Free for academic non-profit institutions. Other users need a Commercial license

Aliases for BACE2 Gene

Aliases for BACE2 Gene

  • Beta-Site APP-Cleaving Enzyme 2 2 3 5
  • Membrane-Associated Aspartic Protease 1 3 4
  • Aspartyl Protease 1 3 4
  • Theta-Secretase 3 4
  • Memapsin-1 3 4
  • AEPLC 3 4
  • ALP56 3 4
  • ASP21 3 4
  • ASP1 3 4
  • DRAP 3 4
  • Beta-Site Amyloid Beta A4 Precursor Protein-Cleaving Enzyme 2 3
  • Beta-Site Amyloid Precursor Protein Cleaving Enzyme 2 4
  • Down Syndrome Region Aspartic Protease 3
  • Transmembrane Aspartic Proteinase Asp1 3
  • Beta-Site APP Cleaving Enzyme 2 4
  • 56 KDa Aspartic-Like Protease 3
  • Aspartic-Like Protease 56 KDa 4
  • Down Region Aspartic Protease 4
  • SLCO3A1/BACE2 Fusion 3
  • Beta-Secretase 2 3
  • EC 4
  • Memapsin 1 2
  • EC 3.4.23 56
  • CDA13 3
  • CEAP1 3
  • Asp 1 4
  • BAE2 3

External Ids for BACE2 Gene

Previous HGNC Symbols for BACE2 Gene


Previous GeneCards Identifiers for BACE2 Gene

  • GC21P039113
  • GC21P041460
  • GC21P041461
  • GC21P042539
  • GC21P028008

Summaries for BACE2 Gene

Entrez Gene Summary for BACE2 Gene

  • This gene encodes an integral membrane glycoprotein that functions as an aspartic protease. The encoded protein cleaves amyloid precursor protein into amyloid beta peptide, which is a critical step in the etiology of Alzheimer's disease and Down syndrome. The protein precursor is further processed into an active mature peptide. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2013]

GeneCards Summary for BACE2 Gene

BACE2 (Beta-Site APP-Cleaving Enzyme 2) is a Protein Coding gene. Diseases associated with BACE2 include Down Syndrome and Alzheimer Disease. Among its related pathways are Alzheimers Disease Pathway and Respiratory electron transport, ATP synthesis by chemiosmotic coupling, and heat production by uncoupling proteins.. Gene Ontology (GO) annotations related to this gene include aspartic-type endopeptidase activity. An important paralog of this gene is BACE1.

UniProtKB/Swiss-Prot for BACE2 Gene

  • Responsible for the proteolytic processing of the amyloid precursor protein (APP). Cleaves APP, between residues 690 and 691, leading to the generation and extracellular release of beta-cleaved soluble APP, and a corresponding cell-associated C-terminal fragment which is later released by gamma-secretase. It has also been shown that it can cleave APP between residues 671 and 672.

Gene Wiki entry for BACE2 Gene

Additional gene information for BACE2 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for BACE2 Gene

Genomics for BACE2 Gene

GeneHancer (GH) Regulatory Elements for BACE2 Gene

Promoters and enhancers for BACE2 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
GH21I041166 Promoter/Enhancer 2.4 EPDnew FANTOM5 Ensembl ENCODE 569.2 +1.7 1664 5.6 ATF1 SIN3A ZBTB7B GLIS2 ZNF213 ZNF143 ZNF202 SP3 REST ZSCAN16 BACE2 MIR3197 PRDM15 LINC00323 GC21P041172
GH21I041246 Enhancer 1.1 FANTOM5 Ensembl ENCODE 71.8 +82.2 82169 6.5 KLF1 ZBTB21 JUN TAL1 INSM2 MAX KLF17 FEZF1 ZNF366 FOS BACE2 PIR40884 GC21P041279
GH21I041206 Enhancer 0.7 Ensembl ENCODE 19.6 +39.9 39932 1.5 NFIC ZBTB48 NFIB HLF ZIC2 PRDM1 BACE2 GC21P041210 ENSG00000225745 GC21P041172
GH21I041112 Enhancer 1.2 FANTOM5 Ensembl ENCODE 11.3 -54.3 -54299 1.6 PKNOX1 NFIB NEUROD1 SIN3A RFX5 ZNF507 CTBP1 GATA3 ZNF362 MAZ BACE2 RIPK4 LINC00323 YRDCP3
GH21I041217 Enhancer 0.7 Ensembl ENCODE 16.1 +50.2 50232 1.8 ZFHX2 EGR1 CEBPB CEBPG NFE2 NR2C2 EGR2 BACE2 PIR47426 PIR40884 GC21P041172
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around BACE2 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the BACE2 gene promoter:

Genomic Locations for BACE2 Gene

Genomic Locations for BACE2 Gene
114,734 bases
Plus strand

Genomic View for BACE2 Gene

Genes around BACE2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
BACE2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for BACE2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for BACE2 Gene

Proteins for BACE2 Gene

  • Protein details for BACE2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Beta-secretase 2
    Protein Accession:
    Secondary Accessions:
    • A8K7P1
    • Q5DIH8
    • Q8N2D4
    • Q9H2V8
    • Q9NZL1
    • Q9NZL2
    • Q9UJT6

    Protein attributes for BACE2 Gene

    518 amino acids
    Molecular mass:
    56180 Da
    Quaternary structure:
    • Monomer. Interacts ith RTN3 and RTN4.

    Three dimensional structures from OCA and Proteopedia for BACE2 Gene

    Alternative splice isoforms for BACE2 Gene


neXtProt entry for BACE2 Gene

Selected DME Specific Peptides for BACE2 Gene


Post-translational modifications for BACE2 Gene

Other Protein References for BACE2 Gene

Antibody Products

  • Abcam antibodies for BACE2

Domains & Families for BACE2 Gene

Gene Families for BACE2 Gene

Human Protein Atlas (HPA):
  • Enzymes
  • Predicted membrane proteins
  • Predicted secreted proteins

Suggested Antigen Peptide Sequences for BACE2 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the peptidase A1 family.
  • Belongs to the peptidase A1 family.
genes like me logo Genes that share domains with BACE2: view

Function for BACE2 Gene

Molecular function for BACE2 Gene

UniProtKB/Swiss-Prot CatalyticActivity:
Broad endopeptidase specificity. Cleaves Glu-Val-Asn-Leu- -Asp-Ala-Glu-Phe in the Swedish variant of Alzheimers amyloid precursor protein.
UniProtKB/Swiss-Prot Function:
Responsible for the proteolytic processing of the amyloid precursor protein (APP). Cleaves APP, between residues 690 and 691, leading to the generation and extracellular release of beta-cleaved soluble APP, and a corresponding cell-associated C-terminal fragment which is later released by gamma-secretase. It has also been shown that it can cleave APP between residues 671 and 672.
UniProtKB/Swiss-Prot Induction:
Up-regulated in primary breast and colon tumors and liver metastasis.

Enzyme Numbers (IUBMB) for BACE2 Gene

Phenotypes From GWAS Catalog for BACE2 Gene

Gene Ontology (GO) - Molecular Function for BACE2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001540 amyloid-beta binding IBA --
GO:0004190 aspartic-type endopeptidase activity IDA 10591213
GO:0008233 peptidase activity IEA --
GO:0016787 hydrolase activity IEA --
genes like me logo Genes that share ontologies with BACE2: view
genes like me logo Genes that share phenotypes with BACE2: view

Animal Models for BACE2 Gene

MGI Knock Outs for BACE2:

Animal Model Products

  • Taconic Biosciences Mouse Models for BACE2

CRISPR Products

miRNA for BACE2 Gene

miRTarBase miRNAs that target BACE2

Inhibitory RNA Products

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for BACE2 Gene

Localization for BACE2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for BACE2 Gene

Membrane; Single-pass type I membrane protein. Golgi apparatus. Endoplasmic reticulum. Endosome. Cell surface.

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 BACE2 gene
Compartment Confidence
endoplasmic reticulum 5
golgi apparatus 5
endosome 5
plasma membrane 4
extracellular 1
mitochondrion 1
peroxisome 1

Gene Ontology (GO) - Cellular Components for BACE2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005768 endosome IEA --
GO:0005783 endoplasmic reticulum IEA --
GO:0005794 Golgi apparatus IEA,IDA 11423558
GO:0009986 cell surface IEA --
GO:0016020 membrane IEA --
genes like me logo Genes that share ontologies with BACE2: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for BACE2 Gene

Pathways & Interactions for BACE2 Gene

genes like me logo Genes that share pathways with BACE2: view

Pathways by source for BACE2 Gene

1 KEGG pathway for BACE2 Gene
1 Qiagen pathway for BACE2 Gene

Gene Ontology (GO) - Biological Process for BACE2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006508 proteolysis NAS 10749877
GO:0006509 membrane protein ectodomain proteolysis IDA 10591213
GO:0016486 peptide hormone processing NAS 10749877
GO:0030163 protein catabolic process IBA --
GO:0042985 negative regulation of amyloid precursor protein biosynthetic process IMP 12801932
genes like me logo Genes that share ontologies with BACE2: view

No data available for SIGNOR curated interactions for BACE2 Gene

Drugs & Compounds for BACE2 Gene

(17) Drugs for BACE2 Gene - From: ApexBio and DGIdb

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Amyloid Beta-Peptide (12-28) (human) Pharma 0
Amyloid Beta-Peptide (1-40) (human) Pharma Amyloid precursor protein 0
Amyloid Beta-peptide (25-35) (human) Pharma Functional domain of Aβ 0
Amyloid β-Peptide (10-20) (human) Pharma Initiates neurodegeneration in Alzheimer disease 0
Amyloid β-Protein (1-15) Pharma Principal component of amyloid 0

(10) ApexBio Compounds for BACE2 Gene

Compound Action Cas Number
Amyloid Beta-Peptide (12-28) (human) 107015-83-8
Amyloid Beta-Peptide (1-40) (human) Amyloid precursor protein 131438-79-4
Amyloid Beta-peptide (25-35) (human) Functional domain of Aβ 131602-53-4
Amyloid β-Peptide (10-20) (human) Initiates neurodegeneration in Alzheimer disease 152286-31-2
Amyloid β-Protein (1-15) Principal component of amyloid 183745-81-5
Beta-Amyloid (1-11) Amyloidogenic peptide 190436-05-6
EHT 1864 Rac family small GTPases inhibitor 754240-09-0
EUK 134 Salen-manganese complexes;SOD mimetic 81065-76-1
LY2886721 BACE inhibitor 1262036-50-9
Pepstatin A Aspartic proteinases inhibitor 26305-03-3
genes like me logo Genes that share compounds with BACE2: view

Drug Products

Transcripts for BACE2 Gene

Unigene Clusters for BACE2 Gene

Beta-site APP-cleaving enzyme 2:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for BACE2 Gene

ExUns: 1 ^ 2 ^ 3a · 3b · 3c ^ 4 ^ 5 ^ 6a · 6b · 6c ^ 7 ^ 8a · 8b · 8c ^ 9a · 9b ^ 10 ^ 11 ^ 12a · 12b
SP1: - - - - - -
SP2: - - - - - - -
SP3: - - - - - - - -
SP4: - -
SP5: - - -
SP6: - -
SP7: - - -
SP8: - -

Relevant External Links for BACE2 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for BACE2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for BACE2 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for BACE2 Gene

This gene is overexpressed in Prostate (38.7) and Pancreas (30.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for BACE2 Gene

Protein tissue co-expression partners for BACE2 Gene

NURSA nuclear receptor signaling pathways regulating expression of BACE2 Gene:


SOURCE GeneReport for Unigene cluster for BACE2 Gene:


mRNA Expression by UniProt/SwissProt for BACE2 Gene:

Tissue specificity: Brain. Present in neurons within the hippocampus, frontal cortex and temporal cortex (at protein level). Expressed at low levels in most peripheral tissues and at higher levels in colon, kidney, pancreas, placenta, prostate, stomach and trachea. Expressed at low levels in the brain. Found in spinal cord, medulla oblongata, substantia nigra and locus coruleus. Expressed in the ductal epithelium of both normal and malignant prostate.

Evidence on tissue expression from TISSUES for BACE2 Gene

  • Skin(4.7)
  • Stomach(4.4)
  • Bone marrow(4.1)
  • Nervous system(2.4)
  • Pancreas(2.2)
genes like me logo Genes that share expression patterns with BACE2: view

No data available for mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for BACE2 Gene

Orthologs for BACE2 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for BACE2 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia BACE2 33 34
  • 99.42 (n)
(Bos Taurus)
Mammalia BACE2 33 34
  • 88.58 (n)
(Canis familiaris)
Mammalia BACE2 33 34
  • 88.43 (n)
(Mus musculus)
Mammalia Bace2 33 16 34
  • 84.58 (n)
(Rattus norvegicus)
Mammalia Bace2 33
  • 83.77 (n)
(Ornithorhynchus anatinus)
Mammalia BACE2 34
  • 83 (a)
(Monodelphis domestica)
Mammalia BACE2 34
  • 67 (a)
(Gallus gallus)
Aves BACE2 33 34
  • 73.62 (n)
(Anolis carolinensis)
Reptilia BACE2 34
  • 69 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia bace2 33
  • 65.56 (n)
Str.2956 33
African clawed frog
(Xenopus laevis)
Amphibia MGC68482 33
(Danio rerio)
Actinopterygii BACE2 (2 of 2) 34
  • 68 (a)
zgc:103530 33
  • 63.37 (n)
bace2 34
  • 52 (a)
wufi26d02 33
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.6129 33
fruit fly
(Drosophila melanogaster)
Insecta Bace 34
  • 25 (a)
CG17134 34
  • 25 (a)
CG5860 34
  • 24 (a)
CG31926 34
  • 23 (a)
CG33128 34
  • 23 (a)
pcl 34
  • 23 (a)
CG6508 34
  • 22 (a)
CG31661 34
  • 21 (a)
CG31928 34
  • 21 (a)
CG5863 34
  • 21 (a)
CG17283 34
  • 20 (a)
(Caenorhabditis elegans)
Secernentea asp-6 34
  • 23 (a)
asp-12 34
  • 22 (a)
asp-5 34
  • 22 (a)
asp-1 34
  • 20 (a)
asp-15 34
  • 20 (a)
asp-17 34
  • 20 (a)
asp-18 34
  • 20 (a)
asp-19 34
  • 20 (a)
asp-13 34
  • 19 (a)
asp-16 34
  • 19 (a)
asp-7 34
  • 19 (a)
asp-9 34
  • 19 (a)
asp-10 34
  • 17 (a)
asp-14 34
  • 17 (a)
asp-2 34
  • 15 (a)
asp-8 34
  • 15 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes PEP4 34
  • 21 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 33 (a)
Species where no ortholog for BACE2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • 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)
  • 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)
  • 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)

Evolution for BACE2 Gene

Gene Tree for BACE2 (if available)
Gene Tree for BACE2 (if available)

Paralogs for BACE2 Gene

Paralogs for BACE2 Gene

(2) SIMAP similar genes for BACE2 Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with BACE2: view

Variants for BACE2 Gene

Sequence variations from dbSNP and Humsavar for BACE2 Gene

SNP ID Clin Chr 21 pos Variation AA Info Type
rs1000008001 -- 41,265,954(+) C/G intron_variant
rs1000019718 -- 41,174,752(+) T/C genic_upstream_transcript_variant, intron_variant
rs1000036431 -- 41,168,999(+) C/T genic_upstream_transcript_variant, intron_variant
rs1000053403 -- 41,239,379(+) T/A intron_variant
rs1000053781 -- 41,172,132(+) AAAAAA/AAAAAAA genic_upstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for BACE2 Gene

Variant ID Type Subtype PubMed ID
esv2236625 CNV deletion 18987734
esv2723482 CNV deletion 23290073
esv2723483 CNV deletion 23290073
esv2723485 CNV deletion 23290073
esv3303127 CNV mobile element insertion 20981092
esv3309043 CNV mobile element insertion 20981092
esv3404742 CNV insertion 20981092
esv3410618 CNV insertion 20981092
esv3557742 CNV deletion 23714750
nsv1072179 CNV deletion 25765185
nsv1136641 CNV deletion 24896259
nsv1144002 CNV deletion 24896259
nsv187046 CNV deletion 16902084
nsv3528 CNV insertion 18451855
nsv519019 CNV loss 19592680
nsv587492 CNV loss 21841781
nsv587493 CNV gain 21841781
nsv7347 OTHER inversion 18451855

Variation tolerance for BACE2 Gene

Residual Variation Intolerance Score: 13.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.78; 16.52% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for BACE2 Gene

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 BACE2 Gene

Disorders for BACE2 Gene

MalaCards: The human disease database

(4) MalaCards diseases for BACE2 Gene - From: DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
down syndrome
  • trisomy 21
alzheimer disease
  • ad
  • myopathy, familial idiopathic inflammatory; iim
inclusion body myositis
  • ibm
- elite association - COSMIC cancer census association via MalaCards
Search BACE2 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for BACE2

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 BACE2: view

No data available for UniProtKB/Swiss-Prot and Genatlas for BACE2 Gene

Publications for BACE2 Gene

  1. A new aspartyl protease on 21q22.3, BACE2, is highly similar to Alzheimer's amyloid precursor protein beta-secretase. (PMID: 10965118) Solans A … de La Luna S (Cytogenetics and cell genetics 2000) 2 3 4 22 58
  2. Lack of association between the polymorphisms of beta-site APP-cleaving enzyme 2 (BACE2) 5'-flanking region and sporadic Alzheimer's disease. (PMID: 19124009) Yu Y … Jia J (Brain research 2009) 3 22 44 58
  3. Crystal structure of human BACE2 in complex with a hydroxyethylamine transition-state inhibitor. (PMID: 16305800) Ostermann N … Gerhartz B (Journal of molecular biology 2006) 3 4 22 58
  4. BACE2, as a novel APP theta-secretase, is not responsible for the pathogenesis of Alzheimer's disease in Down syndrome. (PMID: 16816112) Sun X … Song W (FASEB journal : official publication of the Federation of American Societies for Experimental Biology 2006) 3 4 22 58
  5. Reticulons RTN3 and RTN4-B/C interact with BACE1 and inhibit its ability to produce amyloid beta-protein. (PMID: 16965550) Murayama KS … Araki W (The European journal of neuroscience 2006) 3 4 22 58

Products for BACE2 Gene

Sources for BACE2 Gene

Loading form....