A curated catalogue of human genomic structural variation




Variant Details

Variant: dgv3n17



Internal ID20131569
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
chr1:65756073..65806453hg38UCSC Ensembl
chr1:66221756..66272136hg19UCSC Ensembl
chr1:65994344..66044724hg18UCSC Ensembl
chr1:65591673..65642053hg16UCSC Ensembl
Cytoband1p31.3
Allele length
AssemblyAllele length
hg3850381
hg1950381
hg1850381
hg1650381
Variant TypeCNV loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsnsv437214, nsv437215
SamplesNA18860, NA19173
Known GenesPDE4B
MethodSNP array
AnalysisOur algorithm aims to detect deletions that are transmitted from a hemizygous parent to a child. For each trio, every SNP was coded into one of seven categories: (A) Type I mendelian incompatibility (that is, consistent with deletion) involving mother; (B) Type I mendelian incompatibility involving father; (C) Type II mendelian incompatibility (that is, inconsistent with deletion); (D) child homozygous or missing data, both parents homozygous or missing data; (E) child homozygous or missing data, father heterozygous, mother homozygous or missing data; (F) child homozygous or missing data, mother heterozygous, father homozygous or missing data; (G) child heterozygous or both parents heterozygous (see Supplementary Methods for further details). SNPs were assigned to states D-G only if they did not contain mendelian incompatibilities. A run of consecutive SNPs in a particular trio was considered to be consistent with a maternal transmitted deletion if all SNPs were in states A, D or E, or with a paternal deletion if all SNPs were in states B, D or F.
PlatformNot reported
Comments
ReferenceConrad_et_al_2006
Pubmed ID16327808
Accession Number(s)dgv3n17
Frequency
Sample Size60
Observed Gain0
Observed Loss2
Observed Complex0
Frequencyn/a


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