chr1:227071518:C>T Detail (hg19) (PSEN2)
Information
Genome
Assembly | Position |
---|---|
hg19 | chr1:227,071,518-227,071,518 |
hg38 | chr1:226,883,817-226,883,817 View the variant detail on this assembly version. |
HGVS
Type | Transcript | Protein |
---|---|---|
RefSeq | NM_012486.2:c.254C>T | NP_036618.2:p.Ala85Val |
NM_000447.2:c.254C>T | NP_000438.2:p.Ala85Val | |
Ensemble | ENST00000422240.6:c.254C>T | ENST00000422240.6:p.Ala85Val |
Summary
MGeND
Clinical significance | |
Variant entry | |
GWAS entry | |
Disease area statistics | Show details |
Frequency
JP | HGVD:<0.001 |
ToMMo:<0.001 | |
NCBN:[No Data.] | |
NCBN(Hondo):[No Data.] | |
NCBN(Ryukyu):[No Data.] | |
East asia | ExAC:<0.001 |
Prediction
ClinVar
Clinical Significance |
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Review star | ![]() |
Show details |
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
CIViC
[No Data.]
DisGeNET
Score | Disease name | Description | Source | Pubmed | Links |
---|---|---|---|---|---|
0.360 | Alzheimer disease 4 | NA | CLINVAR | Detail | |
<0.001 | Mild cognitive disorder | Genetic analysis showed a novel PSEN2 A85V mutation present in the proband and i... | BeFree | 18427071 | Detail |
Annotation
Annotations
Descrption | Source | Links |
---|---|---|
NM_000447.3(PSEN2):c.254C>T (p.Ala85Val) AND Alzheimer disease 4 | ClinVar | Detail |
NM_000447.3(PSEN2):c.254C>T (p.Ala85Val) AND not provided | ClinVar | Detail |
NA | DisGeNET | Detail |
Genetic analysis showed a novel PSEN2 A85V mutation present in the proband and in all analyzed affec... | DisGeNET | Detail |
Overlapped Transcript Coordinates
Gene | Transcript ID | Exon Number | Chromosome | Start | Stop | Type | Amino Mutation | Transcript Position | Links |
---|
Overlapped Transcript
Gene | Transcript ID | Chromosome | Start | Stop | Links |
---|
- Gene
- -
- dbSNP
- rs63750048 dbSNP
- Genome
- hg19
- Position
- chr1:227,071,518-227,071,518
- Variant Type
- snv
- Reference Allele
- C
- Alternative Allele
- T
- Filtering Status (HGVD)
- PASS
- Filtering Status (HGVD)
- LowQual
- # of samples (HGVD)
- 1209
- Mean of sample read depth (HGVD)
- 74.17
- Standard deviation of sample read depth (HGVD)
- 34.21
- Number of reference allele (HGVD)
- 2417
- Number of alternative allele (HGVD)
- 1
- Allele Frequency (HGVD)
- 4.1356492969396195E-4
- Gene Symbol (HGVD)
- PSEN2
- ToMMo VCF FILTER column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- PASS
- Total VCF ID column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- rs63750048
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.0002
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 4
- Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16760
- East Asian Chromosome Counts (ExAC)
- 8652
- East Asian Allele Counts (ExAC)
- 0
- East Asian Heterozygous Counts (ExAC)
- 0
- East Asian Homozygous Counts (ExAC)
- 0
- East Asian Allele Frequency (ExAC)
- 0.0
- Chromosome Counts in All Race (ExAC)
- 121282
- Allele Counts in All Race (ExAC)
- 1
- Heterozygous Counts in All Race (ExAC)
- 1
- Homozygous Counts in All Race (ExAC)
- 0
- Allele Frequency in All Race (ExAC)
- 8.245246615326264E-6
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