| Variant ID | 619 |
|---|---|
| Entrez Gene ID | 5664 |
| Gene | PSEN2 (GeneCards) |
| Location | hg19 1:227073271-227073271
hg38 1:226885570-226885570 |
| Disease | Asymptomatic |
| Method | HiSeq2000 MiSeq |
| Mutation(HGVS format) | NC_000001.10:g.227073271 C>T (Genome Assembly: hg19) |
| Exon or Intron | NA |
|---|---|
| Position in protein | 130 |
| Amino acid changes in protein | S > L |
| Position in cDNA | NA |
| Changes in cDNA | NA > NA |
| mRNA accession | NM_000447.2 |
| mRNA length | 21 |
| Reference length | 249250621 |
| MAF in gnomAD genome (version 2.0.1) | 0.0005 |
|---|---|
| SNP ID (dbSNP ID version 137) | rs63750197 |
| EIGEN score | 0.3947 |
| CADD Raw score (version 1.3) | 6.541658 (Deleterious) |
| FATHMM raw prediction score | 0.98268 (Tolerated) |
| SIFT score | 0.012 (Deleterious) |
| LRT score | 0 (Deleterious) |
| MutationTaster score | 1 (Deleterious) |
| MutatioinAssessor score | 3.225 (Deleterious) |
| PROVEAN score | -3.55 (Deleterious) |
| MetaSVM score | 1.134 (Deleterious) |
| MetaLR score | 0.973 (Deleterious) |
| MCAP score | 0.775 (Deleterious) |
| FitCons score | 0.722 (Highly Significant p < 0.003 ) |
| Genomic Evolutionary Rate Profiling (GERP) score | 5.14 |
| PhyloP score based on multiple alignment of 100 vertebrates | 4.677 |
| PhastCons score based on multiple alignment of 100 vertebrates | 0.996 |
| SiPhy log transformed odds ratio on multiple alignment of 29 mammals | 14.349 |
| Deleterious probability by iFish2 | 0.937 (Deleterious) |
| Deleterious probability by DeFine | 0.9578 (Deleterious) |
| Entrez Gene ID | 5664 (NCBI Gene) |
|---|---|
| Official Gene Symbol | PSEN2 (GeneCards) |
| Number of variants in PSEN2 in this database | 3 (view all the variants) |
| Full name | presenilin 2 |
| Band | 1q42.13 |
| Other IDs | Vega: OTTHUMG00000037563 OMIM: 600759 HGNC: HGNC:9509 Ensembl: ENSG00000143801 |
| Other names | 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] |
| Individual ID | 25937274.03 (view all the variants in this individual) |
|---|---|
| Pubmed ID | 25937274 |
| Whose mosaic mutation | Normal |
| Phenotype | 1 |
| Disease | Asymptomatic |
| OMIM ID |
| Pubmed ID | 25937274 |
|---|---|
| Title | On the identification of low allele frequency mosaic mutations in the brains of Alzheimer's disease patients. |
| Journal | Alzheimers Dement |
| Publication date | 2015.11 |
| Disease | Alzheimer disease |