Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene SNPs miRNA Transcription factors Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.	5664
Gene name Gene Name - the full gene name approved by the HGNC.	Presenilin 2
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.	PSEN2
Synonyms (NCBI Gene) Gene synonyms aliases	AD3L, AD4, CMD1V, PS2, STM2
Chromosome Chromosome number	1
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.	1q42.13
Summary Summary of gene provided in NCBI Entrez Gene.	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

Show/Hide all(16)

SNP ID	Visualize variation	Clinical significance	Consequence
rs28936379	A>C,G,T	Pathogenic, not-provided	Coding sequence variant, missense variant, non coding transcript variant
rs28936380	C>G,T	Pathogenic, not-provided	Coding sequence variant, missense variant, non coding transcript variant
rs63749851	A>C	Pathogenic, likely-pathogenic	Missense variant, non coding transcript variant, coding sequence variant
rs63749884	G>A	Pathogenic, not-provided	Missense variant, non coding transcript variant, coding sequence variant
rs63750048	C>T	Pathogenic, not-provided	Missense variant, non coding transcript variant, coding sequence variant
rs63750110	A>C	Uncertain-significance, pathogenic, not-provided	Missense variant, non coding transcript variant, coding sequence variant, intron variant
rs63750197	C>T	Likely-benign, pathogenic	Missense variant, non coding transcript variant, coding sequence variant
rs63750215	A>T	Pathogenic	Missense variant, non coding transcript variant, coding sequence variant
rs63750666	C>T	Pathogenic, not-provided	Missense variant, non coding transcript variant, coding sequence variant, intron variant
rs143912759	C>A,T	Conflicting-interpretations-of-pathogenicity, uncertain-significance	Intron variant, coding sequence variant, non coding transcript variant, missense variant
rs145010538	C>G	Conflicting-interpretations-of-pathogenicity, uncertain-significance	Coding sequence variant, synonymous variant, non coding transcript variant
rs188598190	G>A	Conflicting-interpretations-of-pathogenicity	Missense variant, coding sequence variant, non coding transcript variant
rs200610057	C>T	Conflicting-interpretations-of-pathogenicity, uncertain-significance	Coding sequence variant, synonymous variant, non coding transcript variant
rs202178897	G>A,T	Conflicting-interpretations-of-pathogenicity	Non coding transcript variant, missense variant, coding sequence variant
rs866044092	G>A	Likely-pathogenic, uncertain-significance	Missense variant, coding sequence variant, non coding transcript variant
rs1553268799	TGA>-	Likely-pathogenic	Intron variant, splice donor variant

Show/Hide all(48)

miRTarBase ID	miRNA	Experiments
MIRT1269617	hsa-miR-3163	CLIP-seq
MIRT1269618	hsa-miR-4484	CLIP-seq
MIRT1269619	hsa-miR-548an	CLIP-seq
MIRT1269620	hsa-miR-1276	CLIP-seq
MIRT1269621	hsa-miR-183	CLIP-seq
MIRT1269622	hsa-miR-30a	CLIP-seq
MIRT1269623	hsa-miR-30b	CLIP-seq
MIRT1269624	hsa-miR-30c	CLIP-seq
MIRT1269625	hsa-miR-30d	CLIP-seq
MIRT1269626	hsa-miR-30e	CLIP-seq
MIRT1269627	hsa-miR-3663-3p	CLIP-seq
MIRT1269628	hsa-miR-4487	CLIP-seq
MIRT1269629	hsa-miR-4726-3p	CLIP-seq
MIRT1269630	hsa-miR-4727-5p	CLIP-seq
MIRT1269631	hsa-miR-4755-3p	CLIP-seq
MIRT1269632	hsa-miR-548a-3p	CLIP-seq
MIRT1269633	hsa-miR-548e	CLIP-seq
MIRT1269634	hsa-miR-548f	CLIP-seq
MIRT1269635	hsa-miR-764	CLIP-seq
MIRT2079248	hsa-miR-134	CLIP-seq
MIRT2079249	hsa-miR-3118	CLIP-seq
MIRT2079250	hsa-miR-3164	CLIP-seq
MIRT2079251	hsa-miR-4302	CLIP-seq
MIRT2079252	hsa-miR-4519	CLIP-seq
MIRT2079253	hsa-miR-4530	CLIP-seq
MIRT2079254	hsa-miR-4700-3p	CLIP-seq
MIRT2079255	hsa-miR-4773	CLIP-seq
MIRT2457303	hsa-miR-3183	CLIP-seq
MIRT1269627	hsa-miR-3663-3p	CLIP-seq
MIRT2457304	hsa-miR-3925-3p	CLIP-seq
MIRT2457305	hsa-miR-4723-3p	CLIP-seq
MIRT1269629	hsa-miR-4726-3p	CLIP-seq
MIRT1269635	hsa-miR-764	CLIP-seq
MIRT2457306	hsa-miR-766	CLIP-seq
MIRT1269622	hsa-miR-30a	CLIP-seq
MIRT1269623	hsa-miR-30b	CLIP-seq
MIRT1269624	hsa-miR-30c	CLIP-seq
MIRT1269625	hsa-miR-30d	CLIP-seq
MIRT1269626	hsa-miR-30e	CLIP-seq
MIRT1269620	hsa-miR-1276	CLIP-seq
MIRT1269622	hsa-miR-30a	CLIP-seq
MIRT1269623	hsa-miR-30b	CLIP-seq
MIRT1269624	hsa-miR-30c	CLIP-seq
MIRT1269625	hsa-miR-30d	CLIP-seq
MIRT1269626	hsa-miR-30e	CLIP-seq
MIRT2688821	hsa-miR-4477b	CLIP-seq
MIRT1269628	hsa-miR-4487	CLIP-seq
MIRT1269630	hsa-miR-4727-5p	CLIP-seq

Transcription factors

Show/Hide all(1)

Transcription factor	Regulation	Reference
EGR1	Unknown	14585504

Show/Hide all(48)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000139	Component	Golgi membrane	IEA
GO:0000776	Component	Kinetochore	IDA	9298903
GO:0000776	Component	Kinetochore	IEA
GO:0001666	Process	Response to hypoxia	IEA
GO:0005515	Function	Protein binding	IPI	9223340, 10366599, 10748169, 12297508, 21163940, 32814053
GO:0005637	Component	Nuclear inner membrane	IDA	9298903
GO:0005769	Component	Early endosome	IEA
GO:0005783	Component	Endoplasmic reticulum	IDA	15274632
GO:0005783	Component	Endoplasmic reticulum	IEA
GO:0005789	Component	Endoplasmic reticulum membrane	IEA
GO:0005794	Component	Golgi apparatus	IDA	15274632
GO:0005794	Component	Golgi apparatus	IEA
GO:0005813	Component	Centrosome	IDA	9298903
GO:0005886	Component	Plasma membrane	IDA	15274632
GO:0005886	Component	Plasma membrane	TAS
GO:0006508	Process	Proteolysis	IEA
GO:0006509	Process	Membrane protein ectodomain proteolysis	IBA
GO:0006509	Process	Membrane protein ectodomain proteolysis	IDA	15274632
GO:0006509	Process	Membrane protein ectodomain proteolysis	IEA
GO:0007219	Process	Notch signaling pathway	IBA
GO:0007219	Process	Notch signaling pathway	IEA
GO:0007220	Process	Notch receptor processing	IEA
GO:0007220	Process	Notch receptor processing	TAS	15274632
GO:0008021	Component	Synaptic vesicle	IEA
GO:0008233	Function	Peptidase activity	IEA
GO:0016020	Component	Membrane	HDA	19946888
GO:0016020	Component	Membrane	IEA
GO:0016485	Process	Protein processing	IBA
GO:0016485	Process	Protein processing	IDA	15274632, 27608597
GO:0016485	Process	Protein processing	IEA
GO:0016787	Function	Hydrolase activity	IEA
GO:0031965	Component	Nuclear membrane	IEA
GO:0032991	Component	Protein-containing complex	IDA	9632714
GO:0034205	Process	Amyloid-beta formation	IBA
GO:0034205	Process	Amyloid-beta formation	IDA	27608597
GO:0035556	Process	Intracellular signal transduction	IEA
GO:0042500	Function	Aspartic endopeptidase activity, intramembrane cleaving	IBA
GO:0042500	Function	Aspartic endopeptidase activity, intramembrane cleaving	IEA
GO:0042734	Component	Presynaptic membrane	IEA
GO:0042987	Process	Amyloid precursor protein catabolic process	IDA	27608597
GO:0042987	Process	Amyloid precursor protein catabolic process	IEA
GO:0042987	Process	Amyloid precursor protein catabolic process	TAS	15274632
GO:0055074	Process	Calcium ion homeostasis	IBA
GO:0070765	Component	Gamma-secretase complex	IBA
GO:0070765	Component	Gamma-secretase complex	IDA	12297508
GO:0097060	Component	Synaptic membrane	IEA
GO:0110097	Process	Regulation of calcium import into the mitochondrion	IMP	21285369
GO:1990456	Process	Mitochondrion-endoplasmic reticulum membrane tethering	IMP	21285369

MIM	HGNC	e!Ensembl
600759	9509	ENSG00000143801

Protein

UniProt ID

P49810

Protein name

Presenilin-2 (PS-2) (EC 3.4.23.-) (AD3LP) (AD5) (E5-1) (STM-2) [Cleaved into: Presenilin-2 NTF subunit; Presenilin-2 CTF subunit]

Protein function

Probable catalytic subunit of the gamma-secretase complex, an endoprotease complex that catalyzes the intramembrane cleavage of integral membrane proteins such as Notch receptors and APP (amyloid-beta precursor protein). Requires the other membe

PDB

7Y5X , 7Y5Z

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF01080	Presenilin	82 → 330	Presenilin	Family
PF01080	Presenilin	319 → 438	Presenilin	Family

Tissue specificity

TISSUE SPECIFICITY: 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. {ECO:0000269|PubMed:8574969}.

Sequence

MLTFMASDSEEEVCDERTSLMSAESPTPRSCQEGRQGPEDGENTAQWRSQENEEDGEEDP
DRYVCSGVPGRPPGLEEELTLKYGAKHVIMLFVPVTLCMIVVVATIKSVRFYTEKNGQLI
YTPFTEDTPSVGQRLLNSVLNTLIMISVIVVMTIFLVVLYKYRCYKFIHGWLIMSSLMLL
FLFTYIYLGEVLKTYNVAMDYPTLLLTVWNFGAVGMVCIHWKGPLVLQQAYLIMISALMA
LVFIKYLPEWSAWVILGAISVYDLVAVLCPKGPLRMLVETAQERNEPIFPALIYSSAMVW
TVGMAKLDPSSQGALQLPYDPEMEEDSYDSFGEPSYPEVFEPPLTGYPGEELEEEEERGV
KLGLGDFIFYSVLVGKAAATGSGDWNTTLACFVAILIGLCLTLLLLAVFKKALPALPISI
TFGLIFYFSTDNLVRPFMDTLASHQLYI

Sequence length

448

Interactions

View interactions

	KEGG		Reactome
	Notch signaling pathway Neurotrophin signaling pathway Alzheimer disease Pathways of neurodegeneration - multiple diseases		Nuclear signaling by ERBB4 Regulated proteolysis of p75NTR NRIF signals cell death from the nucleus Constitutive Signaling by NOTCH1 PEST Domain Mutants Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants EPH-ephrin mediated repulsion of cells NOTCH3 Activation and Transmission of Signal to the Nucleus Noncanonical activation of NOTCH3

Show/Hide Causal Diseases (1)

Disease merge term	Disease name	dbSNP ID	References
Causal Diseases caused by PATHOGENIC or LIKELY PATHOGENIC variants from ClinVar only
Alzheimer disease	alzheimer disease 4	rs63750215, rs28936379, rs63749851, rs63749884, rs28936380, rs63750048, rs1553268799	N/A

Show/Hide Unknown Diseases (6)

Disease merge term	Disease name	Evidence	References	Source
Unknown Includes: (1) ClinVar NON-pathogenic variants (Uncertain, Benign, Conflicting, VUS), (2) GenCC associations, (3) GWAS associations, (4) CBGDA evidence-based associations. NOTE: Diseases with pathogenic evidence are excluded to avoid conflicts.
Cardiomyopathy	Primary dilated cardiomyopathy	N/A	N/A	ClinVar
Dilated Cardiomyopathy	Dilated cardiomyopathy 1V, Dilated Cardiomyopathy, Dominant	N/A	N/A	ClinVar
Inflammatory Bowel Disease	Inflammatory bowel disease	N/A	N/A	GWAS
Myopathy	dilated cardiomyopathy	N/A	N/A	GenCC
Ulcerative colitis	Ulcerative colitis	N/A	N/A	GWAS
vascular dementia	Vascular dementia	N/A	N/A	ClinVar

Show/Hide Text Mining Associations (49)

Disease Name	Relationship Type	References
Associations from Text Mining Disease associations identified through Pubtator
AA amyloidosis	Associate	11126197, 28243073, 36120786
Agnosia	Associate	33973882
Agraphia	Associate	35491795
Alzheimer Disease	Associate	10349860, 10366599, 10393846, 10404513, 10409650, 10595683, 10620705, 10652366, 10880397, 11126197, 12754354, 15009634, 15492223, 15569262, 15685448 View all (138 more)
Alzheimer Disease	Stimulate	22312439
Alzheimer disease type 1	Associate	18580586, 30045758, 33678657, 35491795
Amyloid angiopathy	Associate	20375137
Apraxias	Associate	35491795
Asphyxia	Associate	34067945
Atrophy	Associate	26507310, 33973882, 34102969
Autistic Disorder	Inhibit	24853428
CADASIL	Associate	36175824
Cardiomyopathies	Associate	20458009
Cardiomyopathy Dilated	Associate	17186461
Cardiomyopathy Hypertrophic	Associate	28750076, 32344918
Cardiovascular Diseases	Associate	39766777
Cerebral Hemorrhage	Associate	20375137
Cerebral Small Vessel Diseases	Associate	36175824
Cognition Disorders	Associate	35328387
Cognitive Dysfunction	Associate	30104866
Death	Associate	20375137
Dementia	Associate	20375137, 21163230, 21297263, 22312439, 22503161, 24885952, 27901073, 29476165, 29859640, 30530974, 33061333, 33203472, 34444269, 35120450
Depressive Disorder Major	Inhibit	24363250
Disease	Associate	17186461
Dyscalculia	Associate	35491795
Frontotemporal Dementia	Associate	22503161, 35752680
Frontotemporal Lobar Degeneration	Associate	22459598
Genetic Diseases Inborn	Associate	22503161
Genomic Instability	Associate	32397113
Hallucinations	Associate	39273625
Heart Failure	Associate	17186461
Hypoxia	Associate	10349860
Hypoxia Brain	Associate	15569262
Inflammation	Associate	38178159
Intellectual Disability	Associate	35491795
Lewy Body Disease	Associate	31165862, 36362122
Malformations of Cortical Development Group I	Associate	26025363
Malocclusion Angle Class III	Associate	34039391
Melanoma	Associate	39213172
Memory Disorders	Associate	36362122, 39273625
Meningomyelocele	Associate	39774454
Muscle Spasticity	Associate	22503161
Myelodysplastic Syndromes	Associate	32397113
Neoplasms	Associate	24223915
Neurodegenerative Diseases	Associate	17903177, 22489754, 29859640, 36362122
Seizures	Associate	20375137, 22503161
Stomach Neoplasms	Associate	24008668
Ventricular Fibrillation	Associate	29269939
Vision Disorders	Associate	35491795

PSEN2 (presenilin 2)