Variant Detail

Variant Information
ID
DPV: 10938
Chromosome
11
Gene
HGVS (GRCh37/hg19)
NC_000011.9:g.88027665C>T
HGVS (GRCh38/hg38)
NC_000011.10:g.88294497C>T
HGVS (RNA)
NM_001814.4:c.901G>A
HGVS (Protein)
NP_001805.3:p.G301S
dbSNP
-
ClinGen Allele Registry
CA118689
Allele Frequency
Individual Information

ID
DPVS:12831.1
Clinical Significance
Pathogenic
Date Last Evaluated
2020-01-08
Clinical Significance Citation
Nakano, A. Papillon-Lefevre syndrome: mutations and polymorphisms in the cathepsin C gene. 2001 J Invest Dermatol. 2001 Feb;116(2):339-43. doi: 10.1046/j.1523-1747.2001.01244.x. PMID:11180012

Transcript
-
Disease

Phenotype
-
Zygosity
homozygote
Allele Origin
biparental
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
##INFO=<ID=CLNDBN,Number=1,Type=String,Description="calculated by self of overlapping values in field CLNDBN from clinvar/vcf_GRCh37/clinvar.vcf.gz">
##INFO=<ID=CLNDSDB,Number=1,Type=String,Description="calculated by self of overlapping values in field CLNDSDB from clinvar/vcf_GRCh37/clinvar.vcf.gz">
##INFO=<ID=CLNDSDBID,Number=1,Type=String,Description="calculated by self of overlapping values in field CLNDSDBID from clinvar/vcf_GRCh37/clinvar.vcf.gz">
##INFO=<ID=CLNHGVS,Number=.,Type=String,Description="Top-level (primary assembly, alt, or patch) HGVS expression. (from clinvar/vcf_GRCh37/clinvar.vcf.gz)">
##INFO=<ID=CLNSIG,Number=.,Type=String,Description="Clinical significance for this single variant (from clinvar/vcf_GRCh37/clinvar.vcf.gz)">
##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/ExAC.r1.sites.vep.vcf.gz)">
##INFO=<ID=EXAC_AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed (from ExAC/ExAC.r1.sites.vep.vcf.gz)">
##INFO=<ID=EXAC_AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes (from ExAC/ExAC.r1.sites.vep.vcf.gz)">
##INFO=<ID=EXAC_FILTER,Number=1,Type=String,Description="calculated by self of overlapping values in field FILTER from ExAC/ExAC.r1.sites.vep.vcf.gz">
##INFO=<ID=HGVD_AAF,Number=A,Type=Float,Description="Alternative Allele Frequency(s) NA/(NR+NAtotal) (from HGVD/DBexome20170802.tab.vcf.gz)">
##INFO=<ID=HGVD_AC,Number=A,Type=Integer,Description="number(s) of alternative allele(s) (from HGVD/DBexome20170802.tab.vcf.gz)">
##INFO=<ID=HGVD_NR,Number=1,Type=Integer,Description="number of reference allele (from HGVD/DBexome20170802.tab.vcf.gz)">
##INFO=<ID=TOMMO_3_5K_AC,Number=.,Type=Integer,Description="Allele count in genotypes (from ToMMo/tommo-3.5kjpnv2-20181105-af_merged.vcf.gz)">
##INFO=<ID=TOMMO_3_5K_AF,Number=A,Type=Float,Description="Allele frequency, for each ALT allele, in the same order as listed (from ToMMo/tommo-3.5kjpnv2-20181105-af_merged.vcf.gz)">
##INFO=<ID=TOMMO_3_5K_AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes (from ToMMo/tommo-3.5kjpnv2-20181105-af_merged.vcf.gz)">
##INFO=<ID=TOMMO_3_5K_FILTER,Number=1,Type=String,Description="calculated by self of overlapping values in field FILTER from ToMMo/tommo-3.5kjpnv2-20181105-af_merged.vcf.gz">
##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
11	88027665	NC_000011.9:g.88027665C>T	C	T	.	.	EXAC_AF=3.295e-05;EXAC_AC=4;EXAC_AN=121406;CLNSIG=Pathogenic;CLNHGVS=NC_000011.9:g.88027665C>T;TOMMO_3_5K_AF=0.0003;TOMMO_3_5K_AC=2;TOMMO_3_5K_AN=7104;GENEINFO=CTSC:1075;DPVID=10938;DPVSIG=Pathogenic;DPVDSDBID=OMIM:245000;DPVDBN=Papillon-Lefevre_syndrome;DPVHGVS=NC_000011.9:g.88027665C>T	.
VCF (GRCh38/hg38) 
											##fileformat=VCFv4.0
##INFO=<ID=CLNDBN,Number=1,Type=String,Description="calculated by self of overlapping values in field CLNDBN from clinvar/vcf_GRCh38/clinvar.vcf.gz">
##INFO=<ID=CLNDSDB,Number=1,Type=String,Description="calculated by self of overlapping values in field CLNDSDB from clinvar/vcf_GRCh38/clinvar.vcf.gz">
##INFO=<ID=CLNDSDBID,Number=1,Type=String,Description="calculated by self of overlapping values in field CLNDSDBID from clinvar/vcf_GRCh38/clinvar.vcf.gz">
##INFO=<ID=CLNHGVS,Number=.,Type=String,Description="Top-level (primary assembly, alt, or patch) HGVS expression. (from clinvar/vcf_GRCh38/clinvar.vcf.gz)">
##INFO=<ID=CLNSIG,Number=.,Type=String,Description="Clinical significance for this single variant (from clinvar/vcf_GRCh38/clinvar.vcf.gz)">
##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
11	88294497	NC_000011.9:g.88027665C>T	C	T	.	.	CLNSIG=Pathogenic;CLNHGVS=NC_000011.10:g.88294497C>T;GENEINFO=CTSC:1075;DPVID=10938;DPVSIG=Pathogenic;DPVDSDBID=OMIM:245000;DPVDBN=Papillon-Lefevre_syndrome;DPVHGVS=NC_000011.10:g.88294497C>T	.