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PSEN2 presenilin 2 [ Homo sapiens (human) ]

Gene ID: 5664, updated on 28-Mar-2020

Summary

Official Symbol
PSEN2provided by HGNC
Official Full Name
presenilin 2provided by HGNC
Primary source
HGNC:HGNC:9509
See related
Ensembl:ENSG00000143801 MIM:600759
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
AD4; PS2; AD3L; STM2; CMD1V
Summary
Alzheimer's disease (AD) patients with an inherited form of the disease carry mutations in the presenilin proteins (PSEN1 or PSEN2) or the amyloid precursor protein (APP). These disease-linked mutations result in increased production of the longer form of amyloid-beta (main component of amyloid deposits found in AD brains). Presenilins are postulated to regulate APP processing through their effects on gamma-secretase, an enzyme that cleaves APP. Also, it is thought that the presenilins are involved in the cleavage of the Notch receptor such that, they either directly regulate gamma-secretase activity, or themselves act are protease enzymes. Two alternatively spliced transcript variants encoding different isoforms of PSEN2 have been identified. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in testis (RPKM 4.6), prostate (RPKM 4.4) and 25 other tissues See more
Orthologs

Genomic context

See PSEN2 in Genome Data Viewer
Location:
1q42.13
Exon count:
16
Annotation release Status Assembly Chr Location
109.20200228 current GRCh38.p13 (GCF_000001405.39) 1 NC_000001.11 (226870572..226903829)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (227057885..227083804)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 12356 Neighboring gene uncharacterized LOC105373119 Neighboring gene uncharacterized LOC107985354 Neighboring gene coenzyme Q8A Neighboring gene glucose-dependent insulinotropic receptor-like

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

HIV-1 interactions

Replication interactions

Interaction Pubs
Knockdown of presenilin 2 (Alzheimer disease 4, PSEN2) by siRNA inhibits the early stages of HIV-1 replication in 293T cells infected with VSV-G pseudotyped HIV-1 PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
aspartic endopeptidase activity, intramembrane cleaving IEA
Inferred from Electronic Annotation
more info
 
endopeptidase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
Notch receptor processing IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Notch receptor processing TAS
Traceable Author Statement
more info
PubMed 
Notch receptor processing, ligand-dependent TAS
Traceable Author Statement
more info
 
amyloid precursor protein catabolic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
amyloid precursor protein catabolic process TAS
Traceable Author Statement
more info
PubMed 
amyloid-beta metabolic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
calcium ion transport IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
ephrin receptor signaling pathway TAS
Traceable Author Statement
more info
 
intracellular signal transduction IEA
Inferred from Electronic Annotation
more info
 
membrane protein ectodomain proteolysis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
membrane protein ectodomain proteolysis IDA
Inferred from Direct Assay
more info
PubMed 
membrane protein intracellular domain proteolysis TAS
Traceable Author Statement
more info
 
mitochondrion-endoplasmic reticulum membrane tethering IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of apoptotic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of apoptotic process TAS
Traceable Author Statement
more info
 
positive regulation of catalytic activity IDA
Inferred from Direct Assay
more info
PubMed 
protein processing IDA
Inferred from Direct Assay
more info
PubMed 
regulation of calcium import into the mitochondrion IMP
Inferred from Mutant Phenotype
more info
PubMed 
response to hypoxia IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
Golgi apparatus IDA
Inferred from Direct Assay
more info
PubMed 
Golgi membrane IEA
Inferred from Electronic Annotation
more info
 
Z disc IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
apical plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
axon IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cell cortex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cell surface IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
centrosome IDA
Inferred from Direct Assay
more info
PubMed 
ciliary rootlet IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
dendritic shaft IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
early endosome IEA
Inferred from Electronic Annotation
more info
 
endoplasmic reticulum IDA
Inferred from Direct Assay
more info
PubMed 
endoplasmic reticulum membrane IEA
Inferred from Electronic Annotation
more info
 
growth cone IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
integral component of plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
integral component of plasma membrane IDA
Inferred from Direct Assay
more info
PubMed 
integral component of presynaptic membrane IEA
Inferred from Electronic Annotation
more info
 
kinetochore IDA
Inferred from Direct Assay
more info
PubMed 
lysosomal membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
membrane HDA PubMed 
membrane raft IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
mitochondrial inner membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
neuromuscular junction IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
neuronal cell body IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nuclear inner membrane IDA
Inferred from Direct Assay
more info
PubMed 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
perinuclear region of cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
plasma membrane TAS
Traceable Author Statement
more info
 
protein-containing complex IDA
Inferred from Direct Assay
more info
PubMed 
synaptic vesicle IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
presenilin-2
Names
AD3LP
AD5
Alzheimer disease 4
E5-1
PS-2
STM-2
NP_000438.2
NP_036618.2
XP_005273256.1
XP_016857324.1
XP_016857325.1

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_007381.1 RefSeqGene

    Range
    5045..30527
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_000447.3NP_000438.2  presenilin-2 isoform 1

    See identical proteins and their annotated locations for NP_000438.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (1).
    Source sequence(s)
    BT006984, DA198818, DA915823, L43964
    Consensus CDS
    CCDS1556.1
    UniProtKB/Swiss-Prot
    P49810
    Related
    ENSP00000355747.3, ENST00000366783.8
    Conserved Domains (1) summary
    pfam01080
    Location:82438
    Presenilin; Presenilin
  2. NM_012486.2NP_036618.2  presenilin-2 isoform 2

    See identical proteins and their annotated locations for NP_036618.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate splice acceptor site at exon 10 compared to transcript variant 1, resulting in an isoform (2) that is 1 aa shorter than isoform 1.
    Source sequence(s)
    AI091221, DA198818, DA915823, L43964, U34349
    Consensus CDS
    CCDS44324.1
    UniProtKB/Swiss-Prot
    P49810
    Related
    ENSP00000403737.2, ENST00000422240.6
    Conserved Domains (1) summary
    pfam01080
    Location:82437
    Presenilin; Presenilin

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p13 Primary Assembly

    Range
    226870572..226903829
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005273199.4XP_005273256.1  presenilin-2 isoform X1

    See identical proteins and their annotated locations for XP_005273256.1

    UniProtKB/Swiss-Prot
    P49810
    Related
    ENSP00000486498.1, ENST00000626989.2
    Conserved Domains (1) summary
    pfam01080
    Location:82438
    Presenilin; Presenilin
  2. XM_017001836.1XP_016857325.1  presenilin-2 isoform X2

    UniProtKB/Swiss-Prot
    P49810
    Conserved Domains (1) summary
    pfam01080
    Location:82437
    Presenilin; Presenilin
  3. XM_017001835.1XP_016857324.1  presenilin-2 isoform X1

    UniProtKB/Swiss-Prot
    P49810
    Conserved Domains (1) summary
    pfam01080
    Location:82438
    Presenilin; Presenilin

RNA

  1. XR_001737316.2 RNA Sequence

  2. XR_001737317.2 RNA Sequence

  3. XR_949150.3 RNA Sequence

  4. XR_001737318.2 RNA Sequence

  5. XR_949149.2 RNA Sequence

  6. XR_001737321.1 RNA Sequence

  7. XR_001737319.1 RNA Sequence

  8. XR_001737320.1 RNA Sequence

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