nstd89 - de Boer et al 2014 - dbVar Study

nstd89 (de Boer et al. 2014)

Organism:: Human
Study Type:: Case-Set
Submitter:: Martin de Boer
Description:: We report a novel LINE1-mediated insertion of a transcript from the TMF1 gene on chromosome 3 into the CYBB gene on the X chromosome in a Dutch male patient with chronic granulomatous disease. A 5.8-kb, incomplete and partly exonized TMF1 transcript was identified in intron 1 of CYBB in opposite orientation to the host gene. The sequence of the insertion showed the hallmarks of a retrotransposition event, with an antisense poly A tail, target site duplication and a consensus LINE1 endonuclease cleavage site. This insertion induced aberrant CYBB mRNA splicing, with inclusion of an extra 117-bp exon between exons 1 and 2 of CYBB. This extra exon contained a premature stop codon. See Variant Summary counts for nstd89 in dbVar Variant Summary.
Publication(s):: de Boer et al. 2014

Links

Source: NCBI

Detailed Information: Download 1 Variant Region, Download 1 Variant Call, Download Both, FTP

Variant Summary
Samplesets
Experimental Details
Validations

Variant Summary

Assembly used for analysis:
Remapped: GRCh38.p12 (hg38)
Submitted: GRCh37 (hg19)

Variant Summary for:

Sequence ID	Chr	Number of Variant Regions	Number of Variant Calls	Placement type	Link to graphical display
NC_000023.11	ChrX	1	1	Remapped	NC_000023.11

Sequence ID	Chr	Number of Variant Regions	Number of Variant Calls	Placement type	Link to graphical display
NC_000023.10	ChrX	1	1	Submitted	NC_000023.10

Remapping summary:

			Variant Region remap status						Variant Call remap status
Sequence ID	Chr	Variant Regions on source	Perfect	Good	Pass	Fail	Mult	Variant Calls on source	Perfect	Good	Pass	Fail	Mult
NC_000023.10	ChrX	1	1	0	0	0	0	1	1	0	0	0	0

Samplesets

Number of Samplesets: 1

Name:: retrocopy insertion in intron 1 of CYBB gene
Description:: retrocopy insertion of partly exonised TMF1 gene into intron 1 of the CYYB gene
Size:: 1
Organisms:: Homo sapiens
Sampleset Phenotype(s):: Chronic granulomatous disease, X-linked
Sex:: Male

Samples for sampleset 1
Sample ID	Cell Type	Subject ID	Sex	Ethnicity	Subject Age	Subject Phenotype
1	peripheral leukocytes	1	Male	Caucasian	22 years	Chronic granulomatous disease, X-linked

Experimental Details

Experiment ID	Type	Method	Analysis	Platforms	Number of Variant Calls
1	Discovery	Sequencing	Sequence alignment	ABI3130XL	1

dbVar

Database of genomic structural variation

nstd89 (de Boer et al. 2014)

Links

Detailed Information: Download 1 Variant Region, Download 1 Variant Call, Download Both, FTP

Variant Summary

Assembly used for analysis:
Remapped: GRCh38.p12 (hg38)
Submitted: GRCh37 (hg19)

Variant Summary for:

Remapping summary:

Samplesets

Number of Samplesets: 1

Experimental Details

Validations

No validation data were submitted for this study.

dbVar

Database of genomic structural variation

nstd89 (de Boer et al. 2014)

Links

Detailed Information: Download 1 Variant Region, Download 1 Variant Call, Download Both, FTP

Variant Summary

Variant Summary for: GRCh38.p12 (hg38)GRCh37 (hg19)

Remapping summary: GRCh37->GRCh38.p12

Samplesets

Number of Samplesets: 1

Experimental Details

Validations

No validation data were submitted for this study.

Variant Summary for:

Remapping summary: