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PSEN2 (presenilin 2 (Alzheimer disease 4))

Identity

Other namesAD3L
AD4
PS2
STM2
HGNC (Hugo) PSEN2
LocusID (NCBI) 5664
Location 1q42.13
Location_base_pair Starts at 227058273 and ends at 227083804 bp from pter ( according to hg19-Feb_2009)  [Mapping]

DNA/RNA

 
  Presenilin 2 transcript, lines indicate introns and boxes exons. Untranslated regions are represented as yellow boxes and coding regions as red boxes.
Description Twelve exons, spans approximately 26.7 kb of genomic DNA in the centromere to telomere orientation, the translation initation codon is in exon 4 and the stop codon in exon 12.
Transcription mRNA of approximately 2.3 kb. Two alternatively spliced transcript variants encoding different isoforms of PSEN2 have been identified.
Pseudogene Not known.

Protein

 
  Presenilin 2 protein domains, bright blue boxes are transmembrane domains (TM).
Description The open reading frame encodes a 448 amino acid protein, with an estimated molecular weight of 50 kDa. It is a multi-spanning transmembrane protein with a predicted 9 transmembrane domains. Heterogeneous proteolytic processing generates N-terminal and C-terminal fragments.
Expression Neuronal (higher levels in hippocampus and cerebellum). Isoform 1 is seen in the placenta, skeletal muscle and heart while isoform 2 is seen in the heart, brain, placenta, liver, skeletal muscle and kidney. (In isoform 2 amino-acids 263-296 are missing).
Localisation Endoplasmic reticulum, plasma membrane, golgi apparatus.
Function Catalytic core of the gamma-secretase complex. This complex catalyses the intramembrane cleavage of single-pass membrane proteins such as Notch and the Amyloid Precursor Protein (APP) to give intracellular signaling. The released intracellular domains of Notch or APP form complexes with other proteins to regulate gene transcription.
Homology The PSEN2 gene is conserved in chimpanzee, dog, cow, mouse, rat, chicken, and zebrafish.

Mutations

Somatic 23 mutations.
Nucleotide changeDiseaseReference
Arg62HisADCruts et al., 1998; Guerreiro et al., 2008
Arg71Trp ADGuerreiro et al., 2008
Thr122ProADFinckh et al., 2000; 2005
Ser130LeuADSorbi et al., 2002; Tedde et al., 2003; Tomaino et al., 2007
Val139MetADBernardi et al., 2008
Asn141IleADLevy-Lahad et al., 1995; Rogaev et al., 1995
Met174Val ADGuerreiro et al., 2008
Ser175CysADPiscopo et al., 2008
Gln228Leu ADZekanowski et al., 2003
Met239Ile ADFinckh et al., 2000
Met239ValADRogaev et al., 1995; Marcon et al., 2004
Val393Met ADLindquist et al., 2008; 2009
Thr430MetADLleo et al., 2002; Ezquerra et al., 2003
Asp439AlaADLleo et al., 2001; 2002
Arg62HisBreast CancerTo et al., 2006
Arg71TrpBreast CancerTo et al., 2006
Tyr231Cys FTDMarcon et al., 2008; 2009
Ala85ValLBDPiscopo et al., 2008
Thr122ArgAtypical DementiaBinetti et al., 2003

Table. Mutations identified through genetic screening. AD: Alzheimer's Disease, FTD: Frontotemporal Dementia, LBD: Lewy Body Dementia.

Implicated in

Entity Breast cancer
Disease Breast cancer is the most common form of cancer for women. The cancer originates from the breast tissue where it can be a ductal carcinoma or lobular carcinoma. They can be further defined as in situ or invasive cancers.
Oncogenesis Mutations (see above).
  
Entity Alzheimer's disease
Note Mutations (see above) taken from the Alzheimer's Disease and Frontotemporal Dementia Mutation Database. Only pathogenic mutations are included.
Disease Alzheimer's disease is the most prevalent form of dementia. In affected individuals the disease causes a progressive and permanent decline in memory and cognitive abilities. Neuropathogenesis is proposed to be a result of the accumulation of amyloid-beta peptides in the brain together with increased oxidative stress and neuroinflammation. The presenilin proteins are central to the gamma-secretase cleavage of the amyloid precursor protein (APP), releasing the amyloid-beta peptide. Point mutations in the presenilin genes lead to cases of familial Alzheimer's disease (and some sporadic cases) by altering APP cleavage resulting in excess amyloid-beta formation.
 
Diagram taken from http://www.molgen.ua.ac.be/ADMutations. Coloured circles indicate mutation sites. Red: pathogenic, orange: pathogenic nature unclear, green: not pathogenic.
  
Entity Frontotemporal Dementia (FTD)
Note Mutation (see above).
Disease Frontotemporal dementia is a group of related conditions resulting from the progressive degeneration of the temporal and frontal lobes of the brain (frontotemporal lobar degeneration, FTLD), usually with the presence of abnormal intracellular protein accumulations. These areas of the brain play a significant role in decision-making, behavioral control, emotion and language. The disorder is often sporadic, familial FTD has been linked to mutations in several genes, including those encoding the microtubule-associated protein tau (MAPT), progranulin (GRN), valosin-containing protein (VCP) and charged multivescicular body protein 2B (CHMP2B).
  
Entity Lewy body Dementia (DLB)
Note Mutation (see above).
Disease Dementia with Lewy bodies is a neurodegenerative disorder associated with abnormal structures (Lewy bodies) which are clumps of alpha-synuclein and ubiquitin protein in neurons found in certain areas of the brain. In addition to dementia, patients with dementia with Lewy bodies experience hallucinations, motor impairment, and fluctuating alertness.
  

To be noted

Truncated variant PSEN2 protein (PS2V). Variant transcript lacks exon 5 due to alternative splicing. Encodes the first 119 codons of PSEN2 plus a newly generated five amino acids SSMAG. PS2V is detected in sporadic Alzheimer's disease, bi-polar and schizophrenia cases (Sato et al., 1999; Smith et al., 2004). Cell-culture experiments indicate that this variant is upregulated under hypoxic conditions (Sato et al., 1999).

External links

Nomenclature
HGNC (Hugo)PSEN2   9509
Entrez_Gene (NCBI)PSEN2  5664  presenilin 2 (Alzheimer disease 4)
Cards
AtlasPSEN2ID41883ch1q42
GeneCards (Weizmann)PSEN2
Ensembl (Hinxton)ENSG00000143801 [Gene_View]  chr1:227058273-227083804 [Contig_View]  PSEN2 [Vega]
AceView (NCBI)PSEN2
Genatlas (Paris)PSEN2
SOURCE (Stanford)NM_000447 NM_012486
Genomic and cartography
GoldenPath (UCSC)PSEN2  -  1q42.13   chr1:227058273-227083804 +  1q31-q42   [Description]    (hg19-Feb_2009)
EnsemblPSEN2 - 1q31-q42 [CytoView]
Mapping of homologs : NCBIPSEN2 [Mapview]
OMIM600759   606889   613697   
Gene and transcription
Genbank (Entrez)AF416718 AI091221 AK292299 AK301143 BC006365
RefSeq transcript (SRS)NM_000447 NM_012486
RefSeq transcript (Entrez)NM_000447 NM_012486
RefSeq genomic (SRS)AC_000133 NC_000001 NC_018912 NG_007381 NT_167186 NW_001838543 NW_004078000
RefSeq genomic (Entrez)AC_000133 NC_000001 NC_018912 NG_007381 NT_167186 NW_001838543 NW_004078000
Consensus coding sequences : CCDS (NCBI)PSEN2
Cluster EST : UnigeneHs.25363 [ SRS ] Hs.25363 [ NCBI ]
CGAP (NCI)Hs.25363
Alternative Splicing : Fast-db (Paris)GSHG0001497
Alternative Splicing GalleryENSG00000143801
Gene ExpressionPSEN2 [ NCBI-GEO ]   PSEN2 [ EBI - ARRAY_EXPRESS ]
Protein : pattern, domain, 3D structure
UniProt/SwissProtP49810 (SRS) P49810 (Uniprot)
NextProtP49810
With graphics : InterProP49810
Splice isoforms : SwissVarP49810(Swissvar)
Domains : Interpro (SRS)Pept_A22A_PS2    Peptidase_A22    Peptidase_A22A   
Domains : Interpro (EBI)Pept_A22A_PS2    Peptidase_A22    Peptidase_A22A   
Related proteins : CluSTrP49810
Domain families : Pfam (SRS)Presenilin (PF01080)   
Domain families : Pfam (Sanger)Presenilin (PF01080)   
Domain families : Pfam (NCBI)pfam01080   
Domain families : Smart (EMBL)PSN (SM00730)  
DMDM5664
Blocks (Seattle)P49810
Human Protein AtlasENSG00000143801
HPRD02860
IPIIPI00184584   IPI00218471   IPI00952873   IPI00646420   IPI00981899   IPI00377103   IPI00985117   IPI00980574   IPI00983222   
Protein Interaction databases
DIP (DOE-UCLA)P49810
IntAct (EBI)P49810
FunCoupENSG00000143801
REACTOMEPSEN2
Protein Interaction Database5664
BioGRIDPSEN2
InParanoidP49810
Interologous Interaction database P49810
IntegromeDBPSEN2
Polymorphism : SNP, mutations, diseases
SNP Single Nucleotide Polymorphism (NCBI)PSEN2
SNP (GeneSNP Utah)PSEN2
SNP : HGBasePSEN2
Genetic variants : HAPMAPPSEN2
Somatic Mutations in Cancer : COSMICPSEN2 
CONAN: Copy Number AnalysisPSEN2 
Mutations and Diseases : HGMDPSEN2
OMIM600759    606889    613697   
GENETests600759    606889    613697   
Disease Genetic AssociationPSEN2
Huge Navigator PSEN2 [HugePedia]  PSEN2 [HugeCancerGEM]
Genomic VariantsPSEN2  PSEN2 [DGVbeta]
snp3D : Map Gene to Disease5664
General knowledge
Homologs : HomoloGenePSEN2
Homology/Alignments : Family Browser (UCSC)PSEN2
Phylogenetic Trees/Animal Genes : TreeFamPSEN2
Catalytic activity : Enzyme3.4.23.- [ Enzyme-Expasy ]   3.4.23.- [ Enzyme-SRS ]   3.4.23.- [ IntEnz-EBI ]   3.4.23.- [ BRENDA ]   3.4.23.- [ KEGG ]   
Chemical/Protein Interactions : CTD5664
Chemical/Pharm GKB GenePA33856
Clinical trialPSEN2
Cancer Resource (Charite)ENSG00000143801
Ontology : AmiGOGolgi membrane  kinetochore  response to hypoxia  cell fate specification  somitogenesis  negative regulation of protein phosphorylation  hematopoietic progenitor cell differentiation  T cell activation involved in immune response  myeloid leukocyte differentiation  endopeptidase activity  aspartic-type endopeptidase activity  protein binding  nuclear inner membrane  mitochondrial inner membrane  lysosomal membrane  endoplasmic reticulum  endoplasmic reticulum membrane  Golgi apparatus  centrosome  cytosol  plasma membrane  integral to plasma membrane  cell cortex  membrane protein ectodomain proteolysis  calcium ion transport  apoptotic process  regulation of epidermal growth factor-activated receptor activity  Notch signaling pathway  Notch receptor processing  Notch receptor processing  memory  cell surface  protein transport  apical plasma membrane  protein processing  dorsal/ventral neural tube patterning  Z disc  embryonic limb morphogenesis  axon  growth cone  forebrain development  membrane protein intracellular domain proteolysis  neuromuscular junction  endoplasmic reticulum calcium ion homeostasis  ciliary rootlet  intracellular signal transduction  locomotion  anagen  amyloid precursor protein catabolic process  amyloid precursor protein catabolic process  neuronal cell body  positive regulation of apoptotic process  negative regulation of apoptotic process  positive regulation of catalytic activity  dendritic shaft  protein complex  regulation of protein binding  membrane raft  nerve growth factor receptor signaling pathway  regulation of synaptic plasticity  lung alveolus development  perinuclear region of cytoplasm  thymus development  brain morphogenesis  beta-amyloid metabolic process  positive regulation of coagulation  T cell receptor signaling pathway  cardiac muscle contraction  
Ontology : EGO-EBIGolgi membrane  kinetochore  response to hypoxia  cell fate specification  somitogenesis  negative regulation of protein phosphorylation  hematopoietic progenitor cell differentiation  T cell activation involved in immune response  myeloid leukocyte differentiation  endopeptidase activity  aspartic-type endopeptidase activity  protein binding  nuclear inner membrane  mitochondrial inner membrane  lysosomal membrane  endoplasmic reticulum  endoplasmic reticulum membrane  Golgi apparatus  centrosome  cytosol  plasma membrane  integral to plasma membrane  cell cortex  membrane protein ectodomain proteolysis  calcium ion transport  apoptotic process  regulation of epidermal growth factor-activated receptor activity  Notch signaling pathway  Notch receptor processing  Notch receptor processing  memory  cell surface  protein transport  apical plasma membrane  protein processing  dorsal/ventral neural tube patterning  Z disc  embryonic limb morphogenesis  axon  growth cone  forebrain development  membrane protein intracellular domain proteolysis  neuromuscular junction  endoplasmic reticulum calcium ion homeostasis  ciliary rootlet  intracellular signal transduction  locomotion  anagen  amyloid precursor protein catabolic process  amyloid precursor protein catabolic process  neuronal cell body  positive regulation of apoptotic process  negative regulation of apoptotic process  positive regulation of catalytic activity  dendritic shaft  protein complex  regulation of protein binding  membrane raft  nerve growth factor receptor signaling pathway  regulation of synaptic plasticity  lung alveolus development  perinuclear region of cytoplasm  thymus development  brain morphogenesis  beta-amyloid metabolic process  positive regulation of coagulation  T cell receptor signaling pathway  cardiac muscle contraction  
Pathways : BIOCARTAHIV-I Nef: negative effector of Fas and TNF [Genes]   
Pathways : KEGGNeurodegenerative DisordersAlzheimer's diseaseNotch signaling pathway
Other databases
Probes
Litterature
PubMed171 Pubmed reference(s) in Entrez
PubGenePSEN2
iHOPPSEN2

Bibliography

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Estimation of the genetic contribution of presenilin-1 and -2 mutations in a population-based study of presenile Alzheimer disease.
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A novel mutation in the predicted TM2 domain of the presenilin 2 gene in a Spanish patient with late-onset Alzheimer's disease.
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PMID 10732806
 
A novel presenilin-2 splice variant in human Alzheimer's disease brain tissue.
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High prevalence of pathogenic mutations in patients with early-onset dementia detected by sequence analyses of four different genes.
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Variable expression of familial Alzheimer disease associated with presenilin 2 mutation M239I.
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PMID 10822446
 
A novel presenilin 2 gene mutation (D439A) in a patient with early-onset Alzheimer's disease.
Lleo A, Blesa R, Gendre J, Castellvi M, Pastor P, Queralt R, Oliva R.
Neurology. 2001 Nov 27;57(10):1926-8.
PMID 11723295
 
Identification of a second presenilin gene in zebrafish with similarity to the human Alzheimer's disease gene presenilin2.
Groth C, Nornes S, McCarty R, Tamme R, Lardelli M.
Dev Genes Evol. 2002 Nov;212(10):486-90. Epub 2002 Sep 17.
PMID 12424519
 
Frequency of mutations in the presenilin and amyloid precursor protein genes in early-onset Alzheimer disease in Spain.
Lleo A, Blesa R, Queralt R, Ezquerra M, Molinuevo JL, Pena-Casanova J, Rojo A, Oliva R.
Arch Neurol. 2002 Nov;59(11):1759-63.
PMID 12433263
 
Novel presenilin 1 and presenilin 2 mutations in early-onset Alzheimer's disease families.
Sorbi S, Tedde A, Nacmias B, Ciantelli M, Caffarra P, Ghidoni E, Bracco L, Piccini C.
Neurobiology of Aging. 2002; 23(1S):S312.
 
Atypical dementia associated with a novel presenilin-2 mutation.
Binetti G, Signorini S, Squitti R, Alberici A, Benussi L, Cassetta E, Frisoni GB, Barbiero L, Feudatari E, Nicosia F, Testa C, Zanetti O, Gennarelli M, Perani D, Anchisi D, Ghidoni R, Rossini PM.
Ann Neurol. 2003 Dec;54(6):832-6.
PMID 14681895
 
A novel mutation in the PSEN2 gene (T430M) associated with variable expression in a family with early-onset Alzheimer disease.
Ezquerra M, Lleo A, Castellvi M, Queralt R, Santacruz P, Pastor P, Molinuevo JL, Blesa R, Oliva R.
Arch Neurol. 2003 Aug;60(8):1149-51.
PMID 12925374
 
Developmental control of Presenilin1 expression, endoproteolysis, and interaction in zebrafish embryos.
Nornes S, Groth C, Camp E, Ey P, Lardelli M.
Exp Cell Res. 2003 Sep 10;289(1):124-32.
PMID 12941610
 
Identification of new presenilin gene mutations in early-onset familial Alzheimer disease.
Tedde A, Nacmias B, Ciantelli M, Forleo P, Cellini E, Bagnoli S, Piccini C, Caffarra P, Ghidoni E, Paganini M, Bracco L, Sorbi S.
Arch Neurol. 2003 Nov;60(11):1541-4.
PMID 14623725
 
Mutations in presenilin 1, presenilin 2 and amyloid precursor protein genes in patients with early-onset Alzheimer's disease in Poland.
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PMID 14769392
 
Neuropathological and clinical phenotype of an Italian Alzheimer family with M239V mutation of presenilin 2 gene.
Marcon G, Giaccone G, Cupidi C, Balestrieri M, Beltrami CA, Finato N, Bergonzi P, Sorbi S, Bugiani O, Tagliavini F.
J Neuropathol Exp Neurol. 2004 Mar;63(3):199-209.
PMID 15055444
 
Expression of truncated presenilin 2 splice variant in Alzheimer's disease, bipolar disorder, and schizophrenia brain cortex.
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Novel mutations and repeated findings of mutations in familial Alzheimer disease.
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Neurogenetics. 2005 May;6(2):85-9. Epub 2005 Mar 18.
PMID 15776278
 
Functional characterization of novel presenilin-2 variants identified in human breast cancers.
To MD, Gokgoz N, Doyle TG, Donoviel DB, Knight JA, Hyslop PS, Bernstein A, Andrulis IL.
Oncogene. 2006 Jun 15;25(25):3557-64. Epub 2006 Feb 13.
PMID 16474849
 
Presenilin 2 Ser130Leu mutation in a case of late-onset "sporadic" Alzheimer's disease.
Tomaino C, Bernardi L, Anfossi M, Costanzo A, Ferrise F, Gallo M, Geracitano S, Maletta R, Curcio SA, Mirabelli M, Colao R, Frangipane F, Puccio G, Calignano C, Muraca MG, Paonessa A, Smirne N, Leotta A, Bruni AC.
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PMID 17345043
 
Late onset familial Alzheimer's disease: novel presenilin 2 mutation and PS1 E318G polymorphism.
Bernardi L, Tomaino C, Anfossi M, Gallo M, Geracitano S, Puccio G, Colao R, Frangipane F, Mirabelli M, Smirne N, Giovanni Maletta R, Bruni AC.
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PMID 18350357
 
Molecular genetics of Alzheimer's disease: an update.
Brouwers N, Sleegers K, Van Broeckhoven C.
Ann Med. 2008;40(8):562-83. (REVIEW)
PMID 18608129
 
A novel presenilin 2 mutation (V393M) in early-onset dementia with profound language impairment.
Lindquist SG, Hasholt L, Bahl JM, Heegaard NH, Andersen BB, Norremolle A, Stokholm J, Schwartz M, Batbayli M, Laursen H, Pardossi-Piquard R, Chen F, St George-Hyslop P, Waldemar G, Nielsen JE.
Eur J Neurol. 2008 Oct;15(10):1135-9. Epub 2008 Aug 22.
PMID 18727676
 
Interference with splicing of Presenilin transcripts has potent dominant negative effects on Presenilin activity.
Nornes S, Newman M, Verdile G, Wells S, Stoick-Cooper CL, Tucker B, Frederich-Sleptsova I, Martins R, Lardelli M.
Hum Mol Genet. 2008 Feb 1;17(3):402-12. Epub 2007 Nov 2.
PMID 17981814
 
A novel PSEN2 mutation associated with a peculiar phenotype.
Piscopo P, Marcon G, Piras MR, Crestini A, Campeggi LM, Deiana E, Cherchi R, Tanda F, Deplano A, Vanacore N, Tagliavini F, Pocchiari M, Giaccone G, Confaloni A.
Neurology. 2008 Apr 22;70(17):1549-54.
PMID 18427071
 
Genetic testing in familial AD and FTD: mutation and phenotype spectrum in a Danish cohort.
Lindquist SG, Schwartz M, Batbayli M, Waldemar G, Nielsen JE.
Clin Genet. 2009 Aug;76(2):205-9. Epub 2009 Jul 29.
PMID 19659892
 
A novel Italian presenilin 2 gene mutation with prevalent behavioral phenotype.
Marcon G, Di Fede G, Giaccone G, Rossi G, Giovagnoli AR, Maccagnano E, Tagliavini F.
J Alzheimers Dis. 2009 Mar;16(3):509-11.
PMID 19276543
 
Independent and cooperative action of Psen2 with Psen1 in zebrafish embryos.
Nornes S, Newman M, Wells S, Verdile G, Martins RN, Lardelli M.
Exp Cell Res. 2009 Oct 1;315(16):2791-801. Epub 2009 Jun 27.
PMID 19563801
 
Genetic screening of Alzheimer's disease genes in Iberian and African samples yields novel mutations in presenilins and APP.
Guerreiro RJ, Baquero M, Blesa R, Boada M, Bras JM, Bullido MJ, Calado A, Crook R, Ferreira C, Frank A, Gomez-Isla T, Hernandez I, Lleo A, Machado A, Martinez-Lage P, Masdeu J, Molina-Porcel L, Molinuevo JL, Pastor P, Perez-Tur J, Relvas R, Oliveira CR, Ribeiro MH, Rogaeva E, Sa A, Samaranch L, Sanchez-Valle R, Santana I, Tarraga L, Valdivieso F, Singleton A, Hardy J, Clarimon J.
Neurobiol Aging. 2010 May;31(5):725-731. Epub 2008 Jul 30.
PMID 18667258
 
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Contributor(s)

Written04-2010Morgan Newman
School of Molecular and Biomedical Science, The University of Adelaide, Australia

Citation

This paper should be referenced as such :
Newman M . PSEN2 (presenilin 2 (Alzheimer disease 4)). Atlas Genet Cytogenet Oncol Haematol. April 2010 .
URL : http://AtlasGeneticsOncology.org/Genes/PSEN2ID41883ch1q42.html

This paper is referenced by INIST as such :
http://documents.irevues.inist.fr/bitstream/2042/44938/1/04-2010-PSEN2ID41883ch1q42.pdf   [ Bibliographic record ]

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