Variant Detail

Variant Information
ID
DPV: 10919
Chromosome
11
Gene
HGVS (GRCh37/hg19)
NC_000011.9:g.108017088T>C
HGVS (GRCh38/hg38)
NC_000011.10:g.108146361T>C
HGVS (RNA)
NM_000019.3:c.1163+2T>C
HGVS (Protein)
NP_000010.1:p.?
dbSNP
-
ClinGen Allele Registry
CA382508684
Allele Frequency
Individual Information

ID
DPVS:12184.1
Clinical Significance
Pathogenic
Date Last Evaluated
2020-01-08
Clinical Significance Citation
Fukao, T. A common mutation, R208X, identified in Vietnamese patients with mitochondrial acetoacetyl-CoA thiolase (T2) deficiency. 2010 Mol Genet Metab. 2010 May;100(1):37-41. doi: 10.1016/j.ymgme.2010.01.007. Epub 2010 Jan 21. PMID:20156697

Transcript
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Disease

Phenotype
-
Zygosity
compound heterozygote
Allele Origin
maternal
Affected Status
yes
Sample Type
  • DNA
Analysis Type
  • SEQuencing
Collection Method
literature only
Compound heterozygous variant(s)
Data Submitter
Comment
Origin: Dutch|c.[622C>T];[1163+2T>C]

ID
DPVS:12430.1
Clinical Significance
Pathogenic
Date Last Evaluated
2020-01-08
Clinical Significance Citation
Fukao, T. Molecular basis of beta-ketothiolase deficiency: mutations and polymorphisms in the human mitochondrial acetoacetyl-coenzyme A thiolase gene. 1995 Hum Mutat. 1995;5(2):113-20. doi: 10.1002/humu.1380050203. PMID:7749408

Transcript
-
Disease

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
resluts in 1163GCAGins|c.[731-46_752del];[1163+2T>C]

ID
DPVS:12438.1
Clinical Significance
Pathogenic
Date Last Evaluated
2020-01-08
Clinical Significance Citation
Fukao, T. Mitochondrial acetoacetyl-coenzyme A thiolase gene: a novel 68-bp deletion involving 3' splice site of intron 7, causing exon 8 skipping in a Caucasian patient with beta-ketothiolase deficiency. 1995 Hum Mutat. 1995;5(1):94-6. doi: 10.1002/humu.1380050113. PMID:7728155

Transcript
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Disease

Phenotype
-
Zygosity
homozygote
Allele Origin
germline
Affected Status
yes
Sample Type
  • DNA
Analysis Type
  • PCR + restriction enzyme digestion
Collection Method
literature only
Compound heterozygous variant(s)
Data Submitter
Comment
resluts in 1163GCAGins|c.[731-46_752del];[1163+2T>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
11	108017088	NC_000011.9:g.108017088T>C	T	C	.	.	CLNALLELEID=17876;CLNDN=Deficiency_of_acetyl-CoA_acetyltransferase;CLNDISDB=MONDO:MONDO:0008760,MedGen:C1536500,OMIM:203750,Orphanet:ORPHA134,SNOMED_CT:124258007;CLNSIG=Pathogenic;CLNHGVS=NC_000011.9:g.108017088T>C;GENEINFO=93:38;DPVID=10919;DPVSIG=Pathogenic;DPVDSDBID=OMIM:203750;DPVDBN=3-ketothiolase_deficiency;DPVHGVS=NC_000011.9:g.108017088T>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-y4xll121>
##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
11	108146361	NC_000011.9:g.108017088T>C	T	C	.	.	dbSNP_RSID=rs1280110907;CLNALLELEID=17876;CLNDN=Deficiency_of_acetyl-CoA_acetyltransferase;CLNDISDB=MONDO:MONDO:0008760,MedGen:C1536500,OMIM:203750,Orphanet:ORPHA134,SNOMED_CT:124258007;CLNSIG=Pathogenic;CLNHGVS=NC_000011.10:g.108146361T>C;GENEINFO=93:38;DPVID=10919;DPVSIG=Pathogenic;DPVDSDBID=OMIM:203750;DPVDBN=3-ketothiolase_deficiency;DPVHGVS=NC_000011.10:g.108146361T>C	.