer. (PMID:25577248)
  • high expression of Cystatin SN is a significant prognostic indicator of a higher rate of recurrence, metastatic risk, and poor survival in patients with surgically resected NSCLCs. (PMID:25648368)
  • interactions of human family 1 & 2 cystatins with cathepsin L1 (PMID:27764212)
  • These results indicate that CST1-mediated extracellular CatB activity enhances tumor development by preventing cellular senescence. (PMID:28383558)
  • High CST1 expression is negatively correlated with survival of breast cancer patients. CST1 promotes cell proliferation, clone formation, and metastasis in breast cancer cells. CST1 is a novel potential prognostic biomarker and therapeutic target for breast cancer. (PMID:28523467)
  • this results identified cystatin 1 as a biomarker in patients with seasonal allergic rhinitis (PMID:28633877)
  • CST1 may be involved in the pathogenesis of Eosinophilic chronic rhinosinusitis (CRS), and may contribute to the severity and recurrence of CRS with nasal polyps after endoscopic sinus surgery. (PMID:29698614)
  • Results revealed that CST1 expression was upregulated in colon cancer (CC) compared with normal tissues and contributed to CC cell proliferation. (PMID:29845224)
  • Human cystatin SN suppresses allergic rhinitis (AR) symptoms through inhibiting allergen protease activities and protecting the nasal TJ barrier in an allergen-specific manner. We propose that upregulation of nasal endogenous protease inhibitors, including cystatin SN, is a novel therapeutic strategy for protease allergen-induced AR. (PMID:30012514)
  • CST1 enhanced eosinophil activation and recruitment through induction of IL-5. (PMID:30974106)
  • The CST complex (CTC1-STN1-TEN1) maintains genome integrity through resolution of G4 structures both ahead of the replication fork and on the lagging strand template (PMID:30976812)
  • The role of CST1 in hepatocellular carcinoma (HCC) progression and its potential as a latent target for HCC treatment is reported. (PMID:31106426)
  • CST1 was identified as one of the target genes regulated by HOXC10 in gastric cancer. CST1 knockdown represses tumorigenicity of gastric cancer cells. (PMID:31115563)
  • Prognostic and pharmacologic value of cystatin SN for chronic rhinosinusitis with nasal polyps. (PMID:33675819)
  • Cystatin C and cystatin SN as possible soluble tumor markers in malignant uveal melanoma. (PMID:34957724)
  • Cystatin SN promotes epithelial-mesenchymal transition and serves as a prognostic biomarker in lung adenocarcinoma. (PMID:35637432)
  • MicroRNA-375 inhibits laryngeal squamous cell carcinoma progression via targeting CST1. (PMID:35953439)
  • MiR-942-5p inhibits tumor migration and invasion through targeting CST1 in esophageal squamous cell carcinoma. (PMID:36848349)
  • Cystatin SN in type 2 inflammatory airway diseases. (PMID:36958985)
  • Epithelium-derived cystatin SN inhibits house dust mite protease activity in allergic asthma. (PMID:37026502)
  • Meibomian Gland Dysfunction Is Associated with Low Levels of Immunoglobulin Chains and Cystatin-SN. (PMID:37894795)
  • Combination of serum CST1 and HE4 for early diagnosis of endometrial cancer. (PMID:38077439)
  • The functional role of CST1 and CCL26 in asthma development. (PMID:38270326)

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
danio_reriosi:busm1-57f23.1ENSDARG00000074425
caenorhabditis_elegansWBGENE00000534
caenorhabditis_elegansWBGENE00000535
caenorhabditis_elegansWBGENE00023486

Paralogs (11): CST7 (ENSG00000077984), CST9L (ENSG00000101435), CST3 (ENSG00000101439), CST4 (ENSG00000101441), CST8 (ENSG00000125815), CSTL1 (ENSG00000125823), CST11 (ENSG00000125831), CST5 (ENSG00000170367), CST2 (ENSG00000170369), CST9 (ENSG00000173335), CST6 (ENSG00000175315)

Protein

Protein identifiers

Cystatin-SNP01037 (reviewed: P01037)

Alternative names: Cystain-SA-I, Cystatin-1, Salivary cystatin-SA-1

All UniProt accessions (1): P01037

UniProt curated annotations — full annotation on UniProt →

Function. Human saliva appears to contain several cysteine proteinase inhibitors that are immunologically related to cystatin S but that differ in their specificity due to amino acid sequence differences. Cystatin SN, with a pI of 7.5, is a much better inhibitor of papain and dipeptidyl peptidase I than is cystatin S, although both inhibit ficin equally well.

Subcellular location. Secreted.

Tissue specificity. Expressed in submandibular and sublingual saliva but not in parotid saliva (at protein level). Expressed in saliva, tears, urine and seminal fluid.

Similarity. Belongs to the cystatin family.

RefSeq proteins (1): NP_001889* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000010Cystatin_domDomain
IPR018073Prot_inh_cystat_CSConserved_site
IPR046350Cystatin_sfHomologous_superfamily

Pfam: PF00031

UniProt features (11 total): sequence variant 5, disulfide bond 2, signal peptide 1, chain 1, short sequence motif 1, site 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-P01037-F192.690.75

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 (1): 32 (reactive site)

Disulfide bonds (2): 94–104, 118–138

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 67 (showing top): MODULE_255, MODULE_317, GOBP_SENSORY_PERCEPTION_OF_CHEMICAL_STIMULUS, MAHADEVAN_IMATINIB_RESISTANCE_DN, VETTER_TARGETS_OF_PRKCA_AND_ETS1_DN, GOBP_DETECTION_OF_CHEMICAL_STIMULUS_INVOLVED_IN_SENSORY_PERCEPTION_OF_TASTE, GOBP_SENSORY_PERCEPTION_OF_TASTE, MODULE_88, GOBP_DETECTION_OF_STIMULUS, GOBP_SENSORY_PERCEPTION, CHIANG_LIVER_CANCER_SUBCLASS_CTNNB1_UP, MODULE_69, MODULE_55, GOMF_PEPTIDASE_REGULATOR_ACTIVITY, chr20p11

GO Biological Process (1): detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)

GO Molecular Function (3): cysteine-type endopeptidase inhibitor activity (GO:0004869), protein binding (GO:0005515), peptidase inhibitor activity (GO:0030414)

GO Cellular Component (4): obsolete extracellular space (GO:0005615), cytoplasm (GO:0005737), vesicle (GO:0031982), extracellular region (GO:0005576)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure2
detection of chemical stimulus involved in sensory perception of taste1
sensory perception of bitter taste1
cysteine-type endopeptidase activity1
endopeptidase inhibitor activity1
binding1
enzyme inhibitor activity1
peptidase activity1
peptidase regulator activity1
intracellular anatomical structure1
membrane-bounded organelle1

Protein interactions and networks

STRING

633 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
CST1CPPED1Q9BRF8938
CST1PIPP12273696
CST1CSTAP01040629
CST1AZGP1P25311618
CST1STATHP02808580
CST1CSTBP04080565
CST1S100A9P06702520
CST1CA6P23280517
CST1LCN1P31025485
CST1BPIFA2Q96DR5475
CST1LYZL1Q6UWQ5469
CST1DCDP58461451
CST1CTSSP25774447
CST1GZF1Q9H116438
CST1AMY1BP04745434

IntAct

98 interactions, top by confidence:

ABTypeScore
TADA3TADA2Apsi-mi:“MI:0914”(association)0.740
COMMD1VPS26Cpsi-mi:“MI:0914”(association)0.730
TAX1BP3ARVCFpsi-mi:“MI:0914”(association)0.690
NDUFA13NDUFS8psi-mi:“MI:0914”(association)0.640
UQCRQCOX7A2Lpsi-mi:“MI:0914”(association)0.640
ACTR3ARPC2psi-mi:“MI:0914”(association)0.640
C1DZFC3H1psi-mi:“MI:0914”(association)0.640
DNAJC8SF3B1psi-mi:“MI:0914”(association)0.640
SGTACST1psi-mi:“MI:0915”(physical association)0.560
CSNK2BCST1psi-mi:“MI:0915”(physical association)0.560
CST1psi-mi:“MI:0915”(physical association)0.560
CST1UBQLN2psi-mi:“MI:0915”(physical association)0.560
CST1IER3IP1psi-mi:“MI:0915”(physical association)0.560
CST1CSNK2Bpsi-mi:“MI:0915”(physical association)0.560
CST1ASPHpsi-mi:“MI:0915”(physical association)0.560
FTH1A2ML1psi-mi:“MI:0914”(association)0.530
FRMD1A2ML1psi-mi:“MI:0914”(association)0.530
DDX31IGLL5psi-mi:“MI:0914”(association)0.530
CST1CTSVpsi-mi:“MI:0914”(association)0.530
HBMSCGB2A1psi-mi:“MI:0914”(association)0.530
B3GALNT1DUSP14psi-mi:“MI:0914”(association)0.530
RHOBTB1CST4psi-mi:“MI:0914”(association)0.530
GTF2BCST4psi-mi:“MI:0914”(association)0.530
PLEKHG6CST4psi-mi:“MI:0914”(association)0.530
UBTD2CST4psi-mi:“MI:0914”(association)0.530

BioGRID (167): SGTA (Two-hybrid), CST1 (Affinity Capture-MS), CST1 (Affinity Capture-MS), CST1 (Affinity Capture-MS), CST1 (Affinity Capture-MS), CST1 (Affinity Capture-MS), CST1 (Affinity Capture-MS), CST4 (Affinity Capture-MS), CST1 (Affinity Capture-MS), CTSH (Affinity Capture-MS), CST1 (Affinity Capture-MS), CST1 (Affinity Capture-MS), CST1 (Affinity Capture-MS), CST1 (Affinity Capture-MS), CST1 (Affinity Capture-MS)

ESM2 similar proteins: A0A0K0IP23, A0A224AHH8, A0A3S6I186, A0A5C1J0Z8, A0A6B9KZ52, B1P1J3, B2Z450, B7PKZ1, B7PKZ2, E3P6N3, E3P6N4, E3P6N5, E3P6N6, E3P6N7, E3P6N8, E3P6N9, E3P6P0, E3P6P1, E3P6P2, E3P6P3, E3P6P4, G5EDZ9, J3RYX9, J3SE80, O60676, O88969, P01037, P01048, P08935, P0DXA0, P19313, P22085, P28325, P32766, P35481, P81714, P90698, Q15828, Q2XXN5, Q331K1

Diamond homologs: A0A0K0IP23, B1P1J3, G5ECM9, G5EDZ9, O19092, P01034, P01037, P22085, Q6QZV5, Q91195, Q9JM84, B2Z450, E3P6N3, E3P6N4, E3P6N5, E3P6N6, E3P6N7, E3P6N8, E3P6N9, E3P6P0, E3P6P1, E3P6P2, E3P6P3, E3P6P4, J3RYX9, J3SE80, O19093, O97862, P01035, P01038, P08935, P0DXA0, P14841, P19313, P21460, P31726, P35481, P81061, P81714, P90698

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance39
Likely benign8
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

219 predictions. Top by Δscore:

VariantEffectΔscore
20:23747898:TTC:Tacceptor_loss1.0000
20:23747900:C:Aacceptor_loss1.0000
20:23747900:C:CCacceptor_gain1.0000
20:23747902:G:Cacceptor_gain1.0000
20:23749011:CGTA:Cdonor_loss1.0000
20:23749012:GTA:Gdonor_loss1.0000
20:23749013:TACC:Tdonor_loss1.0000
20:23749014:ACCT:Adonor_loss1.0000
20:23749015:CCTT:Cdonor_gain1.0000
20:23749125:ACGGT:Aacceptor_gain1.0000
20:23749126:CGGT:Cacceptor_gain1.0000
20:23749126:CGGTC:Cacceptor_gain1.0000
20:23749128:GT:Gacceptor_gain1.0000
20:23749128:GTC:Gacceptor_loss1.0000
20:23749129:TC:Tacceptor_loss1.0000
20:23749130:C:CCacceptor_gain1.0000
20:23749131:T:Gacceptor_loss1.0000
20:23749133:C:CTacceptor_gain1.0000
20:23749135:C:CTacceptor_gain1.0000
20:23749137:C:CTacceptor_gain1.0000
20:23749138:A:Tacceptor_gain1.0000
20:23750636:TAC:Tdonor_loss1.0000
20:23750637:A:ACdonor_gain1.0000
20:23750638:C:CCdonor_gain1.0000
20:23750638:C:CTdonor_loss1.0000
20:23747895:TGTTT:Tacceptor_gain0.9900
20:23747896:GTTT:Gacceptor_gain0.9900
20:23747897:TTT:Tacceptor_gain0.9900
20:23747898:TT:Tacceptor_gain0.9900
20:23747902:G:GCacceptor_gain0.9900

AlphaMissense

918 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
20:23747861:C:AW127C0.971
20:23747861:C:GW127C0.971
20:23747882:G:CF120L0.960
20:23747882:G:TF120L0.960
20:23747884:A:GF120L0.960
20:23747889:C:GC118S0.959
20:23747890:A:TC118S0.959
20:23747883:A:CF120C0.957
20:23750717:G:CF50L0.949
20:23750717:G:TF50L0.949
20:23750719:A:GF50L0.949
20:23749077:C:GC94S0.946
20:23749078:A:TC94S0.946
20:23749083:G:AT92I0.925
20:23747829:C:GC138S0.924
20:23747830:A:TC138S0.924
20:23750715:G:TA51D0.923
20:23749041:A:CF106C0.921
20:23750640:T:GQ76P0.920
20:23749047:C:GC104S0.916
20:23749048:A:TC104S0.916
20:23749078:A:GC94R0.914
20:23747890:A:GC118R0.912
20:23750699:G:CN56K0.908
20:23750699:G:TN56K0.908
20:23749077:C:TC94Y0.904
20:23750639:C:AQ76H0.904
20:23750639:C:GQ76H0.904
20:23749048:A:GC104R0.903
20:23750718:A:CF50C0.898

dbSNP variants (sampled 300 via entrez): RS1000382148 (20:23747093 T>C,G), RS1001074339 (20:23752920 G>A,C,T), RS1002872823 (20:23748065 G>A,C), RS1003078365 (20:23751268 G>A,T), RS1004075527 (20:23752561 C>G,T), RS1004447204 (20:23748757 T>A,C), RS1004898817 (20:23748298 C>G,T), RS1005113982 (20:23751481 T>C), RS1005901630 (20:23747587 A>T), RS1005928673 (20:23747481 G>C), RS1007523440 (20:23749857 G>A,C), RS1008117728 (20:23749070 C>T), RS1009581787 (20:23752900 C>T), RS1009616220 (20:23752758 G>A,T), RS1011424035 (20:23752648 C>A,G,T)

Disease associations

OMIM: gene MIM:123855 | disease phenotypes:

GenCC curated gene-disease

DiseaseClassificationInheritance
male infertility with azoospermia or oligozoospermia due to single gene mutationLimitedAutosomal recessive

Mondo (1): (MONDO:0018393)

Orphanet (0):

HPO phenotypes

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

GWAS associations

1 associations (top):

StudyTraitp-value
GCST006585_1273Blood protein levels1.000000e-115

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

26 total (human), top 26 by PubMed support.

ChemicalActions (top 5)PubMed papers
Air Pollutantsincreases expression, increases abundance3
Benzo(a)pyrenedecreases expression, increases methylation2
Phenylmercuric Acetateaffects cotreatment, increases expression2
Valproic Acidaffects expression, increases methylation2
bisphenol Aincreases expression1
tris(1,3-dichloro-2-propyl)phosphatedecreases expression1
butyraldehydeincreases expression1
zinc chromateincreases abundance, increases expression1
mercuric bromideaffects cotreatment, increases expression1
chromium hexavalent ionincreases abundance, increases expression1
corosolic acidincreases 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
Diethylhexyl Phthalateincreases expression1
Endosulfandecreases expression1
Estradiolaffects expression, increases reaction1
Etoposideaffects response to substance1
Lipopolysaccharidesaffects expression, affects response to substance1
Lucanthoneincreases expression1
Methotrexateaffects response to substance1
Phosphorusincreases expression1
Silicon Dioxidedecreases expression1
Smokeincreases abundance, increases expression1
Tretinoinincreases expression1
Nanotubes, Carbonincreases expression1
Particulate Matterincreases abundance, increases expression1

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.