Variant Detail

Variant Information
ID
DPV: 10175
Chromosome
11
Gene
HGVS (GRCh37/hg19)
NC_000011.9:g.108004987A>G
HGVS (GRCh38/hg38)
NC_000011.10:g.108134260A>G
HGVS (RNA)
NM_000019.3:c.278A>G
HGVS (Protein)
NP_000010.1:p.N93S
dbSNP
-
ClinGen Allele Registry
CA252469
Allele Frequency
Individual Information

ID
DPVS:11488.2
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. The mitochondrial acetoacetyl-CoA thiolase (T2) deficiency in Japanese patients: urinary organic acid and blood acylcarnitine profiles under stable conditions have subtle abnormalities in T2-deficient patients with some residual T2 activity. 2003 J Inherit Metab Dis. 2003;26(5):423-31. doi: 10.1023/a:1025117226051. PMID:14518824

Transcript
  • NM_000019.3:c.278A>G
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
c.[278A>G];[935T>C]

ID
DPVS:12385.1
Clinical Significance
Pathogenic
Date Last Evaluated
2020-01-08
Clinical Significance Citation
Fukao, T. Characterization of N93S, I312T, and A333P missense mutations in two Japanese families with mitochondrial acetoacetyl-CoA thiolase deficiency. 1998 Hum Mutat. 1998;12(4):245-54. doi: 10.1002/(SICI)1098-1004(1998)12:4<245::AID-HUMU5>3.0.CO;2-E. PMID:9744475
Fukao, T. Mild form of beta-ketothiolase deficiency (mitochondrial acetoacetyl-CoA thiolase deficiency) in two Japanese siblings: identification of detectable residual activity and cross-reactive material in EB-transformed lymphocytes. 1996 Clin Genet. 1996 Oct;50(4):263-6. doi: 10.1111/j.1399-0004.1996.tb02641.x. PMID:9001814

Transcript
-
Disease

Phenotype
-
Zygosity
compound heterozygote
Allele Origin
maternal
Affected Status
yes
Sample Type
  • DNA
Analysis Type
  • HeteroDuplex analysis
Collection Method
literature only
Compound heterozygous variant(s)
Data Submitter
Comment
c.[278A>G];[935T>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	108004987	NC_000011.9:g.108004987A>G	A	G	.	.	CLNALLELEID=17882;CLNDN=Deficiency_of_acetyl-CoA_acetyltransferase;CLNDISDB=MONDO:MONDO:0008760,MedGen:C1536500,OMIM:203750,Orphanet:ORPHA134,SNOMED_CT:124258007;CLNSIG=Likely_pathogenic;CLNHGVS=NC_000011.9:g.108004987A>G;GENEINFO=93:38;DPVID=10175;DPVSIG=Pathogenic;DPVDSDBID=OMIM:203750;DPVDBN=3-ketothiolase_deficiency;DPVHGVS=NC_000011.9:g.108004987A>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-pnm9djv6>
##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	108134260	NC_000011.9:g.108004987A>G	A	G	.	.	dbSNP_RSID=rs120074145;CLNALLELEID=17882;CLNDN=Deficiency_of_acetyl-CoA_acetyltransferase;CLNDISDB=MONDO:MONDO:0008760,MedGen:C1536500,OMIM:203750,Orphanet:ORPHA134,SNOMED_CT:124258007;CLNSIG=Likely_pathogenic;CLNHGVS=NC_000011.10:g.108134260A>G;GENEINFO=93:38;DPVID=10175;DPVSIG=Pathogenic;DPVDSDBID=OMIM:203750;DPVDBN=3-ketothiolase_deficiency;DPVHGVS=NC_000011.10:g.108134260A>G	.