Variant Detail

Variant Information
ID
DPV: 635
Chromosome
21
Gene
HGVS (GRCh37/hg19)
NC_000021.8:g.27264096C>T
HGVS (GRCh38/hg38)
NC_000021.9:g.25891784C>T
HGVS (RNA)
NM_000484.3:c.2149G>A
HGVS (Protein)
NP_000475.1:p.V717I
dbSNP
-
ClinGen Allele Registry
CA127791
Allele Frequency
Individual Information

ID
DPVS:428.1
Clinical Significance
Pathogenic
Date Last Evaluated
2015-06-11
Clinical Significance Citation
Yoshioka, K. The 717Val----Ile substitution in amyloid precursor protein is associated with familial Alzheimer's disease regardless of ethnic groups. 1991 Biochem Biophys Res Commun. 1991 Aug 15;178(3):1141-6. PMID:1908231
Naruse, S. Mis-sense mutation Val----Ile in exon 17 of amyloid precursor protein gene in Japanese familial Alzheimer's disease. 1991 Lancet. 1991 Apr 20;337(8747):978-9. PMID:1678058
Yoshizawa, T. Screening of the mis-sense mutation producing the 717Val-->Ile substitution in the amyloid precursor protein in Japanese familial and sporadic Alzheimer's disease. 1993 J Neurol Sci. 1993 Jul;117(1-2):12-5. PMID:8410047
Katsuya, T. [Affected siblings with Alzheimer's disease had missense mutation of codon 717 in amyloid precursor protein gene]. 1992 Nihon Ronen Igakkai Zasshi. 1992 Feb;29(2):129-34. PMID:1349930
Imagawa, M. Coenzyme Q10, iron, and vitamin B6 in genetically-confirmed Alzheimer's disease. 1992 Lancet. 1992 Sep 12;340(8820):671. PMID:1355228
Pigin, S. A. [Exostoses as a cause of the formation of a false femoral artery aneurysm]. 1977 Khirurgiia (Mosk). 1977 May;(5):120. PMID:864957

Transcript
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Disease

Alzheimer disease 1, early onset familial

Phenotype
-
Zygosity
single heterozygote
Allele Origin
inherited
Affected Status
yes
Sample Type
  • DNA
Analysis Type
  • PCR + restriction enzyme digestion
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

ID
DPVS:5573.1
Clinical Significance
Pathogenic
Date Last Evaluated
2018-11-27
Clinical Significance Citation
Matsumura, Y. Japanese siblings with missense mutation (717Val --> Ile) in amyloid precursor protein of early-onset Alzheimer's disease. 1996 Neurology. 1996 Jun;46(6):1721-3. PMID:8649577

Transcript
-
Disease

Phenotype
-
Zygosity
single heterozygote
Allele Origin
inherited
Affected Status
yes
Sample Type
  • DNA
Analysis Type
  • SEQuencing
Collection Method
literature only
Compound heterozygous variant(s)
Data Submitter
Comment
-

ClinVar
Model Animals
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
21	27264096	NC_000021.8:g.27264096C>T	C	T	.	.	CLNALLELEID=33127;CLNDN=Alzheimer_disease|Alzheimer_disease,_type_1|not_provided;CLNDISDB=Human_Phenotype_Ontology:HP:0002511,Human_Phenotype_Ontology:HP:0006878,Human_Phenotype_Ontology:HP:0007213,MONDO:MONDO:0004975,MedGen:C0002395,OMIM:104300,SNOMED_CT:26929004|MONDO:MONDO:0007088,MedGen:C2931257|MedGen:CN517202;CLNSIG=Pathogenic;CLNHGVS=NC_000021.8:g.27264096C>T;GENEINFO=620:351;DPVID=635;DPVSIG=Pathogenic;DPVDSDBID=OMIM:104300;DPVDBN=Alzheimer_disease_1;DPVHGVS=NC_000021.8:g.27264096C>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-70ak1r20>
##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
21	25891784	NC_000021.8:g.27264096C>T	C	T	.	.	dbSNP_RSID=rs63750264;CLNALLELEID=33127;CLNDN=Alzheimer_disease|Alzheimer_disease,_type_1|not_provided;CLNDISDB=Human_Phenotype_Ontology:HP:0002511,Human_Phenotype_Ontology:HP:0006878,Human_Phenotype_Ontology:HP:0007213,MONDO:MONDO:0004975,MedGen:C0002395,OMIM:104300,SNOMED_CT:26929004|MedGen:C2931257|MedGen:CN517202;CLNSIG=Pathogenic;CLNHGVS=NC_000021.9:g.25891784C>T;GENEINFO=620:351;DPVID=635;DPVSIG=Pathogenic;DPVDSDBID=OMIM:104300;DPVDBN=Alzheimer_disease_1;DPVHGVS=NC_000021.9:g.25891784C>T	.