| Accession | HsInv0201 | Region of the inversion | chr5:147533233-147534971 |
| Status | Validated | Prediction type | Complex |
| Estimated Inversion Size | 1,058 bp | Supporting predictions | 6 |
| Inverted allele frequency | 0.5327 | Mechanism of origin | NHEJ or FoSTeS |
| Functional effect | Inverts a region within an intron of a gene | Breakpoint 1 | chr5:147533233-147534432 |
| Ancestral orientation | Standard | Breakpoint 2 | chr5:147534809-147534971 |
| Comments | There are two small deletions flanking the inverted region that remove exon 3 of the SPINK14 gene
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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 | chr5:147533236-147533236 | Breakpoint 2 | chr5:147534810-147534810 |
| Individuals | |||
| Description | Integrated analysis of structural variants in 2,504 human genomes through short-read and long-read DNA sequencing and statistical imputation using the 1000 Genomes Project data | ||||||||||
| Method | Paired-end mapping (PEM), Long-read sequencing | ||||||||||
| Name | |||
| Breakpoint 1 | chr5:147533059-147533059 | Breakpoint 2 | chr5:147534810-147534810 |
| Individuals | 1735 out of 2504 individuals
 | ||
| Description | Next generation sequencing and analysis by paired-end mapping of an individual genome of African origin | ||||||||||||||
| Method | Paired-end mapping (PEM) | ||||||||||||||
| Name | |||||||
| Breakpoint 1 | chr5:147533908-147534427 | Breakpoint 2 | chr5:147534807-147535132 | ||||
| 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 | chr5:147532995-147533235 | Breakpoint 2 | chr5:147534546-147534801 | ||||
| Individuals |
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| Name | |||||||
| Breakpoint 1 | chr5:147534427-147534639 | Breakpoint 2 | chr5:147534984-147535190 | ||||
| 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 | chr5:147493556-147534433 | Breakpoint 2 | chr5:147534773-147575793 | ||||||||||||||||||||
| D/C Score | NA | Disc. Support Prob. | 0.99918 | ||||||||||||||||||||
| 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 | Validated |
| Comment | Tested in sample A105c |
| Description | Integrated analysis of structural variants in 2,504 human genomes through short-read and long-read DNA sequencing and statistical imputation using the 1000 Genomes Project data | ||||
| Method | Sequence analysis |
| Status | Validated |
| Comment | Inversion flanked by more than one deletion validated by sequence analysis of PacBio long reads from fosmids |
| Description | Population genetic analysis of an inversion by bioinformatic identification of its breakpoints and experimental genotyping by PCR | ||||
| Method | Polymerase chain reaction (PCR) |
| Status | Validated |
| Genotyping | 271 individuals: 270 HapMap/1000GP, 1 Other 61 STD/STD - 121 STD/INV - 87 INV/INV - 2 ND |
-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 2 STD/STD - 5 STD/INV - 3 INV/INV |
- 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 | 60 | 83 | 0.3083 | 0.6917 | > 0.5 |
| Africa (AFR)
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Africa (AFR) summary | 60 | 83 | 0.3083 | 0.6917 | > 0.5 |
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+ Europe (EUR)
| Population | Sample and Study | Independent individuals | Inverted alleles | Standard frequency | Inverted frequency | HWE p-value |
|---|---|---|---|---|---|---|
| Northwestern European
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All samples and studies | 63 | 66 | 0.4762 | 0.5238 | > 0.5 |
| Europe (EUR)
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Europe (EUR) summary | 63 | 66 | 0.4762 | 0.5238 | > 0.5 |
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+ East Asia (EAS)
| Population | Sample and Study | Independent individuals | Inverted alleles | Standard frequency | Inverted frequency | HWE p-value |
|---|---|---|---|---|---|---|
| Han Chinese
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All samples and studies | 44 | 44 | 0.5000 | 0.5000 | > 0.2 |
| Japanese
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All samples and studies | 45 | 33 | 0.6333 | 0.3667 | > 0.5 |
| East Asia (EAS)
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East Asia (EAS) summary | 89 | 77 | 0.5674 | 0.4326 | > 0.5 |
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+ 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 | > 0.1 |
| Unknown
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Unknown summary | 2 | 2 | 0.5000 | 0.5000 | > 0.1 |
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+ Breakpoints
| Breakpoint 1 | chr5:147533233-147534432 | Breakpoint 2 | chr5:147534809-147534971 | ||
| Study | Martinez-Fundichely et al. 2014 (in preparation) | ||||
| Description | Breakpoints defined by comparison with Celera Human Genome assembly and sequencing of inverted PCR fragments | ||||
| Definition method | Manual curation | ||||
| Mechanism of origin |
NHEJ or FoSTeS
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| Flexibility | 11.18 | GC content | 0.38 | Stability | 1.74 |
| Comments |
Inverted region is flanked by two deletions of 1.2 kb and 0.2 kb and was probably generated by NHEJ or FoSTeS with no microhomology. Breakpoint positions comprise each deleted sequence. |
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+ Evolutionary history
| Ancestral allele | Standard | Age | ND |
| Derived allele | Inverted | Origin | Unique |
+ Orientation in other species
| Species | Orientation | Method | Study |
| Chimpanzee | Standard | Comparison between sequences | INVFEST curation |
| Rhesus macaque | Standard | Comparison between sequences | INVFEST curation |
+ Age
Not defined
+ Origin
| Origin | Method | Study |
| Unique | Analysis of breakpoints sequences | Lucas-Lledo et al. 2014 |
+ Functional effects
- SPINK14
| Gene position | chr5:147529488-147535154 |
| Mechanism | Inverts a region within an intron of a gene |
| Study | INVFEST curation |
| Effect | One of the deletions flanking the inverted region remove exon 3 of the SPINK5L2 gene |
| Functional consequences | Unknown |
+ Inversion phenotypical effects
Not defined
+ Report history
HsInv0749 incorporated information to HsInv0201
- 2017-09-29 00:00:00
| Breakpoint 1 | chr5:147528236-147538059 | Breakpoint 2 | chr5:147529810-147539810 |
| Assembly | hg18 | ||
| Definition method | Default informatic definition | ||
- 2017-09-18 00:00:00
| Breakpoint 1 | chr5:147528059-147538059 | Breakpoint 2 | chr5:147529810-147539810 |
| Assembly | hg18 | ||
| Definition method | Default informatic definition | ||
- 2016-12-09 18:59:43
| Breakpoint 1 | chr5:147533233-147534432 | Breakpoint 2 | chr5:147534809-147534971 |
| Study | Martinez-Fundichely et al. 2014 (in preparation) | ||
| Assembly | hg18 | ||
| Description | Breakpoints defined by comparison with Celera Human Genome assembly and sequencing of inverted PCR fragments | ||
| Definition method | Manual curation | ||
- 2015-02-23 10:14:33
| Breakpoint 1 | chr5:147532635-147533595 | Breakpoint 2 | chr5:147534201-147535146 |
| Assembly | hg18 | ||
| Definition method | Default informatic definition | ||
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