Database of Pathogenic Variants

Individual Information

DPVS:11491.2

ID

DPVS:11491.2

Clinical Significance

Pathogenic

Date Last Evaluated

2019-07-21

Clinical Significance Citation

Hori, T. Inborn errors of ketone body utilization. 2015 Pediatr Int. 2015;57(1):41-8. doi: 10.1111/ped.12585. PMID:25559898

Fukao, T. Ketone body metabolism and its defects. 2014 J Inherit Metab Dis. 2014 Jul;37(4):541-51. doi: 10.1007/s10545-014-9704-9. Epub 2014 Apr 8. PMID:24706027

Fukao, T. A novel mutation (c.951C>T) in an exonic splicing enhancer results in exon 10 skipping in the human mitochondrial acetoacetyl-CoA thiolase gene. 2010 Mol Genet Metab. 2010 Aug;100(4):339-44. doi: 10.1016/j.ymgme.2010.03.012. Epub 2010 Mar 19. PMID:20488739

Transcript

NM_000019.3:c.951C>T

Disease

3-ketothiolase deficiency
OMIM:203750
Orphanet:134
MedGen:C1536500

Phenotype

Zygosity

compound heterozygote

Allele Origin

germline

Affected Status

yes

Sample Type

Analysis Type

SEQuencing

Collection Method

literature only

Compound heterozygous variant(s)

Data Submitter

Comment

c.[556G>T];[951C>T]

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	108014720	NC_000011.9:g.108014720C>T	C	T	.	.	EXAC_AF=8.236e-06;EXAC_AC=1;EXAC_AN=121412;GNOMAD_AF=1.5987e-05;GNOMAD_AC=4;GNOMAD_AN=250210;TOMMO_4_7K_AF=0.0001;TOMMO_4_7K_AC=1;TOMMO_4_7K_AN=9330;CLNALLELEID=654064;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.108014720C>T;GENEINFO=93:38;DPVID=10182;DPVSIG=Pathogenic;DPVDSDBID=OMIM:203750;DPVDBN=3-ketothiolase_deficiency;DPVHGVS=NC_000011.9:g.108014720C>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-n6av7rmb>
##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	108143993	NC_000011.9:g.108014720C>T	C	T	.	.	dbSNP_RSID=rs747714452;GNOMAD_AF=1.5987e-05;GNOMAD_AC=4;GNOMAD_AN=250210;CLNALLELEID=654064;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.108143993C>T;GENEINFO=93:38;DPVID=10182;DPVSIG=Pathogenic;DPVDSDBID=OMIM:203750;DPVDBN=3-ketothiolase_deficiency;DPVHGVS=NC_000011.10:g.108143993C>T	.

Variant Detail