Variant Detail

Variant Information
ID
DPV: 531
Chromosome
17
Gene
HGVS (GRCh37/hg19)
NC_000017.10:g.44087690T>G
HGVS (GRCh38/hg38)
NC_000017.11:g.46010324T>G
HGVS (RNA)
NM_005910:c.837T>G
HGVS (Protein)
NP_005901:p.N279K
dbSNP
-
ClinGen Allele Registry
CA225424
Allele Frequency
Individual Information

ID
DPVS:416.1
Clinical Significance
Pathogenic
Date Last Evaluated
2015-06-11
Clinical Significance Citation
Paloyan, D. The timing of biliary tract operations in patients with pancreatitis associated with gallstones. 1975 Surg Gynecol Obstet. 1975 Nov;141(5):737-9. PMID:1198310
Ogaki, K. Analyses of the MAPT, PGRN, and C9orf72 mutations in Japanese patients with FTLD, PSP, and CBS. 2013 Parkinsonism Relat Disord. 2013 Jan;19(1):15-20. doi: 10.1016/j.parkreldis.2012.06.019. Epub 2012 Jul 18. PMID:22818528

Transcript
-
Disease

Frontotemporal lobar degeneration|progressive supranuclear palsy

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
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:1872.1
Clinical Significance
Pathogenic
Date Last Evaluated
2018-03-30
Clinical Significance Citation
Ogaki, K. Analyses of the MAPT, PGRN, and C9orf72 mutations in Japanese patients with FTLD, PSP, and CBS. 2013 Parkinsonism Relat Disord. 2013 Jan;19(1):15-20. doi: 10.1016/j.parkreldis.2012.06.019. Epub 2012 Jul 18. PMID:22818528

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
17	44087690	NC_000017.10:g.44087690T>G	T	G	.	.	CLNALLELEID=29292;CLNDN=Frontotemporal_dementia|Parkinson_disease,_late-onset|Pick_disease|Parkinson-dementia_syndrome|Progressive_supranuclear_ophthalmoplegia|not_provided;CLNDISDB=Human_Phenotype_Ontology:HP:0002145,MONDO:MONDO:0017276,MedGen:C0338451,OMIM:600274,Orphanet:ORPHA282,SNOMED_CT:230270009|MONDO:MONDO:0008199,MedGen:C3160718,OMIM:168600,SNOMED_CT:49049000|MONDO:MONDO:0008243,MedGen:C0236642,OMIM:172700,SNOMED_CT:13092008|MONDO:MONDO:0009839,MedGen:C1850077,OMIM:260540,Orphanet:ORPHA240085|MedGen:C4551862,OMIM:601104,Orphanet:ORPHA683,SNOMED_CT:28978003|MedGen:CN517202;CLNSIG=Pathogenic;CLNHGVS=NC_000017.10:g.44087690T>G;GENEINFO=6893:4137;DPVID=531;DPVSIG=Pathogenic;DPVDSDBID=OMIM:104300|OMIM:601104|OMIM:600274;DPVDBN=Alzheimer_disease_1|Progressive_supranuclear_palsy_1|Frontotemporal_dementia;DPVHGVS=NC_000017.10:g.44087690T>G	.
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-ews95qs3>
##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
17	46010324	NC_000017.10:g.44087690T>G	T	G	.	.	dbSNP_RSID=rs63750756;CLNALLELEID=29292;CLNDN=Frontotemporal_dementia|Parkinson_disease,_late-onset|Pick's_disease|Parkinson-dementia_syndrome|Progressive_supranuclear_ophthalmoplegia|not_provided;CLNDISDB=Human_Phenotype_Ontology:HP:0002145,MONDO:MONDO:0017276,MedGen:C0338451,OMIM:600274,Orphanet:ORPHA282,SNOMED_CT:230270009|MONDO:MONDO:0008199,MedGen:C3160718,OMIM:168600,SNOMED_CT:49049000|MONDO:MONDO:0008243,MedGen:C0236642,OMIM:172700,SNOMED_CT:13092008|MONDO:MONDO:0009839,MedGen:C1850077,OMIM:260540,Orphanet:ORPHA240085|MedGen:C4551863,OMIM:601104,Orphanet:ORPHA683,SNOMED_CT:28978003|MedGen:CN517202;CLNSIG=Pathogenic;CLNHGVS=NC_000017.11:g.46010324T>G;GENEINFO=6893:4137;DPVID=531;DPVSIG=Pathogenic;DPVDSDBID=OMIM:104300|OMIM:601104|OMIM:600274;DPVDBN=Alzheimer_disease_1|Progressive_supranuclear_palsy_1|Frontotemporal_dementia;DPVHGVS=NC_000017.11:g.46010324T>G	.