| Accession | HsInv0073 | Region of the inversion | chrX:46694748-46716632 |
| Status | Validated | Prediction type | Simple |
| Estimated Inversion Size | 20,166 bp | Supporting predictions | 5 |
| Inverted allele frequency | 1.0000 | Mechanism of origin | NAHR |
| Functional effect | Inverts a region within an intron of a gene | Breakpoint 1 | chrX:46694748-46696216 |
| Ancestral orientation | NA | Breakpoint 2 | chrX:46714661-46716632 |
| Comments | Standard orientation is possibly a low frequency variant or HG18 assembly error
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Human Polymorphic Inversion DataBase
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General information
- Region map
+ Predictions
| 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 | chrX:46695609-46695938 | Breakpoint 2 | chrX:46715443-46716144 | ||||
| Individuals |
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| Description | Paired-end mapping of 3-kb fragments in an African and in a putatively European individual with some predictions validated by PCR, fiber-FISH or comparison with Celera assembly | ||||||||||||||||||||||||||||||||||
| Method | Paired-end mapping (PEM) | ||||||||||||||||||||||||||||||||||
| Name | |||||||||
| Breakpoint 1 | chrX:46694985-46694985 | Breakpoint 2 | chrX:46714070-46714070 | ||||||
| Individuals |
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| Name | |||||||||
| Breakpoint 1 | chrX:46695472-46695472 | Breakpoint 2 | chrX:46713315-46713315 | ||||||
| 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 | chrX:46695748-46695748 | Breakpoint 2 | chrX:46715632-46715632 | ||||
| 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:46680192-46696216 | Breakpoint 2 | chrX:46714661-46736381 | ||||||||||||||||||||
| D/C Score | NA | Disc. Support Prob. | 1 | ||||||||||||||||||||
| Support | 88 probes  | ||||||||||||||||||||||
| Individuals |
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+ Validation and genotyping
| Description | Sequence analysis of structural variant breakpoints and experimental genotyping of inversions by PCR | ||||||
| Method | Polymerase chain reaction (PCR) |
| Status | Validated |
| Genotyping | 42 individuals (No genotypes available) |
| Comment | Inversion genotyped in 42 individuals of diverse origin (63 INV alleles) |
| Description | Paired-end mapping of 3-kb fragments in an African and in a putatively European individual with some predictions validated by PCR, fiber-FISH or comparison with Celera assembly | ||
| Method | Polymerase chain reaction (PCR) |
| Status | Validated |
- 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) (Pang et al. 2013) | 10 | NA | 0.0000 | 1.0000 | NA |
| Africa (AFR) | Africa (AFR) summary | 10 | NA | 0.0000 | 1.0000 | NA |
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+ 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) (Pang et al. 2013) | 12 | NA | 0.0000 | 1.0000 | NA |
| Europe (EUR) | Europe (EUR) summary | 12 | NA | 0.0000 | 1.0000 | NA |
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+ 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) (Pang et al. 2013) | 10 | NA | 0.0000 | 1.0000 | NA |
| Japanese | Japanese in Tokyo, Japan (JPT) (Pang et al. 2013) | 10 | NA | 0.0000 | 1.0000 | NA |
| East Asia (EAS) | East Asia (EAS) summary | 10 | NA | 0.0000 | 1.0000 | NA |
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+ Breakpoints
| Breakpoint 1 | chrX:46694748-46696216 | Breakpoint 2 | chrX:46714661-46716632 | ||
| Definition method | Default informatic definition | ||||
| Mechanism of origin |
NAHR
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| Flexibility | 10.08 | GC content | 0.58 | Stability | 2.09 |
| Comments |
Inversion generated by non-allelic homologous recombination (NAHR) between inverted AluSq2 and AluSz elements with ~90% identity |
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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
- PHF16
| Gene position | chrX:46656679-46805585 |
| Mechanism | Inverts a region within an intron of a gene |
+ Inversion phenotypical effects
Not defined
+ Report history
- 2015-02-23 10:14:37
| Breakpoint 1 | chrX:46694748-46696216 | Breakpoint 2 | chrX:46714661-46716632 |
| Assembly | hg18 | ||
| Definition method | Default informatic definition | ||
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Contact us at invfestdb@uab.cat
This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.