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Aliases for HPSE2 Gene

Aliases for HPSE2 Gene

  • Heparanase 2 (Inactive) 2 3 5
  • HPA2 3 4
  • Heparanase-Like Protein 3
  • Inactive Heparanase-2 3
  • Urofacial Syndrome 2
  • Heparanase 3 3
  • Heparanase 2 2
  • HPR2 3
  • UFS1 3
  • Hpa2 4
  • UFS 3

External Ids for HPSE2 Gene

Previous HGNC Symbols for HPSE2 Gene

  • UFS

Previous GeneCards Identifiers for HPSE2 Gene

  • GC10M099112
  • GC10M099452
  • GC10M100350
  • GC10M099883
  • GC10M100208
  • GC10M093841

Summaries for HPSE2 Gene

Entrez Gene Summary for HPSE2 Gene

  • This gene encodes a heparanase enzyme. The encoded protein is a endoglycosidase that degrades heparin sulfate proteoglycans located on the extracellular matrix and cell surface. This protein may be involved in biological processes involving remodeling of the extracellular matrix including angiogenesis and tumor progression. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Oct 2009]

GeneCards Summary for HPSE2 Gene

HPSE2 (Heparanase 2 (Inactive)) is a Protein Coding gene. Diseases associated with HPSE2 include Urofacial Syndrome 1 and Uterine Benign Neoplasm. Among its related pathways are Chondroitin sulfate/dermatan sulfate metabolism and Glycosaminoglycan degradation. Gene Ontology (GO) annotations related to this gene include heparan sulfate proteoglycan binding and heparanase activity. An important paralog of this gene is HPSE.

UniProtKB/Swiss-Prot for HPSE2 Gene

  • Binds heparin and heparan sulfate with high affinity, but lacks heparanase activity. Inhibits HPSE, possibly by competing for its substrates (in vitro).

Gene Wiki entry for HPSE2 Gene

Additional gene information for HPSE2 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for HPSE2 Gene

Genomics for HPSE2 Gene

GeneHancer (GH) Regulatory Elements for HPSE2 Gene

Promoters and enhancers for HPSE2 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH10J099235 Promoter/Enhancer 1.1 EPDnew ENCODE 650.7 -0.2 -233 1.4 SP3 ZNF362 SUZ12 SIN3A ZNF398 ZNF518A SP1 ZNF335 GLIS2 KLF16 HPSE2 GC10M099245
GH10J099328 Promoter/Enhancer 1.6 EPDnew Ensembl ENCODE 16.9 -93.9 -93879 1.8 CLOCK MLX ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 ZNF121 GLIS2 CNNM1 PIR44588 HPSE2 SPCS2P2 TPM4P1 CWF19L1 SLC25A28 HPS1 GOT1
GH10J098919 Enhancer 0.7 ENCODE 32 +315.0 315017 2 ATF1 CTBP1 ZNF316 NFE2 ATF7 MAFK CREM CBFA2T3 MAFG ZEB2 HPSE2 MIR6507 GC10P098899
GH10J098910 Enhancer 0.9 ENCODE 11.4 +325.6 325636 0.2 PKNOX1 SMAD1 ATF1 ARNT NCOA2 TCF12 ZNF766 GATA2 FOS ATF7 HPSE2 MIR6507 GC10P098899
GH10J099231 Enhancer 0.9 Ensembl ENCODE 8.5 +2.3 2296 3.2 MXI1 USF1 SUZ12 MAX STAT5A IRF4 POLR2A EED ETV6 BCLAF1 HPSE2 CNNM1 RPL7P36
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around HPSE2 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the HPSE2 gene promoter:
  • N-Myc
  • GATA-2
  • c-Jun
  • ATF-2
  • Evi-1
  • HNF-1A
  • USF-1
  • USF1
  • LyF-1
  • HNF-1

Genomic Locations for HPSE2 Gene

Genomic Locations for HPSE2 Gene
778,799 bases
Minus strand
778,799 bases
Minus strand

Genomic View for HPSE2 Gene

Genes around HPSE2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
HPSE2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for HPSE2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for HPSE2 Gene

Proteins for HPSE2 Gene

  • Protein details for HPSE2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Inactive heparanase-2
    Protein Accession:
    Secondary Accessions:
    • Q5VUH4
    • Q5VUH5
    • Q5VUH6
    • Q8WWQ1
    • Q9HB37
    • Q9HB38
    • Q9HB39

    Protein attributes for HPSE2 Gene

    592 amino acids
    Molecular mass:
    66596 Da
    Quaternary structure:
    • Interacts with HPSE. Interacts with SDC1 (via glycan chains).

    Alternative splice isoforms for HPSE2 Gene


neXtProt entry for HPSE2 Gene

Post-translational modifications for HPSE2 Gene

  • Glycosylation at Asn392 and isoforms=2254
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for HPSE2 Gene

Domains & Families for HPSE2 Gene

Gene Families for HPSE2 Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins
  • Predicted secreted proteins

Protein Domains for HPSE2 Gene

Suggested Antigen Peptide Sequences for HPSE2 Gene

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the glycosyl hydrolase 79 family.
  • Belongs to the glycosyl hydrolase 79 family.
genes like me logo Genes that share domains with HPSE2: view

Function for HPSE2 Gene

Molecular function for HPSE2 Gene

UniProtKB/Swiss-Prot Function:
Binds heparin and heparan sulfate with high affinity, but lacks heparanase activity. Inhibits HPSE, possibly by competing for its substrates (in vitro).

Phenotypes From GWAS Catalog for HPSE2 Gene

Gene Ontology (GO) - Molecular Function for HPSE2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0016798 hydrolase activity, acting on glycosyl bonds IEA --
GO:0030305 heparanase activity TAS 11027606
GO:0043395 heparan sulfate proteoglycan binding IDA 20576607
genes like me logo Genes that share ontologies with HPSE2: view
genes like me logo Genes that share phenotypes with HPSE2: view

Human Phenotype Ontology for HPSE2 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for HPSE2

Clone Products

No data available for Enzyme Numbers (IUBMB) , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for HPSE2 Gene

Localization for HPSE2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for HPSE2 Gene

Secreted, extracellular space, extracellular matrix.

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for HPSE2 gene
Compartment Confidence
plasma membrane 5
extracellular 5
nucleus 2
golgi apparatus 2
cytoskeleton 1
mitochondrion 1
peroxisome 1
endoplasmic reticulum 1

Gene Ontology (GO) - Cellular Components for HPSE2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005622 intracellular TAS 11027606
GO:0005886 plasma membrane TAS --
GO:0016020 membrane IEA --
genes like me logo Genes that share ontologies with HPSE2: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for HPSE2 Gene

Pathways & Interactions for HPSE2 Gene

genes like me logo Genes that share pathways with HPSE2: view

Interacting Proteins for HPSE2 Gene

Gene Ontology (GO) - Biological Process for HPSE2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006027 glycosaminoglycan catabolic process TAS --
GO:0008150 biological_process ND --
GO:0008284 positive regulation of cell proliferation IEA --
GO:0030198 extracellular matrix organization IEA --
genes like me logo Genes that share ontologies with HPSE2: view

No data available for SIGNOR curated interactions for HPSE2 Gene

Drugs & Compounds for HPSE2 Gene

(1) Drugs for HPSE2 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Water Approved Pharma 0
genes like me logo Genes that share compounds with HPSE2: view

Transcripts for HPSE2 Gene

mRNA/cDNA for HPSE2 Gene

Unigene Clusters for HPSE2 Gene

Heparanase 2:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for HPSE2

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for HPSE2 Gene

No ASD Table

Relevant External Links for HPSE2 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for HPSE2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for HPSE2 Gene

mRNA differential expression in normal tissues according to GTEx for HPSE2 Gene

This gene is overexpressed in Esophagus - Muscularis (x6.9) and Esophagus - Gastroesophageal Junction (x5.7).

Protein differential expression in normal tissues from HIPED for HPSE2 Gene

This gene is overexpressed in Heart (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for HPSE2 Gene

Protein tissue co-expression partners for HPSE2 Gene

NURSA nuclear receptor signaling pathways regulating expression of HPSE2 Gene:


SOURCE GeneReport for Unigene cluster for HPSE2 Gene:


mRNA Expression by UniProt/SwissProt for HPSE2 Gene:

Tissue specificity: Widely expressed, with the highest expression in brain, mammary gland, prostate, small intestine, testis and uterus. In the central nervous system, expressed in the spinal chord, caudate nucleus, thalamus, substantia nigra, medulla oblongata, putamen and pons. In the urinary bladder, expressed in longitudinal and circular layers of detrusor muscle. Found both in normal and cancer tissues.

Evidence on tissue expression from TISSUES for HPSE2 Gene

  • Heart(4.1)

Phenotype-based relationships between genes and organs from Gene ORGANizer for HPSE2 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
  • digestive
  • immune
  • nervous
  • reproductive
  • skeletal muscle
  • skeleton
  • urinary
Head and neck:
  • cranial nerve
  • face
  • head
  • skull
  • intestine
  • kidney
  • large intestine
  • rectum
  • testicle
  • ureter
  • urethra
  • urinary bladder
  • blood
  • peripheral nerve
  • peripheral nervous system
  • white blood cell
genes like me logo Genes that share expression patterns with HPSE2: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery for HPSE2 Gene

Orthologs for HPSE2 Gene

This gene was present in the common ancestor of chordates.

Orthologs for HPSE2 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia HPSE2 34 33
  • 99.72 (n)
(Ornithorhynchus anatinus)
Mammalia HPSE2 34
  • 98 (a)
(Monodelphis domestica)
Mammalia -- 34
  • 98 (a)
-- 34
  • 72 (a)
(Bos Taurus)
Mammalia HPSE2 33
  • 96.17 (n)
(Canis familiaris)
Mammalia HPSE2 34 33
  • 95.33 (n)
(Mus musculus)
Mammalia Hpse2 16 34 33
  • 93.19 (n)
(Rattus norvegicus)
Mammalia Hpse2 33
  • 89.08 (n)
(Gallus gallus)
Aves HPSE2 34 33
  • 80.47 (n)
(Anolis carolinensis)
Reptilia HPSE2 34
  • 86 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia hpse2 33
  • 75.29 (n)
(Danio rerio)
Actinopterygii hpse2 34 33
  • 69.96 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 35 (a)
Species where no ortholog for HPSE2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for HPSE2 Gene

Gene Tree for HPSE2 (if available)
Gene Tree for HPSE2 (if available)
Evolutionary constrained regions (ECRs) for HPSE2: view image

Paralogs for HPSE2 Gene

Paralogs for HPSE2 Gene

(1) SIMAP similar genes for HPSE2 Gene using alignment to 3 proteins:

  • F8S1G9_HUMAN
  • Q2M1H9_HUMAN
genes like me logo Genes that share paralogs with HPSE2: view

Variants for HPSE2 Gene

Sequence variations from dbSNP and Humsavar for HPSE2 Gene

SNP ID Clin Chr 10 pos Variation AA Info Type
rs267606864 pathogenic, Ochoa syndrome 98,490,103(-) G/A/C coding_sequence_variant, genic_downstream_transcript_variant, missense_variant, non_coding_transcript_variant, stop_gained
rs267606865 pathogenic, Ochoa syndrome 99,144,391(-) G/A 5_prime_UTR_variant, coding_sequence_variant, intron_variant, non_coding_transcript_variant, stop_gained
rs267606866 pathogenic, Ochoa syndrome 98,482,733(-) G/A coding_sequence_variant, genic_downstream_transcript_variant, intron_variant, non_coding_transcript_variant, stop_gained
rs397515338 pathogenic, Ochoa syndrome 98,490,051(-) TT/ coding_sequence_variant, frameshift, genic_downstream_transcript_variant, non_coding_transcript_variant
rs397515452 pathogenic, Ochoa syndrome 98,459,725(-) T/A 3_prime_UTR_variant, coding_sequence_variant, genic_downstream_transcript_variant, missense_variant, non_coding_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for HPSE2 Gene

Variant ID Type Subtype PubMed ID
dgv1370n54 CNV loss 21841781
dgv1371n54 CNV loss 21841781
dgv1372n54 CNV loss 21841781
dgv165e199 CNV deletion 23128226
dgv505n106 CNV deletion 24896259
dgv8n50 CNV loss 21212237
esv1004375 CNV deletion 20482838
esv1474285 CNV insertion 17803354
esv23306 CNV loss 19812545
esv2448524 OTHER inversion 19546169
esv2482496 CNV deletion 19546169
esv25039 CNV loss 19812545
esv2522473 CNV loss 19546169
esv2665040 CNV deletion 23128226
esv26720 CNV loss 19812545
esv2674577 CNV deletion 23128226
esv2740017 CNV deletion 23290073
esv2740029 CNV deletion 23290073
esv2740040 CNV deletion 23290073
esv32597 CNV gain+loss 17666407
esv3431730 CNV insertion 20981092
esv3546737 CNV deletion 23714750
esv3624337 CNV loss 21293372
esv3624339 CNV loss 21293372
esv3624340 CNV loss 21293372
esv3624342 CNV loss 21293372
esv3624343 CNV loss 21293372
esv3624344 CNV loss 21293372
esv3624346 CNV loss 21293372
nsv1038634 CNV gain 25217958
nsv1045593 CNV gain 25217958
nsv1053992 CNV gain 25217958
nsv1070884 CNV deletion 25765185
nsv1075421 CNV duplication 25765185
nsv1076944 CNV deletion 25765185
nsv1130907 CNV deletion 24896259
nsv1137950 CNV deletion 24896259
nsv1137951 CNV deletion 24896259
nsv1145477 CNV deletion 24896259
nsv1152639 CNV deletion 26484159
nsv1159760 CNV duplication 26073780
nsv436692 OTHER inversion 17901297
nsv436820 CNV insertion 17901297
nsv478233 CNV novel sequence insertion 20440878
nsv498739 CNV loss 21111241
nsv507573 OTHER sequence alteration 20534489
nsv508602 CNV deletion 20534489
nsv513014 CNV insertion 21212237
nsv514537 CNV loss 21397061
nsv517710 CNV gain+loss 19592680
nsv518822 CNV gain 19592680
nsv520353 CNV gain 19592680
nsv521748 CNV gain 19592680
nsv552030 CNV loss 21841781
nsv552035 CNV loss 21841781
nsv552042 CNV loss 21841781
nsv552043 CNV loss 21841781
nsv552044 CNV loss 21841781
nsv7209 OTHER inversion 18451855
nsv7511 CNV deletion 18451855
nsv7513 CNV deletion 18451855
nsv7514 CNV deletion 18451855
nsv825536 CNV loss 20364138
nsv825537 CNV loss 20364138
nsv825538 CNV loss 20364138
nsv831955 CNV gain 17160897
nsv831956 CNV loss 17160897
nsv831957 CNV gain 17160897
nsv948160 CNV duplication 23825009
nsv948161 CNV duplication 23825009
nsv956971 CNV deletion 24416366

Variation tolerance for HPSE2 Gene

Residual Variation Intolerance Score: 41.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.16; 51.74% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for HPSE2 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for HPSE2 Gene

Disorders for HPSE2 Gene

MalaCards: The human disease database

(9) MalaCards diseases for HPSE2 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
urofacial syndrome 1
  • ufs1
uterine benign neoplasm
reproductive organ benign neoplasm
endometriosis of uterus
  • adenomyosis
neurogenic bladder
  • neurogenic dysfunction of the urinary bladder
- elite association - COSMIC cancer census association via MalaCards
Search HPSE2 in MalaCards View complete list of genes associated with diseases


  • Urofacial syndrome 1 (UFS1) [MIM:236730]: A rare autosomal recessive disorder characterized by facial grimacing when attempting to smile and failure of the urinary bladder to void completely despite a lack of anatomical bladder outflow obstruction or overt neurological damage. Affected individuals often have reflux of infected urine from the bladder to the upper renal tract, with a risk of kidney damage and renal failure. {ECO:0000269 PubMed:20560209, ECO:0000269 PubMed:20560210}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for HPSE2

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with HPSE2: view

No data available for Genatlas for HPSE2 Gene

Publications for HPSE2 Gene

  1. Cloning and expression profiling of Hpa2, a novel mammalian heparanase family member. (PMID: 11027606) McKenzie E … Page M (Biochemical and biophysical research communications 2000) 2 3 4 22 58
  2. Mutations in HPSE2 cause urofacial syndrome. (PMID: 20560210) Daly SB … Newman WG (American journal of human genetics 2010) 2 3 4 58
  3. Heparanase 2 interacts with heparan sulfate with high affinity and inhibits heparanase activity. (PMID: 20576607) Levy-Adam F … Vlodavsky I (The Journal of biological chemistry 2010) 2 3 4 58
  4. A genome-wide meta-analysis of six type 1 diabetes cohorts identifies multiple associated loci. (PMID: 21980299) Bradfield JP … Hakonarson H (PLoS genetics 2011) 3 44 58
  5. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 44 58

Products for HPSE2 Gene

Sources for HPSE2 Gene

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