TABLE 5.
Size of the deletions and haploinsufficient genes located within the atypical NF1 deletions.
| Patient | Deletion size (Mb) | Haploinsufficient genes (by gnomAD pLI) | References |
| BUD | 4.7 | ATAD5, NF1, OMG, RAB11FIP4, SUZ12, PSMD11, CDK5R1, ASIC2 | Kehrer-Sawatzki et al., 2003 |
| 3724A | 2.0-3.1 | ATAD5, NF1, OMG, RAB11FIP4, SUZ12, PSMD11, CDK5R1, ASIC2 | Cnossen et al., 1997 |
| 6 | 3 | ATAD5, NF1, OMG, RAB11FIP4, SUZ12, PSMD11, CDK5R1, ASIC2 | Venturin et al., 2004a, b |
| UWA106-3 | 3.2-3.7 | ATAD5, NF1, OMG, RAB11FIP4, SUZ12, PSMD11, CDK5R1, ASIC2 | Dorschner et al., 2000; Kayes et al., 1992; Kayes et al., 1994 |
| 442 | 2 | ATAD5, NF1, OMG, RAB11FIP4, SUZ12 | Kehrer-Sawatzki et al., 2005 |
| BL | ∼3 | ATAD5, NF1, OMG, RAB11FIP4, SUZ12, PSMD11, CDK5R1, ASIC2 | Riva et al., 2000 |
| ID806 | ∼7 | ATAD5, NF1, OMG, RAB11FIP4, SUZ12, PSMD11, CDK5R1, ASIC2 | Upadhyaya et al., 1996 |
| UWA155-1 | 2.1-2.7 | NF1, OMG, RAB11FIP4, SUZ12, PSMD11, CDK5R1, ASIC2 | Upadhyaya et al., 1996 |
| 118 | N/A | ATAD5, NF1 | Venturin et al., 2004b |
| 282775 | > 1.33 | NF1, OMG, RAB11FIP4, SUZ12 | Mantripragada et al., 2006 |
| 552 | 2.7 | NF1, OMG, RAB11FIP4, SUZ12, PSMD11, CDK5R1, ASIC2 | Kehrer-Sawatzki et al., 2008 |
| 40 | 1.27-1.46* | NF1, OMG, RAB11FIP4, SUZ12, | Zhang et al., 2015 |
| 56 | 0.60-1.14* | ATAD5, NF1, OMG | |
| 73 | 0.93-1.28* | NF1, OMG, RAB11FIP4, SUZ12 | |
| 76 | 1.26-1.63* | ATAD5, NF1, OMG, RAB11FIP4, SUZ12 | |
| 556/NF | 1.122 | ATAD5, NF1, OMG, RAB11FIP4, SUZ12 | This study |
| 125/NF | 1.635* | ATAD5, NF1, OMG, RAB11FIP4, SUZ12 | |
| 134/NF | 0.618* | ATAD5, NF1, OMG | |
| 260/NF | 0.618* | ATAD5, NF1, OMG |
*Results originated from MLPA probes location. The probability of loss of function (pLI) metric were provided by the gnomAD browser (https://gnomad.broadinstitute.org/). According to official description, a transcript’s intolerance to variation is measured by predicting the number of variants expected to be seen in the gnomAD dataset and comparing those expectations to the observed amount of variation. The range scales from 0 to 1, where the closer the pLI value is to 1, the more intolerant the gene appears to be to loss of function (LoF) variants. We determined as haploinsufficient a gene if the pLI value was above 0.9, which indicates extreme intolerance to LoF variants (Karczewski et al., 2020).