Variant Detail

Variant Information
ID
DPV: 384
Chromosome
1
Gene
HGVS (GRCh37/hg19)
NC_000001.10:g.22412944A>G
HGVS (GRCh38/hg38)
NC_000001.11:g.22086451A>G
HGVS (RNA)
NM_001039802.1:c.191A>G
HGVS (Protein)
NP_001034891.1:p.Y64C
dbSNP
-
ClinGen Allele Registry
CA278804
Allele Frequency
Individual Information

ID
DPVS:24.1
Clinical Significance
Pathogenic
Date Last Evaluated
2017-03-30
Clinical Significance Citation
Takenouchi, T. Further evidence of a mutation in CDC42 as a cause of a recognizable syndromic form of thrombocytopenia. 2016 Am J Med Genet A. 2016 Apr;170A(4):852-5. doi: 10.1002/ajmg.a.37526. Epub 2015 Dec 28. PMID:26708094
Takenouchi, T. Macrothrombocytopenia and developmental delay with a de novo CDC42 mutation: Yet another locus for thrombocytopenia and developmental delay. 2015 Am J Med Genet A. 2015 Nov;167A(11):2822-5. doi: 10.1002/ajmg.a.37275. Epub 2015 Aug 6. PMID:26386261

Transcript
-
Disease

Phenotype
-
Zygosity
single heterozygote
Allele Origin
de novo
Affected Status
yes
Sample Type
  • DNA
Analysis Type
  • Next-Generation Sequencing - Illumina/Solexa
Collection Method
clinical testing
Compound heterozygous variant(s)
Data Submitter
Comment
-

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
1	22412944	NC_000001.10:g.22412944A>G	A	G	.	.	CLNALLELEID=215784;CLNDN=Abnormality_of_blood_and_blood-forming_tissues|Abnormal_facial_shape|Abnormality_of_the_immune_system|Postnatal_growth_retardation|Neurodevelopmental_abnormality|Takenouchi-Kosaki_syndrome|Inborn_genetic_diseases|not_provided;CLNDISDB=Human_Phenotype_Ontology:HP:0001871,Human_Phenotype_Ontology:HP:0003135,MedGen:C0850715|Human_Phenotype_Ontology:HP:0001999,Human_Phenotype_Ontology:HP:0002004,Human_Phenotype_Ontology:HP:0002260,Human_Phenotype_Ontology:HP:0004643,Human_Phenotype_Ontology:HP:0004649,Human_Phenotype_Ontology:HP:0004652,Human_Phenotype_Ontology:HP:0004655,Human_Phenotype_Ontology:HP:0004675,Human_Phenotype_Ontology:HP:0005124,MedGen:C0424503|Human_Phenotype_Ontology:HP:0002715,Human_Phenotype_Ontology:HP:0003257,Human_Phenotype_Ontology:HP:0003346,Human_Phenotype_Ontology:HP:0010986,MedGen:C4021753|Human_Phenotype_Ontology:HP:0008844,Human_Phenotype_Ontology:HP:0008865,Human_Phenotype_Ontology:HP:0008868,Human_Phenotype_Ontology:HP:0008897,Human_Phenotype_Ontology:HP:0008901,Human_Phenotype_Ontology:HP:0008918,MedGen:C1859778|Human_Phenotype_Ontology:HP:0012759,MedGen:C4022737|MONDO:MONDO:0014757,MedGen:C4225222,OMIM:616737,Orphanet:ORPHA487796|MeSH:D030342,MedGen:C0950123|MedGen:CN517202;CLNSIG=Pathogenic/Likely_pathogenic;CLNHGVS=NC_000001.10:g.22412944A>G;GENEINFO=1736:998;DPVID=384;DPVSIG=Pathogenic;DPVDSDBID=OMIM:616737;DPVDBN=Takenouchi-Kosaki_syndrome;DPVHGVS=NC_000001.10:g.22412944A>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-1bd2hcxc>
##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
1	22086451	NC_000001.10:g.22412944A>G	A	G	.	.	dbSNP_RSID=rs864309721;CLNALLELEID=215784;CLNDN=Takenouchi-Kosaki_syndrome|Inborn_genetic_diseases|not_provided;CLNDISDB=MONDO:MONDO:0014757,MedGen:C4225222,OMIM:616737,Orphanet:ORPHA487796|MeSH:D030342,MedGen:C0950123|MedGen:CN517202;CLNSIG=Pathogenic/Likely_pathogenic;CLNHGVS=NC_000001.11:g.22086451A>G;GENEINFO=1736:998;DPVID=384;DPVSIG=Pathogenic;DPVDSDBID=OMIM:616737;DPVDBN=Takenouchi-Kosaki_syndrome;DPVHGVS=NC_000001.11:g.22086451A>G	.