CRISP3

gene
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Also known as SGP28CRISP-3CRS3dJ442L6.3Aeg2

Summary

CRISP3 (cysteine rich secretory protein 3, HGNC:16904) is a protein-coding gene on chromosome 6p12.3, encoding Cysteine-rich secretory protein 3 (P54108).

This gene encodes a member of the cysteine-rich secretory protein (CRISP) family within the CRISP, antigen 5 and pathogenesis-related 1 proteins superfamily. The encoded protein has an N-terminal CRISP, antigen 5 and pathogenesis-related 1 proteins domain, a hinge region, and a C-terminal ion channel regulator domain. This protein contains cysteine residues, located in both the N- and C-terminal domains, that form eight disulfide bonds, a distinguishing characteristic of this family. This gene is expressed in the male reproductive tract where it plays a role in sperm function and fertilization, and the female reproductive tract where it plays a role in endometrial receptivity for embryo implantation. This gene is upregulated in certain types of prostate cancer. Alternative splicing results in multiple transcript variants.

Source: NCBI Gene 10321 — RefSeq curated summary.

At a glance

  • Clinical variants (ClinVar): 43 total
  • MANE Select transcript: NM_006061

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:16904
Approved symbolCRISP3
Namecysteine rich secretory protein 3
Location6p12.3
Locus typegene with protein product
StatusApproved
AliasesSGP28, CRISP-3, CRS3, dJ442L6.3, Aeg2
Ensembl geneENSG00000096006
Ensembl biotypeprotein_coding
OMIM618062
Entrez10321

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 4 protein_coding

ENST00000263045, ENST00000354620, ENST00000371159, ENST00000433368

RefSeq mRNA: 3 — MANE Select: NM_006061 NM_001190986, NM_001368123, NM_006061

CCDS: CCDS4929, CCDS55019, CCDS93932

Canonical transcript exons

ENST00000263045 — 8 exons

ExonStartEnd
ENSE000008504404972737649728857
ENSE000011387504973116349731251
ENSE000011387614973319549733292
ENSE000022193704974433149744388
ENSE000023112104973732549737398
ENSE000024865184973639149736507
ENSE000024884424973370349733848
ENSE000036480104973550449735591

Expression profiles

Bgee: expression breadth ubiquitous, 185 present calls, max score 99.67.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 10.0421 / max 4077.1644, expressed in 152 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter IDTPM avgSamples expressed
739238.6927115
739220.831945
739240.300642
739250.161729
739260.055215

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
pancreatic ductal cellCL:000207999.67gold quality
right uterine tubeUBERON:000130299.54gold quality
lower esophagus mucosaUBERON:003583498.94gold quality
olfactory segment of nasal mucosaUBERON:000538698.83gold quality
trabecular bone tissueUBERON:000248398.57gold quality
pharyngeal mucosaUBERON:000035598.43gold quality
tongue squamous epitheliumUBERON:000691998.28gold quality
bone marrowUBERON:000237198.04gold quality
minor salivary glandUBERON:000183097.83gold quality
seminal vesicleUBERON:000099897.63gold quality
oral cavityUBERON:000016797.54gold quality
bone marrow cellCL:000209297.43gold quality
saliva-secreting glandUBERON:000104496.35gold quality
esophagus squamous epitheliumUBERON:000692096.28gold quality
buccal mucosa cellCL:000233696.15gold quality
mouth mucosaUBERON:000372996.04gold quality
epithelium of esophagusUBERON:000197695.68gold quality
oviduct epitheliumUBERON:000480495.07gold quality
bone elementUBERON:000147494.80gold quality
tracheaUBERON:000312693.36gold quality
cervix epitheliumUBERON:000480193.27gold quality
cervix squamous epitheliumUBERON:000692292.85gold quality
body of tongueUBERON:001187692.78gold quality
urethraUBERON:000005792.44gold quality
amniotic fluidUBERON:000017392.22gold quality
upper leg skinUBERON:000426291.89gold quality
esophagus mucosaUBERON:000246991.20gold quality
epithelial cell of pancreasCL:000008390.91gold quality
fallopian tubeUBERON:000388990.44gold quality
tongueUBERON:000172390.03gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-MTAB-9801yes6220.75
E-HCAD-1yes11.54
E-ANND-3yes10.31

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): AR, ERG, HOXC13, POU2F1, POU2F2

miRNA regulators (miRDB)

54 targeting CRISP3, 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-4668-3P100.0068.742635
HSA-MIR-656-3P100.0072.152788
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-33A-5P99.9968.621055
HSA-MIR-33B-5P99.9968.581062
HSA-MIR-428299.9975.366408
HSA-MIR-493-5P99.9672.472382
HSA-MIR-551B-5P99.9671.283493
HSA-MIR-548AT-5P99.9670.832666
HSA-MIR-552-5P99.9368.561583
HSA-MIR-335-3P99.9373.364958
HSA-MIR-1213399.9271.822006
HSA-MIR-182-5P99.8774.032589
HSA-MIR-5002-5P99.7670.841763
HSA-MIR-7856-5P99.7569.992901
HSA-MIR-4755-5P99.7170.342716
HSA-MIR-5006-3P99.7170.262728
HSA-MIR-4677-5P99.7070.091940
HSA-MIR-545-5P99.6670.182308
HSA-MIR-432899.5771.064094
HSA-MIR-203A-3P99.4970.562806
HSA-MIR-582-5P99.4770.792635
HSA-MIR-508-5P99.4164.251248
HSA-MIR-428499.3665.251293
HSA-MIR-3606-5P99.3169.671168
HSA-MIR-3614-5P99.3065.25837
HSA-MIR-3160-5P99.2869.071938
HSA-MIR-520E-5P99.2768.901513

Literature-anchored findings (GeneRIF, showing 26)

  • The presence of CRISP-3 in peroxidase-negative granules of neutrophils, in granules of eosinophils, and in exocrine secretions indicates a role in the innate host defense. (PMID:12223513)
  • in situ hybridization experiments indicated that CRISP-3 mRNA is epithelial-specific and is up-regulated in prostate adenocarcinoma compared with benign prostate tissue; a potential biomarker for prostate cancer (PMID:12433721)
  • high levels of CRISP-3 in acinar cells dedifferentiating into small proliferating ductal cells in chronic pancreatitis suggests a role of this molecule in the pathophysiology of chronic pancreatitis (PMID:12647793)
  • alpha-1-B glycoprotein-CRISP-3 complex displays a similar function in protecting the circulation from a potentially harmful effect of free CRISP-3 (PMID:15461460)
  • Human CRISP-3 is a quantitatively minor seminal plasma protein not associated with prostasomes. CRISP-3 was found in secretory epithelium throughout the male genital tract, with particularly high expression in cauda epididymis and ampulla vas deferens. (PMID:15867000)
  • Structural similarity with an MSP-binding protein from blood plasma suggests that CRISP-3 binds MSP through its aminoterminal SCP-domain. (PMID:15950934)
  • Strong immunostaining for CRISP-3 is common in high-grade prostatic-intraepithelial-neoplasia and preserved in prostatic csncer. (PMID:16388501)
  • Predictor of recurrence after radical prostatectomy for localized prostate cancer. (PMID:17634540)
  • CRISP-3 pathology occurred in acini remote from lymphocyte foci and may represent some systemic effect in Sjogren Syndrome. (PMID:17665393)
  • A tentative structure for the hMSP-CRISP-3 complex using the known crystal structure of triflin as a model of CRISP-3 was presented. (PMID:19026612)
  • Results suggest that absence of a local reduction in expression of CRISP-3 in decidualized endometrium of women with EP may be due to reduced exposure to hCG due to the ectopic location of the trophoblast. (PMID:19282327)
  • Complex binding of CRISP proteins by A1BG and other proteins may interfere with the detection and function of these proteins. (PMID:20116414)
  • Additional transcription changes likely associated with Th2-like eosinophilic inflammation were prominent and included decreased CRISP2&3. (PMID:20625511)
  • Either PSP94 or CRISP-3 alone can induce growth inhibition in prostate cancer cells in a cell line specific manner. (PMID:20676114)
  • Expression levels of AR and CRISP3 were not affected by short-term ADT but were high in castration-resistant prostate cancer (CRPC) and metastases. (PMID:20680031)
  • We found no correlation between CRISP3 expression and biochemical recurrence. (PMID:21240253)
  • up-regulation of CRISP3 is associated with prostate carcinomas with the TMPRSS2-ERG fusion gene. (PMID:21814574)
  • MSMB and CRISP3 were widely distributed in ovaries and in ovarian tumors; the expression of MSMB fits well with a tumor-suppressor function in ovarian carcinogenesis. (PMID:22993349)
  • Strong CRISP3 expression is associated with unfavorable tumor phenotype and early recurrence in prostate cancers (PMID:23196798)
  • terminal beta-strands of PSP94 contact the first alpha-helix and the hinge region of CRISP-3 (PMID:23375721)
  • up-regulation of the mRNA encoding cysteine-rich secretory protein 3 (CRISP3), a glycoprotein with unknown function that is secreted from multiple exocrine glands, was correlated with HCV resistance. (PMID:24978310)
  • These data suggest roles for epithelial and neutrophil-derived CRISP3 in postmenstrual endometrial repair and regeneration (PMID:25715794)
  • results suggest that overexpression of CRISP-3 in prostate tumor may maintain higher PSA expression and lower ANXA1 expression (PMID:26369530)
  • in the presence of varicocoele, there is a marked increase in seminal CRISP-3 levels. Surgical intervention (varicocelectomy) decreases CRISP-3 levels and improves semen quality. (PMID:30354034)
  • In this study, we found obvious differences in the expression of CRISP3 between different mammary carcinoma cells, which is related to the prognosis of patients with mammary carcinoma (PMID:30609035)
  • EP300 promotes tumor stemness via epigenetic activation of CRISP3 leading to lobaplatin resistance in triple-negative breast cancer. (PMID:38879857)

Cross-species orthologs

47 orthologs

OrganismSymbolGene ID
mus_musculusCrisp1ENSMUSG00000025431
mus_musculusCrisp3ENSMUSG00000025433
rattus_norvegicusCrisp3ENSRNOG00000013496
drosophila_melanogasterAg5rFBGN0015010
drosophila_melanogasterAg5r2FBGN0020508
drosophila_melanogasterCG9400FBGN0030562
drosophila_melanogasterCG10651FBGN0032853
drosophila_melanogasterCG9822FBGN0034623
drosophila_melanogasterCG17974FBGN0034624
drosophila_melanogasterCG3640FBGN0035042
drosophila_melanogasterCG8072FBGN0036070
drosophila_melanogasterCG6628FBGN0036072
drosophila_melanogasterscpr-CFBGN0037879
drosophila_melanogasterscpr-BFBGN0037888
drosophila_melanogasterscpr-AFBGN0037889
drosophila_melanogasterCG8483FBGN0038126
drosophila_melanogasterCG30486FBGN0050486
drosophila_melanogasterantrFBGN0050488
drosophila_melanogasterCG31286FBGN0051286
drosophila_melanogasterCG32313FBGN0052313
drosophila_melanogasterCG32679FBGN0052679
drosophila_melanogasterCG34002FBGN0054002
drosophila_melanogasterCG17575FBGN0250842
drosophila_melanogasterCG42564FBGN0260766
drosophila_melanogasterCG42780FBGN0261848
drosophila_melanogasterCG43775FBGN0264297
drosophila_melanogasterCG43776FBGN0264298
drosophila_melanogasterCG43777FBGN0264299
caenorhabditis_elegansWBGENE00004742
caenorhabditis_elegansWBGENE00007397
caenorhabditis_elegansWBGENE00008027
caenorhabditis_elegansWBGENE00008028
caenorhabditis_elegansWBGENE00008029
caenorhabditis_elegansWBGENE00008030
caenorhabditis_elegansWBGENE00008625
caenorhabditis_elegansWBGENE00009891
caenorhabditis_elegansWBGENE00009895
caenorhabditis_elegansWBGENE00009896
caenorhabditis_elegansWBGENE00012816
caenorhabditis_elegansWBGENE00013971
caenorhabditis_elegansWBGENE00013972
caenorhabditis_elegansWBGENE00015246
caenorhabditis_elegansWBGENE00017055
caenorhabditis_elegansWBGENE00017183
caenorhabditis_elegansWBGENE00019178
caenorhabditis_elegansWBGENE00019179
caenorhabditis_elegansWBGENE00021780

Paralogs (13): R3HDML (ENSG00000101074), CRISPLD2 (ENSG00000103196), CRISPLD1 (ENSG00000121005), GLIPR2 (ENSG00000122694), CRISP2 (ENSG00000124490), CRISP1 (ENSG00000124812), PI15 (ENSG00000137558), GLIPR1 (ENSG00000139278), CLEC18B (ENSG00000140839), CLEC18A (ENSG00000157322), CLEC18C (ENSG00000157335), GLIPR1L1 (ENSG00000173401), GLIPR1L2 (ENSG00000180481)

Protein

Protein identifiers

Cysteine-rich secretory protein 3P54108 (reviewed: P54108)

Alternative names: Specific granule protein of 28 kDa

All UniProt accessions (3): P54108, I3L0A1, J3KPA1

UniProt curated annotations — full annotation on UniProt →

Subunit / interactions. Interacts with A1BG.

Subcellular location. Secreted.

Tissue specificity. Salivary gland, pancreas and prostate > epididymis, ovary, thymus and colon.

Similarity. Belongs to the CRISP family.

Isoforms (3)

UniProt IDNamesCanonical?
P54108-11yes
P54108-22
P54108-33

RefSeq proteins (3): NP_001177915, NP_001355052, NP_006052* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001283CRISP-relatedFamily
IPR003582ShKT_domDomain
IPR013871Cysteine_rich_secretoryDomain
IPR014044CAP_domDomain
IPR018244Allrgn_V5/Tpx1_CSConserved_site
IPR034117SCP_CRISPDomain
IPR035940CAP_sfHomologous_superfamily
IPR042076Crisp-like_domHomologous_superfamily

Pfam: PF00188, PF08562

UniProt features (16 total): disulfide bond 5, splice variant 2, sequence variant 2, sequence conflict 2, domain 2, signal peptide 1, chain 1, glycosylation site 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-P54108-F192.650.89

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 (5): 191–198, 194–203, 207–240, 216–234, 225–238

Glycosylation sites (1): 239

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

IDPathway
R-HSA-6798695Neutrophil degranulation

MSigDB gene sets: 116 (showing top): GSE37336_LY6C_POS_VS_NEG_NAIVE_CD4_TCELL_DN, REACTOME_INNATE_IMMUNE_SYSTEM, GOCC_SECRETORY_GRANULE, GOZGIT_ESR1_TARGETS_DN, ACEVEDO_LIVER_CANCER_WITH_H3K27ME3_UP, chr6p12, GOBP_DEFENSE_RESPONSE_TO_OTHER_ORGANISM, SHETH_LIVER_CANCER_VS_TXNIP_LOSS_PAM1, CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_5, HANSON_HRAS_SIGNALING_VIA_NFKB, BRUNO_HEMATOPOIESIS, TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_16D_DN, GOCC_SECRETORY_VESICLE, GOCC_VESICLE_LUMEN, TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_8D_UP

GO Biological Process (2): defense response (GO:0006952), innate immune response (GO:0045087)

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (7): extracellular region (GO:0005576), obsolete extracellular space (GO:0005615), extracellular matrix (GO:0031012), specific granule lumen (GO:0035580), specific granule (GO:0042581), tertiary granule lumen (GO:1904724), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-1 pathways:

CategoryPathways
Innate Immune System1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure2
response to stress1
immune response1
defense response to symbiont1
binding1
external encapsulating structure1
secretory granule lumen1
specific granule1
secretory granule1
intracellular organelle lumen1
tertiary granule1

Protein interactions and networks

STRING

1088 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
CRISP3A1BGP04217920
CRISP3MTDHQ86UE4758
CRISP3MSMBP08118720
CRISP3IL4I1Q96RQ9621
CRISP3PLB1Q6P1J6619
CRISP3LTA4HP09960548
CRISP3LCN2P30150527
CRISP3PLA2G2AP14555507
CRISP3ACHEP22303504
CRISP3PGLYRP1O75594478
CRISP3BPIFB1Q8TDL5466
CRISP3OLFM4Q6UX06465
CRISP3CEBPBP17676455
CRISP3FGFBP1Q14512442
CRISP3QPCTQ16769424
CRISP3NPPCP23582424

IntAct

2 interactions, top by confidence:

ABTypeScore
CRISP3ADD2psi-mi:“MI:0914”(association)0.350

BioGRID (14): A1BG (Affinity Capture-MS), CRISP3 (Affinity Capture-MS), GPR152 (Two-hybrid), ADD2 (Affinity Capture-MS), ADD3 (Affinity Capture-MS), SLC2A8 (Affinity Capture-MS), HSPA1A (Affinity Capture-MS), CRISP3 (Phenotypic Suppression), CRISP3 (Phenotypic Suppression), CRISP3 (Phenotypic Suppression), CRISP3 (Phenotypic Suppression), MSMB (Reconstituted Complex), CRISP3 (Affinity Capture-MS), CRISP3 (Affinity Capture-MS)

ESM2 similar proteins: A0A0D3QS98, A0A0D3QS99, A2A5I3, O19010, O19011, O42596, P01137, P04202, P04629, P07200, P09533, P16562, P17246, P18341, P35739, P50414, P54108, P54831, P57110, Q01974, Q38HS2, Q3KPV7, Q3UFB7, Q505J3, Q5R7Y0, Q5T4F7, Q60477, Q658N2, Q6UWX4, Q7T141, Q7TSQ1, Q80XH4, Q8BG58, Q91009, Q99JR5, Q9CXM0, Q9D2G9, Q9EQT5, Q9GZM7, Q9H3Y0

Diamond homologs: A0A182GL09, A0A1S4EWW7, A0A218QX58, A1BQQ5, A6MFK9, A6QLZ7, A8S6B6, A9QQ26, A9YME1, B2MVK7, B9URJ1, C0ITL3, D4B327, D4P2Y4, F8J2D4, G3CJR9, O19010, O43692, P0CB15, P0DMB9, P0DMT4, P0DPU0, P0DPU1, P0DPU2, P0DPU5, P0DPV2, P0DSI3, P10736, P10737, P12020, P16562, P16563, P35759, P35760, P35778, P35779, P35780, P35781, P35782, P35783

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance36
Likely benign3
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1005 predictions. Top by Δscore:

VariantEffectΔscore
6:49731249:CCA:Cacceptor_gain1.0000
6:49731250:CAC:Cacceptor_gain1.0000
6:49731252:C:CCacceptor_gain1.0000
6:49733850:T:Aacceptor_loss1.0000
6:49735499:CATA:Cdonor_gain1.0000
6:49735500:ATAC:Adonor_loss1.0000
6:49735501:TACT:Tdonor_loss1.0000
6:49735502:A:ACdonor_gain1.0000
6:49735503:C:CGdonor_gain1.0000
6:49735503:CTTGT:Cdonor_gain1.0000
6:49735587:CATTC:Cacceptor_gain1.0000
6:49735589:TTC:Tacceptor_gain1.0000
6:49735590:TC:Tacceptor_gain1.0000
6:49735591:CC:Cacceptor_gain1.0000
6:49735592:C:CAacceptor_loss1.0000
6:49735592:C:CCacceptor_gain1.0000
6:49735593:T:Aacceptor_loss1.0000
6:49736390:CCAT:Cdonor_gain1.0000
6:49731161:A:ACdonor_gain0.9900
6:49731162:C:CCdonor_gain0.9900
6:49731162:CTG:Cdonor_gain0.9900
6:49731250:CA:Cacceptor_gain0.9900
6:49731259:T:Cacceptor_gain0.9900
6:49731259:T:TCacceptor_gain0.9900
6:49731923:ATCT:Adonor_gain0.9900
6:49731924:T:Cdonor_gain0.9900
6:49733187:ATAC:Adonor_loss0.9900
6:49733188:TACT:Tdonor_loss0.9900
6:49733189:ACTT:Adonor_loss0.9900
6:49733190:C:CTdonor_loss0.9900

AlphaMissense

1703 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000128570 (6:49730240 A>G), RS1000204340 (6:49739207 A>C), RS1001513815 (6:49741623 T>G), RS1001599520 (6:49743055 T>A), RS1001632082 (6:49742737 G>C), RS1001680230 (6:49730270 C>G), RS1001752562 (6:49742844 G>A), RS1001934764 (6:49741581 A>G), RS1001965925 (6:49741249 C>G,T), RS1001979761 (6:49729131 A>G), RS1002144627 (6:49732974 T>C), RS1002146143 (6:49734949 A>G), RS1002194294 (6:49736327 T>A), RS1002498564 (6:49735302 G>A), RS1002815802 (6:49746051 A>G)

Disease associations

OMIM: gene MIM:618062 | 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: no

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

CTD chemical–gene interactions

17 total (human), top 17 by PubMed support.

ChemicalActions (top 5)PubMed papers
Benzo(a)pyreneincreases methylation, increases mutagenesis2
Nickeldecreases expression2
sodium arsenitedecreases expression1
CGP 52608affects binding, increases reaction1
rofecoxibincreases expression1
enzalutamidedecreases expression1
Arsenicalsdecreases expression1
Estradiolaffects cotreatment, increases expression1
Lipopolysaccharidesincreases expression1
Malathiondecreases expression1
N-Nitrosopyrrolidineincreases expression1
Dihydrotestosteroneincreases expression1
Tetrachlorodibenzodioxinincreases expression, affects cotreatment1
Tobacco Smoke Pollutiondecreases expression1
Valproic Acidincreases expression1
Aflatoxin B1increases methylation1
Okadaic Aciddecreases 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.