| Accession | HsInv1122 | Region of the inversion | chr3:164008437-164030349 |
| Status | Validated | Prediction type | Complex |
| Estimated Inversion Size | 12,096 bp | Supporting predictions | 6 |
| Inverted allele frequency | 0.2945 | Mechanism of origin | FoSTeS |
| Functional effect | Intergenic breakpoints | Breakpoint 1 | chr3:164008437-164028058 |
| Ancestral orientation | Standard | Breakpoint 2 | chr3:164030336-164030349 |
| Comments | Region comprises 3 different alleles: a 114.2 kb deletion removing the entire inversion region, the ancestral orientation and the derived orientation with the inversion. The derived allele includes two deletions of 19.6 kb and 14 bp flanking the inverted region (which make that some of the predictions are not consistent).
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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 | chr3:164008441-164008441 | Breakpoint 2 | chr3:164030344-164030344 |
| Individuals | |||
| Name | |||
| Breakpoint 1 | chr3:164028053-164028053 | Breakpoint 2 | chr3:164030345-164030345 |
| Individuals | |||
| Description | Paired-end mapping analysis of the J. Craig Venter genome (HuRef) | ||||||||||||||
| Method | Paired-end mapping (PEM) | ||||||||||||||
| Name | |||||||
| Breakpoint 1 | chr3:164007964-164009561 | Breakpoint 2 | chr3:164030337-164031814 | ||||
| Individuals |
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| Description | Next generation sequencing and analysis by paired-end mapping of a Korean individual genome | ||||||||||||||||||||||||||||||
| Method | Paired-end mapping (PEM) | ||||||||||||||||||||||||||||||
| Name | |||||||
| Breakpoint 1 | chr3:164008271-164008434 | Breakpoint 2 | chr3:164030071-164030328 | ||||
| Individuals |
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| Name | |||||||
| Breakpoint 1 | chr3:164028057-164028258 | Breakpoint 2 | chr3:164030368-164030612 | ||||
| Individuals |
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| Description | Sequencing and analysis of the independently assembled diploid J. Craig Venter genome (HuRef) | ||||||||||||||
| Method | Genome sequence comparison | ||||||||||||||
| Name | |||||||
| Breakpoint 1 | chr3:164028056-164028056 | Breakpoint 2 | chr3:164030335-164030335 | ||||
| Individuals |
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+ Validation and genotyping
| Description | Validation and characterization of human inversions predicted by comparison of two independently assembled human genomes | ||||||
| Method | Inverse polymerase chain reaction (iPCR) |
| Status | Validated |
| Genotyping | 98 individuals: 96 HapMap/1000GP, 2 Other 27 STD/DEL - 16 DEL/DEL - 19 INV/DEL - 7 STD/STD - 16 STD/INV - 13 INV/INV  |
| Comment | 114.2 kb deletion including the entire inversion region was genotyped independently by regular PCR |
| 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 | Validated |
| Comment | Tested in sample A105c |
| Method | Polymerase chain reaction (PCR) |
| Status | Validated |
| Comment | Tested in sample A105c |
| Description | Sequence analysis of structural variant breakpoints and experimental genotyping of inversions by PCR | ||||||
| Method | Polymerase chain reaction (PCR) |
| Status | Validated |
| Genotyping | 6 individuals: 4 HapMap/1000GP, 2 Other 1 STD/DEL - 1 DEL/DEL - 1 INV/DEL - 1 STD/STD - 1 STD/INV - 1 INV/INV |
| Comment | Quantitative and regular PCR confirmed the presence of a 19.6 kb deletion associated to the inverted allele and the existence of an additional 114.2 kb deletion including the entire inversion region |
- Frequency
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+ Africa (AFR)
| Population | Sample and Study | Independent individuals | Inverted alleles | Standard frequency | Inverted frequency | HWE p-value |
|---|---|---|---|---|---|---|
Yoruba
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All samples and studies | 5 | 0 | 1.0000 | 0.0000 | NA |
| Africa (AFR)
|
Africa (AFR) summary | 5 | 0 | 1.0000 | 0.0000 | NA |
|---|
+ Europe (EUR)
| Population | Sample and Study | Independent individuals | Inverted alleles | Standard frequency | Inverted frequency | HWE p-value |
|---|---|---|---|---|---|---|
| Northwestern European
|
All samples and studies | 64 | 41 | 0.6797 | 0.3203 | < 0.05 |
| Europe (EUR)
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Europe (EUR) summary | 64 | 41 | 0.6797 | 0.3203 | < 0.05 |
|---|
+ 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) (Vicente-Salvador et al. 2017) | 1 | 0 | 1.0000 | 0.0000 | NA |
| Japanese
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Japanese in Tokyo, Japan (JPT) (Vicente-Salvador et al. 2017) | 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
|
All samples and studies | 2 | 2 | 0.5000 | 0.5000 | 0 |
| Unknown
|
Unknown summary | 2 | 2 | 0.5000 | 0.5000 | 0 |
|---|
+ Breakpoints
| Breakpoint 1 | chr3:164008437-164028058 | Breakpoint 2 | chr3:164030336-164030349 | ||
| Study | Vicente-Salvador et al. 2017 | ||||
| Description | Breakpoints defined by comparison with HuRef Human Genome assembly | ||||
| Definition method | Manual curation | ||||
| Mechanism of origin |
FoSTeS
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| Flexibility | 11.17 | GC content | 0.28 | Stability | 1.75 |
| Comments |
Inverted region is flanked by two deletions of 19.6 kb and 14 bp, and was probably generated by two fork stalling and template switching (FoSTeS) events mediated by microhomology. Breakpoint positions comprise the deleted sequence. |
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+ Evolutionary history
| Ancestral allele | Standard | Age | ND |
| Derived allele | Inverted | Origin | ND |
+ Orientation in other species
| Species | Orientation | Method | Study |
| Chimpanzee | Standard | Polymerase chain reaction (PCR) | Pang et al. 2013 |
| Chimpanzee | Standard | Inverse polymerase chain reaction (iPCR) | Vicente-Salvador et al. 2017 |
| Gorilla | Standard | Inverse polymerase chain reaction (iPCR) | Vicente-Salvador et al. 2017 |
| Rhesus macaque | Standard | Genome sequence comparison | Vicente-Salvador et al. 2017 |
+ Age
Not defined
+ Origin
Not defined
+ Functional effects
No genes disrupted by the inversion breakpoints
+ Inversion phenotypical effects
Not defined
+ Report history
HsInv1000 and HsInv0052 merge into HsInv1122
- 2018-11-07 13:47:05
| Breakpoint 1 | chr3:164008437-164028058 | Breakpoint 2 | chr3:164030336-164030349 |
| Study | Vicente-Salvador et al. 2017 | ||
| Assembly | hg18 | ||
| Description | Breakpoints defined by comparison with HuRef Human Genome assembly | ||
| Definition method | Manual curation | ||
- 2017-12-15 00:00:00
| Breakpoint 1 | chr3:164003441-164033053 | Breakpoint 2 | chr3:164025345-164035344 |
| Assembly | hg18 | ||
| Definition method | Default informatic definition | ||
- 2017-12-14 14:17:12
| Breakpoint 1 | chr3:164008435-164028058 | Breakpoint 2 | chr3:164030336-164030351 |
| Assembly | hg18 | ||
| Description | Breakpoints defined by comparison with HuRef Human Genome assembly | ||
| Definition method | Manual curation | ||
- 2017-09-29 00:00:00
| Breakpoint 1 | chr3:164003441-164013441 | Breakpoint 2 | chr3:164025344-164035344 |
| Assembly | hg18 | ||
| Definition method | Default informatic definition | ||
- 2016-11-28 16:28:19
| Breakpoint 1 | chr3:164008436-164008437 | Breakpoint 2 | chr3:164030337-164030338 |
| Study | Pang et al. 2013 | ||
| Assembly | hg18 | ||
| Description | Breakpoints defined by comparison with HuRef Human Genome assembly | ||
| Definition method | Manual curation | ||
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Contact us at invfestdb@uab.cat
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