Table 3.
List of rare SVs impacting genes implicated in NTD pathways
| Case ID | NTD type | Variant | Nomenclature | Gene(s) | Region(s) | Size (bp) | Variant confirmation | Inheritance | Evidence (literature/ internal database) | Evidence for association with NTDs |
|---|---|---|---|---|---|---|---|---|---|---|
| 18 | Anencephaly | Inversion | ogm[GRCh38] inv(2)(p11.2p11.2)(87,054,207_86,742,515) |
RMND5A | Gene disruption | 311,692 | _ | Not maternal | Vogel et al. (2012); Pfirrmann et al. (2015) | S |
| 19 | Encephalocele (Meckel syndrome) | Inversion | ogm[GRCh38] inv(2)(p11.2p11.2)(87,054,207_86,742,515) |
RMND5A | Gene disruption | 311,693 | _ | Not determined | S | |
| 20 | Anencephaly | Duplication | ogm[GRCh38] 14q11.2(21,253,761_21,311,033) × 3 |
HNRNPC | Exon 1 and 2 (both noncoding) | 57,272 | qPCR | de novo | MIM # 620688; Liu et al. (2020); Niggl et al. (2023) |
S |
| 21 | Spina bifida (OEIS) | Duplication | ogm[GRCh38] 14q11.2q11.2(20,990,605_21,390,099) × 3 |
HNRNPC | Whole gene | 399,494 | qPCR | Not determined | S | |
| 22 | Anencephaly | Deletion | ogm[GRCh38] 3p21.31(48,540,706_48,558,562) × 1 |
PFKFB4 | Exon 2 and 3 deletion | 3260 | qPCR | de novo | Pegoraro et al. (2015) | M |
| 23 | Encephalocele | Deletion | ogm[GRCh38] 19p13.2(9,370,139_9,529,559) × 1 |
ZNF266 | Whole gene | 147,320 | qPCR | Not determined | Internal database: Two cases with similar deletion: 1 with MCA; 2 in fetal demise | W |
| 24 | Spina bifida (OEIS) | Deletion | ogm[GRCh38] 15q25.3(85,036,822_85,102,540) × 1 |
PDE8A | Exons 2–10 | 50,956 | qPCR | Not determined | Internal database: same deletion in a case of fetal demise | W |
| Deletion | ogm[GRCh38] 18p11.21(10,982,344_11,061,530) × 1 |
PIEZO2 | Intron 2 | 72,238 | qPCR | Not determined | (MIM# 248700, 114300, 108145) | W | ||
| 25 | Anencephaly | Deletion | ogm[GRCh38] 5p13.2(34,009,171_34,049,829) × 1 |
C1QTNF3 | Whole gene | 30,311 | qPCR | Not determined | MIM# 612045 | W |
| 26 | Anencephaly | Deletion | ogm[GRCh38] 5q35.1(173,140,602_173,149,664) × 1 |
BNIP1 | Exon 1 and 2 | 3853 | _ | MIM# 603291 | W | |
| 27 | Anencephaly | Duplication | ogm[GRCh38] Xp22.2(11,017,889_11,437,394) × 3 |
HCCS, AMELX | Whole genes | 419,505 | qPCR | Maternal | HCCS: MIM# 309801, AMELX: MIM# 301200 | W |
| 28 | Anencephaly | Rearrangement | ogm[GRCh38] dup(1)(p36.13p36.13) |
SDHB, MFAP2 | Multiple genes | 378,106 | _ | Not determined | MIM# 185470 | W |
| 29 | Anencephaly | Duplication | ogm[GRCh38] 8p21.2(23,701,105_24,412,415) × 2∼3 |
NKX2-6 | Whole gene | 711,311 | qPCR | Not determined | MIM #217095 | W |
| 30 | Anencephaly | Duplication | ogm[GRCh38] dup(10)(q22.3q22.3) |
KCNMA1 | Exon 1 and 2 | 371,692 | _ | Not determined | MIM #618729 | W |
| 31 | Anencephaly | Duplication | ogm[GRCh38] 1q21.1(145,497,462_145,815,386) × 3 |
_ | Partial locus-mosaic | 317,924 | qPCR | Not determined | Partial duplication of 1q21.1 locus | W |
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(S) Strong, (M) moderate, (W) weak, (OEIS) omphalocele-exstrophy-imperforate anus-spinal defects.
