Table 2.
List of rare SVs impacting genes associated with NTDs in mouse
| Case ID | Mouse NTD | NTD observed in this study | Variant | Nomenclature | Gene | Size (bp) | Region(s) | Variant confirmation | Inheritance | Evidence (literature/ internal database) | Evidence for association with NTDs |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 9 | Open NTD | Spina bifida | Deletion | ogm[GRCh38] 9p24.3(82,669_173,653) × 1 |
FOXD4 | 54,206 | Whole gene | qPCR | Not maternal | Neilson et al. (2012); McMohan et al. (2022) | S |
| 10 | Open NTD | Spina bifida (OEIS) | Deletion | ogm[GRCh38] 1p35.1(32,671,257_32,688,145) × 1 |
RBBP4 | 4904 | 3′ UTR | qPCR | Not determined | Miao et al. (2020) | S |
| 11 | Exencephaly | Anencephaly | Deletion | ogm[GRCh38] 18p11.31(3,151,509_3,517,870) × 1 |
TGIF1 | 334,545 | Whole gene | CMA | Paternal | MIM# 142946 | S |
| 12 | Exencephaly | Anencephaly | Insertion | ogm[GRCh38] ins(13)(q12.11)(20,599,264_20,606,931) |
IFT88 | 2707 | Intron 11 | _ | Not determined | Pazour et al. (2000); Ohazama et al. (2009); Tian et al. (2017); Au et al. (2021) | M |
| Deletion | ogm[GRCh38] 1p34.2(42,442,313_42,468,422) × 1 |
ZMYND12 | 6794 | Exons 2 and 3 | qPCR | Not determined | Wang et al. (2022) | ||||
| 13 | Anencephaly | Craniorachischisis | Deletion | ogm[GRCh38] 8q24.3(144,474,228_144,518,767) × 1 |
FOXH1 | 2759 | Regulatory region | CMA* | Not determined | Roessler et al. (2008); Internal database: One anencephaly case with FOXH1 deletion | M |
| Deletion | ogm[GRCh38] 16p12.2(21,660,813_22,434,434) × 1 |
16p12.2 | 773,622 | CMA | Not determined | 16p12.2-p11.2 deletion syndrome (MIM# 613604) | |||||
| 14 | Abnormal neural tube closure | Meroacrania Type Anencephaly | Insertion | ogm[GRCh38] ins(3)(p22.3;p22.3)(32,703,720–32,716,482) |
CNOT10 | 3236 | Intragenic | _ | Not determined | Internal database: One fetal demise case carries a heterozygous deletion of CNOT10 | M |
| 15 | Exencephaly | Anencephaly | Duplication | ogm[GRCh38] dup(7)(p21.1p21.1)(18,813,738_19,816,010) × 3 |
TWIST1 | 1,002,272 | Whole gene | CMA | Paternal | MIM# 601622 | W |
| 16 | Open neural tube | Spina bifida | Duplication | ogm[GRCh38] 19q13.43q13.43(58,513,157_58,564,834) × 3 | TRIM28 | 51,677 | Whole gene | qPCR | Paternal | Lee and Gleeson (2020) | W |
| 17 | Exencephaly | Spina bifida | Duplication | ogm[GRCh38] 1p36.33(1,624,078_1,691,055) × 3 |
MIB2 | 66,977 | Whole gene | _ | Not determined | Wu et al. (2007) | W |
-
(S) Strong, (M) moderate, (W) weak; CMA*(CMA was indicative of the copy number loss), (OEIS) omphalocele-exstrophy-imperforate anus-spinal defects.
