| Accession | HsInv0389 | Region of the inversion | chrX:153219602-153275629 |
| Status | Validated | Prediction type | Simple |
| Estimated Inversion Size | 46,822 bp | Supporting predictions | 2 |
| Inverted allele frequency | 0.2105 | Mechanism of origin | NAHR |
| Functional effect | Intergenic breakpoints | Breakpoint 1 | chrX:153219602-153228808 |
| Ancestral orientation | ND | Breakpoint 2 | chrX:153266422-153275629 |
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Human Polymorphic Inversion DataBase
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General information
- Region map
+ Predictions
| Description | Identification of a common X-chromosome inversion by analysis of EMD deletions | ||||||||||
| Method | Southern blot analysis | ||||||||||
| Name | |||
| Breakpoint 1 | chrX:153217480-153228808 | Breakpoint 2 | chrX:153266422-153277757 |
| Individuals | |||
- 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:153218406-153229208 | Breakpoint 2 | chrX:153265868-153274315 | ||||||||||||||||||||
| D/C Score | 1.5 | Disc. Support Prob. | 1 | ||||||||||||||||||||
| Support | 95 probes  | ||||||||||||||||||||||
| Individuals |
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+ Validation and genotyping
| Description | Identification of a common X-chromosome inversion by analysis of EMD deletions | ||||
| Method | Southern blot analysis |
| Status | Validated |
| Genotyping | 85 individuals: 85 unknown 14 STD/STD - 7 STD/INV - 52 STD - 12 INV |
| Description | Validation and genotyping of 22 inversion predictions by inverse PCR | ||||
| Method | Inverse polymerase chain reaction (iPCR) |
| Status | Validated |
| Genotyping | 77 individuals: 76 HapMap/1000GP, 1 Other 31 STD/STD - 8 STD/INV - 5 INV/INV - 23 STD - 9 INV - 1 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 | Fosmid sequence analysis |
| 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
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Yoruba in Ibadan, Nigeria (YRI) (Aguado et al. 2014) | 4 | 7 | 0.0000 | 1.0000 | NA |
| Africa (AFR)
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Africa (AFR) summary | 4 | 7 | 0.0000 | 1.0000 | NA |
|---|
+ 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) (Aguado et al. 2014) | 48 | 13 | 0.8169 | 0.1831 | > 0.05 |
| Europe (EUR)
|
Europe (EUR) summary | 48 | 13 | 0.8169 | 0.1831 | > 0.05 |
|---|
+ East Asia (EAS)
| Population | Sample and Study | Independent individuals | Inverted alleles | Standard frequency | Inverted frequency | HWE p-value |
|---|---|---|---|---|---|---|
| Han Chinese
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Han Chinese in Beijing, China (CHB) (Aguado et al. 2014) | 1 | 0 | 1.0000 | 0.0000 | NA |
| Japanese
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Japanese in Tokyo, Japan (JPT) (Aguado et al. 2014) | 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 | 86 | 20 | 0.8148 | 0.1852 | > 0.2 |
| Unknown
|
Unknown summary | 86 | 20 | 0.8148 | 0.1852 | > 0.2 |
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+ Breakpoints
| Breakpoint 1 | chrX:153219602-153228808 | Breakpoint 2 | chrX:153266422-153275629 | |||||||||||||
| Study | Martinez-Fundichely et al. 2014 (in preparation) | |||||||||||||||
| Description | Breakpoints defined by comparison with four sequenced fosmids | |||||||||||||||
| Definition method | Manual curation | |||||||||||||||
| Mechanism of origin |
NAHR
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| Flexibility | 10.67 | GC content | 0.51 | Stability | 2.01 |
| Comments |
Inversion generated by non-allelic homologous recombination (NAHR) between 11.3 kb inverted SDs with 99% identity |
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Sequence features |
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Segmental duplications:
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+ Evolutionary history
| Ancestral allele | ND | Age | ND |
| Derived allele | NA | Origin | Recurrent |
+ Orientation in other species
| Species | Orientation | Method | Study |
| Chimpanzee | Inverted | Paired-end mapping (PEM) | Caceres et al. 2007 |
| Orangutan | Standard | Paired-end mapping (PEM) | Caceres et al. 2007 |
| Rhesus macaque | Inverted | Paired-end mapping (PEM) | Caceres et al. 2007 |
| Gibbon | Inverted | Paired-end mapping (PEM) | Caceres et al. 2007 |
| Chimpanzee | Inverted | Inverse polymerase chain reaction (iPCR) | Aguado et al. 2014 |
| Gorilla | Inverted | Inverse polymerase chain reaction (iPCR) | Aguado et al. 2014 |
+ Age
Not defined
+ Origin
| Origin | Method | Study |
| Recurrent | Paired-end mapping (PEM) | Caceres et al. 2007 |
| Recurrent | Inverted polymerase chain reaction (iPCR) | Aguado et al. 2014 |
+ Functional effects
No genes disrupted by the inversion breakpoints
+ Inversion phenotypical effects
| The presence of the inversion has been associated with EMD deletions causing Emery Dreifuss muscular dystrophy | Small et al. 1997 |
+ Report history
- 2015-02-23 10:14:38
| Breakpoint 1 | chrX:153218406-153228808 | Breakpoint 2 | chrX:153266422-153274315 |
| Assembly | hg18 | ||
| Definition method | Default informatic definition | ||
- 2015-02-23 10:14:38
| Breakpoint 1 | chrX:153219602-153228808 | Breakpoint 2 | chrX:153266422-153275629 |
| Study | Martinez-Fundichely et al. 2014 (in preparation) | ||
| Assembly | hg18 | ||
| Description | Breakpoints defined by comparison with four sequenced fosmids | ||
| Definition method | Manual curation | ||
- 2015-02-23 10:14:38
| Breakpoint 1 | chrX:153218406-153229208 | Breakpoint 2 | chrX:153265868-153274315 |
| Assembly | hg18 | ||
| Definition method | Default informatic definition | ||
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Contact us at invfestdb@researchmar.net
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