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 Pathogenic
Review star
Show details
Links
Type Database ID Link
Gene MIM 600759 OMIM
HGNC 9509 HGNC
Ensembl ENSG00000143801 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv5030084 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Pathogenic 2008-04-22 no assertion criteria provided Alzheimer disease 4 germline Detail
not provided no assertion provided not provided not provided Detail
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

DescrptionSourceLinks
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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