Table 1. Prioritized de novo variants.
| Ext-Code | Phenotype | Variant | HGNC | Refseq | gnomAD (MAF) | MutCDNA | MutProt | Mm | Gg | Dr | Xt |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 4_501 | VATER/VACTERL-like association | 1 | EEF1D | NM_032378.4 | c.874C>T | p.Arg292* | K | E | K | ||
| 2 | CELSR1 | NM_014246.1 | 3/282,594 (0.00001) | c.4357G>A | p.Val1453Ile | V | I | I | |||
| 21_501 | nonsyndromic | 3 | HPS3 | NM_032383.3 | 10/282,776 (0.00004) | c.1189C>T | p.Arg397Trp | H | R | R | R |
| 27_501 | nonsyndromic | 4 | PIGC | NM_153747.1 | c.716C>T | p.Ala239Val | A | G | A | ||
| 35_501 | VATER/VACTERL-like association | 5 | NFX1 | NM_002504.4 | c.1723G>A | p.Val575Met | V | V | |||
| 36_501 | nonsyndromic | 6 | ZFHX3 | NM_006885.3 | c.1601C>G | p.Pro534Arg | P | P | P | N | |
| 41_501 | VATER/VACTERL-like association | 7 | MTA3 | NM_020744.2 | 1/237,600 (0.000004) | c.393C>A | p.Phe131Leu | F | F | ||
| 46_501 | nonsyndromic | 8 | FANCB | NM_152633.2 | c.782G>A | p.Arg261Gln | R | Q | S | ||
| 9 | PLEC | NM_201379.1 | 17/272,690 (0.00006) | c.6704G>A | p.Arg2394His | R | R | K | R | ||
| 63_501 | VATER/VACTERL-like association | 10 | PPIP5K2 | NM_015216.2 | 2/247,732 (0.000008) | c.686G>A | p.Arg229Gln | R | R | R | R |
| 88_501 | nonsyndromic | 11 | CLP1 | NM_006831.2 | 1/251,486 (0.000003) | c.814C>A | p.His272Asn | H | H | H | H |
| 12 | GPR133 | NM_198827.3 | 6/282,534 (0.00002) | c.1033G>A | p.Ala345Thr | A | |||||
| 13 | SLC5A2 | NM_003041.3 | c.644T>C | p.Leu215Pro | L | L | L | ||||
| 90_501 | VATER/VACTERL-like association | 14 | KIAA0556 | NM_015202.2 | c.3730C>T | p.His1244Tyr | H | H | H | H | |
| 141_501 | VATER/VACTERL-like association | 15 | STAB1 | NM_015136.2 | 9/278,948 (0.00003) | c.6145C>T | p.Arg2049Cys | R | S | ||
| 154_501 | VATER/VACTERL association | 16 | GGT6 | NM_153338.2 | c.1045A>G | p.Ser349Gly | S | ||||
| 167_501 | nonsyndromic | 17 | CHD7 | NM_017780.3 | c.4187C>G | p.Ala1396Gly | A | A | A | ||
| 172_501 | VATER/VACTERL-like association | 18 | NPR2 | NM_003995.3 | c.952C>G | p.Arg318Gly | R | K | T | ||
| 174_501 | nonsyndromic | 19 | UBA3 | NM_198195.1 | c.1088C>T | p.Ser363Phe | S | S | T | P | |
| 181_501 | nonsyndromic | 20 | TANC2 | NM_025185.3 | c.2357C>T | p.Pro786Leu | P | P | P | ||
| 288_501 | VATER/VACTERL association | 21 | TRPS1 | NM_014112.2 | c.1630C>T | p.Arg544* | R | R | R | ||
| 22 | APOL2 | NM_145637.1 | c.319G>C | p.Glu107Gln | D | ||||||
| 750_501* | VATER/VACTERL association | 23 | ZFHX3 | NM_006885.3 | 5/250,880 (0.00002) | c.6377C>T | p.Ala2126Val | A | T | T | A |
Annotations marked in bold red represent: “known disease genes” involved in the formation of congenital malformations, variants with truncating consequence, variants in highly conserved regions of the protein, or novel variants (not found in (n.f.i.), gnomAD (MAF)).