Database of Pathogenic Variants

Individual Information

DPVS:429.1

ID

DPVS:429.1

Clinical Significance

Pathogenic

Date Last Evaluated

2015-06-11

Clinical Significance Citation

Yagi, R. Detecting gene mutations in Japanese Alzheimer's patients by semiconductor sequencing. 2014 Neurobiol Aging. 2014 Jul;35(7):1780.e1-5. doi: 10.1016/j.neurobiolaging.2014.01.023. Epub 2014 Jan 25. PMID:24559647

Transcript

Disease

Alzheimer disease 1
OMIM:104300
MedGen:C1863052

Early onset Alzheimer's disease

Phenotype

Zygosity

single heterozygote

Allele Origin

de novo

Affected Status

yes

Sample Type

Analysis Type

SEQuencing

Collection Method

literature only

Compound heterozygous variant(s)

Data Submitter

Comment

Kensaku Kasuga, Masataka Kikuchi, Takayoshi Tokutake, Akihiro Nakaya, Toshiyuki Tezuka, Tamao Tsukie, Norikazu Hara, Akinori Miyashita, Ryozo Kuwano and Takeshi Ikeuchi. Systematic review and meta-analysis of Japanese familial Alzheimer's disease and FTDP-17. Journal of Human Genetics (2015) 60, 281-283; doi:10.1038/jhg.2015.15

VCF

VCF (GRCh37/hg19)

											##fileformat=VCFv4.0
##reference=GRCh37
##INFO=<ID=CLNALLELEID,Number=1,Type=Integer,Description="the ClinVar Allele ID">
##INFO=<ID=CLNDISDB,Number=.,Type=String,Description="Tag-value pairs of disease database name and identifier, e.g. OMIM:NNNNNN (from ClinVar)">
##INFO=<ID=CLNDN,Number=.,Type=String,Description="ClinVar's preferred disease name for the concept specified by disease identifiers in CLNDISDB (from ClinVar)">
##INFO=<ID=CLNHGVS,Number=.,Type=String,Description="Top-level (primary assembly, alt, or patch) HGVS expression.(from ClinVar)">
##INFO=<ID=CLNSIG,Number=.,Type=String,Description="Clinical significance for this single variant (from ClinVar)">
##INFO=<ID=EXAC_AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed (from ExAC r1)">
##INFO=<ID=EXAC_AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed (from ExAC r1)">
##INFO=<ID=EXAC_AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes (from ExAC r1)">
##INFO=<ID=EXAC_FILTER,Number=1,Type=String,Description="calculated by self of overlapping values in field FILTER (from ExAC r1)">
##INFO=<ID=GNOMAD_AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed (from gnomAD v2.1.1 )">
##INFO=<ID=GNOMAD_AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed (from gnomAD v2.1.1 )">
##INFO=<ID=GNOMAD_AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes (from gnomAD v2.1.1 )">
##INFO=<ID=HGVD_AAF,Number=A,Type=Float,Description="Alternative Allele Frequency(s) NA/(NR+NAtotal) (from HGVD/DBexome20170802)">
##INFO=<ID=HGVD_AC,Number=A,Type=Integer,Description="number(s) of alternative allele(s) (from HGVD/DBexome20170802)">
##INFO=<ID=HGVD_NR,Number=1,Type=Integer,Description="number of reference allele (from HGVD/DBexome20170802)">
##INFO=<ID=TOMMO_4_7K_AC,Number=A,Type=Integer,Description="Allele count in genotypes (from ToMMo 4.7KJPN (20190826))">
##INFO=<ID=TOMMO_4_7K_AF,Number=A,Type=Float,Description="Allele frequency, for each ALT allele, in the same order as listed  (from ToMMo 4.7KJPN (20190826))">
##INFO=<ID=TOMMO_4_7K_AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes (from ToMMo 4.7KJPN (20190826))">
##INFO=<ID=dbSNP_RSID,Number=1,Type=String,Description="dbSNP ID (from dbSNP b151 )">
##INFO=<ID=GENEINFO,Number=1,Type=String,Description="Pairs each of gene symbol:gene id. The gene symbol and id are delimited by a colon (:)">
##INFO=<ID=DPVID,Number=.,Type=String,Description="DPV Variant ID">
##INFO=<ID=DPVSIG,Number=.,Type=String,Description="Variant Clinical Significance">
##INFO=<ID=DPVDSDBID,Number=.,Type=String,Description="Variant disease database ID">
##INFO=<ID=DPVDBN,Number=.,Type=String,Description="Variant disease name">
##INFO=<ID=DPVHGVS,Number=.,Type=String,Description="Variant in HGVS.">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
1	227083195	NC_000001.10:g.227083195C>T	C	T	.	.	EXAC_AF=3.295e-05;EXAC_AC=4;EXAC_AN=121412;GNOMAD_AF=2.7884e-05;GNOMAD_AC=7;GNOMAD_AN=251036;TOMMO_4_7K_AF=0.0018;TOMMO_4_7K_AC=17;TOMMO_4_7K_AN=9546;CLNALLELEID=863807;CLNDN=Alzheimer_disease,_type_4|Dilated_cardiomyopathy_1V;CLNDISDB=MONDO:MONDO:0011743,MedGen:C1847200,OMIM:606889|MONDO:MONDO:0013373,MedGen:C3150958,OMIM:613697;CLNSIG=Uncertain_significance;CLNHGVS=NC_000001.10:g.227083195C>T;HGVD_AAF=0.00124;HGVD_NR=2417;HGVD_AC=3;GENEINFO=9509:5664;DPVID=401;DPVSIG=Pathogenic;DPVDSDBID=OMIM:104300;DPVDBN=Alzheimer_disease_1;DPVHGVS=NC_000001.10:g.227083195C>T	.

VCF (GRCh38/hg38)

											##fileformat=VCFv4.0
##reference=GRCh38
##INFO=<ID=CLNALLELEID,Number=1,Type=Integer,Description="the ClinVar Allele ID">
##INFO=<ID=CLNDISDB,Number=.,Type=String,Description="Tag-value pairs of disease database name and identifier, e.g. OMIM:NNNNNN (from ClinVar)">
##INFO=<ID=CLNDN,Number=.,Type=String,Description="ClinVar's preferred disease name for the concept specified by disease identifiers in CLNDISDB (from ClinVar)">
##INFO=<ID=CLNHGVS,Number=.,Type=String,Description="Top-level (primary assembly, alt, or patch) HGVS expression.(from ClinVar)">
##INFO=<ID=CLNSIG,Number=.,Type=String,Description="Clinical significance for this single variant (from ClinVar)">
##INFO=<ID=GNOMAD_AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed (from gnomAD v2.1.1 )">
##INFO=<ID=GNOMAD_AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed (from gnomAD v2.1.1 )">
##INFO=<ID=GNOMAD_AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes (from gnomAD v2.1.1 )">
##INFO=<ID=dbSNP_RSID,Number=1,Type=String,Description="dbSNP ID (from dbSNP b151 )">
##originalFile=</tmp/crossmap-input-0kyvmcvk>
##targetRefGenome=</usr/lib64/python2.7/site-packages/transvar/transvar.download/hg38.fa>
##INFO=<ID=GENEINFO,Number=1,Type=String,Description="Pairs each of gene symbol:gene id. The gene symbol and id are delimited by a colon (:)">
##INFO=<ID=DPVID,Number=.,Type=String,Description="DPV Variant ID">
##INFO=<ID=DPVSIG,Number=.,Type=String,Description="Variant Clinical Significance">
##INFO=<ID=DPVDSDBID,Number=.,Type=String,Description="Variant disease database ID">
##INFO=<ID=DPVDBN,Number=.,Type=String,Description="Variant disease name">
##INFO=<ID=DPVHGVS,Number=.,Type=String,Description="Variant in HGVS.">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
1	226895494	NC_000001.10:g.227083195C>T	C	T	.	.	dbSNP_RSID=rs756609078;GNOMAD_AF=2.7884e-05;GNOMAD_AC=7;GNOMAD_AN=251036;CLNALLELEID=863807;CLNDN=Alzheimer_disease,_type_4|Dilated_cardiomyopathy_1V;CLNDISDB=MONDO:MONDO:0011743,MedGen:C1847200,OMIM:606889|MONDO:MONDO:0013373,MedGen:C3150958,OMIM:613697;CLNSIG=Uncertain_significance;CLNHGVS=NC_000001.11:g.226895494C>T;GENEINFO=9509:5664;DPVID=401;DPVSIG=Pathogenic;DPVDSDBID=OMIM:104300;DPVDBN=Alzheimer_disease_1;DPVHGVS=NC_000001.11:g.226895494C>T	.

Variant Detail