| Accession | HsInv0409 | Region of the inversion | chrX:6147047-6148392 |
| Status | Validated | Prediction type | Simple |
| Estimated Inversion Size | 1,345 bp | Supporting predictions | 4 |
| Inverted allele frequency | 0.3889 | Mechanism of origin | FoSTeS or NHEJ |
| Functional effect | Inverts a region within an intron of a gene | Breakpoint 1 | chrX:6147047-6147049 |
| Ancestral orientation | NA | Breakpoint 2 | chrX:6148391-6148392 |
| Comments | Standard allele includes two small deletions and a 6 bp duplication flanking the inverted region
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Human Polymorphic Inversion DataBase
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General information
- Region map
+ Predictions
| Description | Discovery, genotyping and phasing of structural variants detected from Illumina whole genome sequencing data of 769 individuals from 250 Dutch families belonging to the GoNL project | ||||||||||
| Method | Paired-end mapping (PEM) | ||||||||||
| Name | |||
| Breakpoint 1 | chrX:6147134-6147134 | Breakpoint 2 | chrX:6148479-6148479 |
| Individuals | |||
| Description | Identification and resolution of sequence gaps and structural variants in the euchromatic regions of the reference human assembly through single-molecule, real-time (SMRT) DNA sequencing of an haploid human genome (CHM1) | ||||||||||||||
| Method | Long-read sequencing | ||||||||||||||
| Name | |||||||
| Breakpoint 1 | chrX:6147046-6147046 | Breakpoint 2 | chrX:6148384-6148384 | ||||
| Individuals |
| ||||||
| Description | Next generation sequencing and analysis by paired-end mapping of a Korean individual genome | ||||||||||||||
| Method | Paired-end mapping (PEM) | ||||||||||||||
| Name | |||||||
| Breakpoint 1 | chrX:6146833-6146975 | Breakpoint 2 | chrX:6148211-6148382 | ||||
| Individuals |
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- Martinez-Fundichely et al. 2014 (in preparation)
| Description | Accurate prediction of inversions in the human genome from Kidd et al. 2008 fosmid paired-end mapping data using the GRIAL algorithm, and validation of some predictions by sequence analysis and PCR | ||||||||||||||||||||||||||||||||||||||
| Method | Paired-end mapping (PEM) | ||||||||||||||||||||||||||||||||||||||
| Name | |||||||||||||||||||||||
| Breakpoint 1 | chrX:6106097-6147760 | Breakpoint 2 | chrX:6147959-6186777 | ||||||||||||||||||||
| D/C Score | NA | Disc. Support Prob. | 0.99991 | ||||||||||||||||||||
| Support | 2 probes  | ||||||||||||||||||||||
| Individuals |
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+ Validation and genotyping
| Description | Discovery, genotyping and phasing of structural variants detected from Illumina whole genome sequencing data of 769 individuals from 250 Dutch families belonging to the GoNL project | ||||
| Method | Polymerase chain reaction (PCR) |
| Status | Inconclusive |
| Comment | Tested in sample A139c. PCR assay failed. |
| Description | Identification and resolution of sequence gaps and structural variants in the euchromatic regions of the reference human assembly through single-molecule, real-time (SMRT) DNA sequencing of an haploid human genome (CHM1) | ||||
| Method | Sequence analysis |
| Status | Validated |
| Comment | Inversion validated by analysis of CH17-285M6 BAC sequence (AC255440) obtained with PacBio long reads |
-Martinez-Fundichely et al. 2014 (in preparation)
| Description | Accurate prediction of inversions in the human genome from Kidd et al. 2008 fosmid paired-end mapping data using the GRIAL algorithm, and validation of some predictions by sequence analysis and PCR | ||||
| Method | Polymerase chain reaction (PCR) |
| Status | Validated |
| Genotyping | 10 individuals: 8 HapMap/1000GP, 2 Other 4 STD/STD - 1 STD/INV - 3 INV/INV - 2 STD |
- Frequency
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+ Africa (AFR)
| Population | Sample and Study | Independent individuals | Inverted alleles | Standard frequency | Inverted frequency | HWE p-value |
|---|---|---|---|---|---|---|
Yoruba
|
Yoruba in Ibadan, Nigeria (YRI) (Martinez-Fundichely et al. 2014 (in preparation)) | 4 | 4 | 0.4286 | 0.5714 | < 0.05 |
| Africa (AFR)
|
Africa (AFR) summary | 4 | 4 | 0.4286 | 0.5714 | < 0.05 |
|---|
+ Europe (EUR)
| Population | Sample and Study | Independent individuals | Inverted alleles | Standard frequency | Inverted frequency | HWE p-value |
|---|---|---|---|---|---|---|
| Northwestern European
|
Utah residents with Northern and Western European ancestry (CEU) (Martinez-Fundichely et al. 2014 (in preparation)) | 2 | 1 | 0.7500 | 0.2500 | > 0.5 |
| Europe (EUR)
|
Europe (EUR) summary | 2 | 1 | 0.7500 | 0.2500 | > 0.5 |
|---|
+ East Asia (EAS)
| Population | Sample and Study | Independent individuals | Inverted alleles | Standard frequency | Inverted frequency | HWE p-value |
|---|---|---|---|---|---|---|
| Han Chinese
|
Han Chinese in Beijing, China (CHB) (Martinez-Fundichely et al. 2014 (in preparation)) | 1 | 0 | 1.0000 | 0.0000 | NA |
| Japanese
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Japanese in Tokyo, Japan (JPT) (Martinez-Fundichely et al. 2014 (in preparation)) | 1 | 0 | 1.0000 | 0.0000 | NA |
| East Asia (EAS)
|
East Asia (EAS) summary | 2 | 0 | 1.0000 | 0.0000 | NA |
|---|
+ Unknown
| Population | Sample and Study | Independent individuals | Inverted alleles | Standard frequency | Inverted frequency | HWE p-value |
|---|---|---|---|---|---|---|
| Unknown
|
Unknown (Martinez-Fundichely et al. 2014 (in preparation)) | 2 | 2 | 0.3333 | 0.6667 | NA |
| Unknown
|
Unknown summary | 2 | 2 | 0.3333 | 0.6667 | NA |
|---|
+ Breakpoints
| Breakpoint 1 | chrX:6147047-6147049 | Breakpoint 2 | chrX:6148391-6148392 | ||
| Study | Martinez-Fundichely et al. 2014 (in preparation) | ||||
| Description | Breakpoints defined by sequencing of inverted PCR fragments | ||||
| Definition method | Manual curation | ||||
| Mechanism of origin |
FoSTeS or NHEJ
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| Flexibility | 11.14 | GC content | 0.33 | Stability | 1.78 |
| Comments |
Inverted region is flanked by two small deletions of 8 bp and 0.4 kb and a 6 bp duplication, and was probably generated by several FoSTeS events mediated by microhomology or NHEJ followed by a deletion |
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+ Evolutionary history
| Ancestral allele | NA | Age | ND |
| Derived allele | NA | Origin | ND |
+ Orientation in other species
Not defined
+ Age
Not defined
+ Origin
Not defined
+ Functional effects
- NLGN4X
| Gene position | chrX:5818082-6156706 |
| Mechanism | Inverts a region within an intron of a gene |
+ Inversion phenotypical effects
Not defined
+ Report history
- 2017-09-29 00:00:00
| Breakpoint 1 | chrX:6146375-6147433 | Breakpoint 2 | chrX:6147959-6148811 |
| Assembly | hg18 | ||
| Definition method | Default informatic definition | ||
- 2017-09-29 00:00:00
| Breakpoint 1 | chrX:6146375-6147433 | Breakpoint 2 | chrX:6147959-6148811 |
| Assembly | hg18 | ||
| Definition method | Default informatic definition | ||
- 2015-02-23 10:14:36
| Breakpoint 1 | chrX:6146375-6147433 | Breakpoint 2 | chrX:6147959-6148811 |
| Assembly | hg18 | ||
| Definition method | Default informatic definition | ||
- 2015-02-23 10:14:36
| Breakpoint 1 | chrX:6147047-6147049 | Breakpoint 2 | chrX:6148391-6148392 |
| Study | Martinez-Fundichely et al. 2014 (in preparation) | ||
| Assembly | hg18 | ||
| Description | Breakpoints defined by sequencing of inverted PCR fragments | ||
| Definition method | Manual curation | ||
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Contact us at invfestdb@researchmar.net
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