Table 6.
DGAP268, DGAP285, DGAP288, DGAP290, and DGAP295: Significant Protein-Coding Genes Surrounding the Breakpoints according to TADs and Convergent Genomic Evidence
| Gene | Nucleotides (GRCh37/hg19) | Description | OMIM37 | OMIM Morbid37 | DDG2P39 | HI (%)36 | Notes |
|---|---|---|---|---|---|---|---|
| DGAP268: 10p12.31 Breakpoints on Rearrangement_B (21,606,655) and Rearrangement_C (21,606,63{4-2}) | |||||||
| No significant gene within the same TAD as the breakpoints | |||||||
| DGAP268: 10p12.2 Breakpoints on Rearrangement_A (23,659,495∼) and Rearrangement_C (23,659,20{0-2}) | |||||||
| No significant gene within the same TAD as the breakpoints | |||||||
| DGAP268: 10q23.32 Breakpoints on Rearrangement_A (93,983,897∼) and Rearrangement_B (93,982,408) | |||||||
|
CPEB3 (disrupted) |
93,806,449–94,050,844 | cytoplasmic polyadenylation element binding protein 3 | 610606 | − | − | 12.96 | no reported phenotype association |
| DGAP285: Xp11.21 Breakpoints on Rearrangement_A (55,174,723∼) and Rearrangement_B (55,174,381∼) | |||||||
|
FAM104B (disrupted) |
55,169,535–55,187,743 | family with sequence similarity 104 member B | − | − | − | 93.08 | no reported phenotype association |
| DGAP285: Xq28 Breakpoints on Rearrangement_A (150,286,207∼) and Rearrangement_B (150,284,569∼) | |||||||
| MTM1 | 149,737,069–149,841,795 | myotubularin 1 | 300415 | + | + | 12.54 | hemizygous loss of function (X-linked recessive) associated with X-linked myotubular myopathy69 (overlapping the phenotype of DGAP285) |
| DGAP288: 6q21 Breakpoints on Rearrangement_A (112,976,04{2-4}) and Rearrangement_B (112,976,031) | |||||||
| No significant gene within the same TAD as the breakpoints | |||||||
| DGAP288: 17q24.3 Breakpoints on Rearrangement_A (69,728,01{7-9}) and Rearrangement_B (69,728,006) | |||||||
| SOX9 | 70,117,161–70,122,561 | SRY-box 9 | 608160 | + | + | 0.56 | haploinsufficient (autosomal dominant, monoallelic) long-range cis-regulation associated with Pierre Robin sequence28 (overlapping the phenotype of DGAP288) |
| DGAP290: 2q32.3 Breakpoints on Rearrangement_A (197,164,194) and Rearrangement_B (197,164,206) | |||||||
|
HECW2 (disrupted) |
197,059,094–197,458,416 | HECT, C2, and WW domain containing E3 ubiquitin protein ligase 2 | − | − | − | 18.5 | no reported phenotype association |
| DGAP290: 7q33 Breakpoints on Rearrangement_A (135,905,923), Rearrangement_B (135,299,810), and Rearrangement_C (135,299,81{2} and 135,905,92{4}) | |||||||
|
NUP205 (disrupted) |
135,242,667–135,333,505 | nucleoporin 205 | 614352 | − | − | 11.41 | no reported phenotype association |
| DGAP295: 2p13.3 Breakpoints on Rearrangement_D (69,588,420∼) and Rearrangement_E (69,588,264∼) | |||||||
|
GFPT1 (disrupted) |
69,546,905–69,614,382 | glutamine-fructose-6-phosphate transaminase 1 | 138292 | + | − | 22.36 | biallelic loss of function (autosomal recessive) associated with congenital myasthenia type 1270 (no overlap with the phenotype of DGAP295) |
| DGAP295: 11p15.5 Breakpoints on Rearrangement_A (1,915,057∼ and 1,936,993∼), Rearrangement_B (1,960,727∼ and 1,936,668∼), Rearrangement_C (1,915,843∼ and 1,961,361∼), Rearrangement_D (1,984,895∼), and Rearrangement_E (1,985,019∼) | |||||||
| IGF2 | 2,150,342–2,170,833 | insulin-like growth factor 2 | 147470 | + | + | 79.01 | imprinted loss of function (epimutation) associated with GRDF71 and Silver-Russell syndrome72 (overlapping the phenotype of DGAP295) |
Abbreviations are as follows: DDG2P, Developmental Disorders Genotype-to-Phenotype database; GRDF, growth restriction with distinctive facies; and HI, haploinsufficiency index.