A curated catalogue of human genomic structural variation




Variant Details

Variant: dgv20n17



Internal ID20131586
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
chr1:248324336..248684068hg38UCSC Ensembl
chr1:248487638..248847369hg19UCSC Ensembl
chr1:246554261..246913992hg18UCSC Ensembl
chr1:245385231..245782548hg16UCSC Ensembl
Cytoband1q44
Allele length
AssemblyAllele length
hg38359733
hg19359732
hg18359732
hg16397318
Variant TypeCNV loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsnsv437274, nsv437273
SamplesNA19103, NA19221
Known GenesOR14C36, OR14I1, OR2G6, OR2M7, OR2T1, OR2T10, OR2T11, OR2T2, OR2T27, OR2T29, OR2T3, OR2T34, OR2T35, OR2T4, OR2T5, OR2T6
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)dgv20n17
Frequency
Sample Size60
Observed Gain0
Observed Loss2
Observed Complex0
Frequencyn/a


Hosted by The Centre for Applied Genomics
Grant support for DGV
Please read the usage disclaimer