Variant Detail

Variant Information
ID
DPV: 5844
Chromosome
10
Gene
HGVS (GRCh37/hg19)
NC_000010.10:g.101571361T>C
HGVS (GRCh38/hg38)
NC_000010.11:g.99811604T>C
HGVS (RNA)
NM_000392.4:c.1967+2T>C
HGVS (Protein)
dbSNP
-
ClinGen Allele Registry
CA119601
Allele Frequency
Individual Information

ID
DPVS:5921.1
Clinical Significance
Pathogenic
Date Last Evaluated
2018-12-04
Clinical Significance Citation
Togawa, T. Clinical, Pathologic, and Genetic Features of Neonatal Dubin-Johnson Syndrome: A Multicenter Study in Japan. 2018 J Pediatr. 2018 May;196:161-167.e1. doi: 10.1016/j.jpeds.2017.12.058. Epub 2018 Feb 28. PMID:29499989
Kajihara, S. A splice mutation in the human canalicular multispecific organic anion transporter gene causes Dubin-Johnson syndrome. 1998 Biochem Biophys Res Commun. 1998 Dec 18;253(2):454-7. doi: 10.1006/bbrc.1998.9780. PMID:9878557

Togawa et al. J Pediatr (Epub ahead of print)

Transcript
-
Disease

Dubin-Johnson syndrome

Phenotype
-
Zygosity
compound heterozygote
Allele Origin
germline
Affected Status
yes
Sample Type
  • DNA
Analysis Type
  • SEQuencing
Collection Method
literature only
Compound heterozygous variant(s)
Data Submitter
Comment
c.351_355dup(;)1967+2T>C

ID
DPVS:5924.1
Clinical Significance
Pathogenic
Date Last Evaluated
2018-12-04
Clinical Significance Citation
Togawa, T. Clinical, Pathologic, and Genetic Features of Neonatal Dubin-Johnson Syndrome: A Multicenter Study in Japan. 2018 J Pediatr. 2018 May;196:161-167.e1. doi: 10.1016/j.jpeds.2017.12.058. Epub 2018 Feb 28. PMID:29499989
Kajihara, S. A splice mutation in the human canalicular multispecific organic anion transporter gene causes Dubin-Johnson syndrome. 1998 Biochem Biophys Res Commun. 1998 Dec 18;253(2):454-7. doi: 10.1006/bbrc.1998.9780. PMID:9878557

Togawa et al. J Pediatr (Epub ahead of print)

Transcript
-
Disease

Dubin-Johnson syndrome

Phenotype
-
Zygosity
compound heterozygote
Allele Origin
germline
Affected Status
yes
Sample Type
  • DNA
Analysis Type
  • SEQuencing
Collection Method
literature only
Compound heterozygous variant(s)
Data Submitter
Comment
c.1967+2T>C(;)2125T>C

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
10	101571361	NC_000010.10:g.101571361T>C	T	C	.	.	TOMMO_4_7K_AF=0.0002;TOMMO_4_7K_AC=2;TOMMO_4_7K_AN=9546;CLNALLELEID=23456;CLNDN=Dubin-Johnson_syndrome;CLNDISDB=MONDO:MONDO:0009380,MedGen:C0022350,OMIM:237500,Orphanet:ORPHA234,SNOMED_CT:44553005;CLNSIG=Pathogenic;CLNHGVS=NC_000010.10:g.101571361T>C;HGVD_AAF=0.000826;HGVD_NR=2418;HGVD_AC=2;GENEINFO=53:1244;DPVID=5844;DPVSIG=Pathogenic;DPVDSDBID=OMIM:237500;DPVDBN=Dubin-Johnson_syndrome;DPVHGVS=NC_000010.10:g.101571361T>C	.
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-5m_c842u>
##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
10	99811604	NC_000010.10:g.101571361T>C	T	C	.	.	dbSNP_RSID=rs387906396;CLNALLELEID=23456;CLNDN=Dubin-Johnson_syndrome;CLNDISDB=MONDO:MONDO:0009380,MedGen:C0022350,OMIM:237500,Orphanet:ORPHA234,SNOMED_CT:44553005;CLNSIG=Pathogenic;CLNHGVS=NC_000010.11:g.99811604T>C;GENEINFO=53:1244;DPVID=5844;DPVSIG=Pathogenic;DPVDSDBID=OMIM:237500;DPVDBN=Dubin-Johnson_syndrome;DPVHGVS=NC_000010.11:g.99811604T>C	.