Table 2.
List of all confirmed exonic and splice region de novo variants.
| Trio ID | Trio in Rovelet-Lecrux et al., [7] | Consequence | Gene symbol | Nomenclature (cDNA level) | Nomenclature (protein level) | Identifier of existing variations | CADD | REVEL | Allele frequency in gnomAD v2.1 |
|---|---|---|---|---|---|---|---|---|---|
| EFA-362 | No | missense | ZSWIM8 | NM_001242488.2:c.5563A>G | NP_001229417.1:p.(Ile1855Val) | - | - | - | - |
| EFA-787 | No | splice region | NUP54 | NM_017426.4:c.67+5G>C | - | - | - | - | - |
| EFA-787 | No | splice region | CNTFR | NM_147164.3:c.86-10C>T | - | rs573942894 | - | - | 6.894e-05 |
| EFA-435 | No | synonymous | SSH3 | NM_017857.4:c.1260A>G | NP_060327.3:p.(Ser420Ser) | - | - | - | - |
| EFA-435 | No | missense | RRP7A | NM_015703.5:c.211A>C | NP_056518.2:p.(Thr71Pro) | - | 20.4 | 0.098 | - |
| EFA-848 | No | missense | LOC400499 | NM_001370704.1:c.3319G>A | NP_001357633.1:p.(Val1107Ile) | rs1482886742 | 0.006 | - | 7.49e-06 |
| EFA-848 | No | missense | SYNJ2 | NM_003898.4:c.3200C>T | NP_003889.1:p.(Thr1067Met) | rs140015862 | 23.8 | 0.437 | 3.987e-06 |
| EFA-667 | No | missense | RREB1 | NM_001003699.4:c.1984G>A | NP_001003699.1:p.(Val662Met) | rs777379568 | 20.3 | 0.145 | 2.45e-05 |
| EFA-667 | No | missense | SLC7A13 | NM_138817.3:c.906C>A | NP_620172.2:p.(Asn302Lys) | - | 8.079 | 0.395 | - |
| EXT-0395 | Yes | missense | CPM | NM_001874.5:c.352C>T | NP_001865.1:p.(Arg118Trp) | - | 25.0 | 0.589 | - |
| EXT-0395 | Yes | missense | RNF213 | NM_001256071.3:c.5114C>T | NP_001243000.2:p.(Thr1705Met) | rs147868237,COSV60393253 | 24.6 | 0.277 | 3.527e-05 |
| EXT-0941 | No | missense | EME2 | NM_001257370.2:c.1063G>C | NP_001244299.1:p.(Gly355Arg) | - | 24.5 | - | - |
| EXT-0941 | No | inframe insertion | TBL1X | NM_001139467.1:c.342_350dup | NP_001132939,1:p.(Ala115_Ala117dup) | ||||
| EXT-1340 | No | missense | IER5 | NM_016545.5:c.136G>A | NP_057629.2:p.(Val46Ile) | - | 24.7 | 0.128 | - |
| EXT-1340 | No | missense | MCTP1 | NM_024717.6:c.326C>T | NP_078993.4:p.(Pro109Leu) | - | 22.4 | 0.211 | - |
| EXT-0222 | No | missense | KCNJ3 | NM_002239.4:c.1214A>G | NP_002230.1:p.(Lys405Arg) | - | 22.2 | 0.221 | - |
| EXT-1289 | No | missense | LPAR6*,** | NM_005767.7:c.614G>A | NP_005758.2:p.(Ser205Asn) | rs780139124 | 23.0 | 0.375 | 3.998e-06 |
| EXT-1289 | No | synonymous | GABRB3*,** | NM_000814.6:c.249C>T | NP_000805.1:p.(Thr83Thr) | rs1476625006 | - | - | 3.989e-06 |
| EXT-1289 | No | missense | STARD9 | NM_020759.3:c.2909C>G | NP_065810.2:p.(Ser970Cys) | - | 18.61 | 0.053 | - |
| EXT-1289 | No | missense | TOMM70*,** | NM_014820.5:c.1795A>G | NP_055635.3:p.(Lys599Glu) | rs1270426552 | 22.6 | 0.130 | - |
| EXT-1289 | No | frameshift | TET2*,** | NM_001127208.3:c.1328_1341del | NP_001120680.1:p.(Thr443ArgfsTer7) | - | - | - | - |
| EXT-1549 | No | missense | ATG2B | NM_018036.7:c.5716_5717delinsAT | NP_060506.6:p.(Asp1906Ile) | - | 33 | 0.732 | - |
| EXT-1549 | No | synonymous | EHMT2 | NM_001363689.1:c.2232G>A | NP_001350618.1:p.(Thr744Thr) | rs762523692 | - | - | 4.456e-05 |
| EXT-0893 | No | missense | CEP112* | NM_001199165.4:c.2018C>T | NP_001186094.1:p.(Thr673Met) | ||||
| EXT-0893 | No | splice region | TACC1 | NM_001352778.2:c.1887+8C>T | - | - | - | - | - |
| EXT-0848 | No | missense | FASN | NM_004104.5:c.4874C>T | NP_004095.4:p.(Ser1625Phe) | - | 22.6 | 0.118 | - |
| EXT-1244 | No | missense | TTN | NM_001267550.2:c.88820G>A | NP_001254479.2:p.(Arg29607Gln) | rs755212831 | 23.7 | 0.424 | 4.839e-05 |
| EXT-1244 | No | missense | DDR1 | NM_013994.3:c.2155C>T | NP_054700.2:p.(Leu719Phe) | - | 28.2 | 0.874 | - |
| EXT-1301 | No | missense | IL27RA | NM_004843.4:c.1216T>C | NP_004834.1:p.(Ser406Pro) | - | 3.751 | 0.014 | - |
| EXT-344 | Yes | frameshift | LPIN3 | NM_001301860.2:c.335dup | NP_001288789.1:p.(Leu113SerfsTer15) | rs756955559 | - | - | 0.0001159 |
| EXT-0804 | Yes | missense | SPEG | NM_005876.5:c.2929G>A | NP_005867.3:p.(Val977Met) | rs770098499 | 25.6 | 0.592 | 8.299e-06 |
| EXT-0854 | No | missense | MKI67 | NM_002417.5:c.5194A>G | NP_002408.3:p.(Thr1732Ala) | rs768117451 | 6.276 | 0.036 | 2.388e-05 |
| EXT-0854 | No | synonymous | TRABD2B | NM_001194986.2:c.774A>T | NP_001181915.1:p.(Gly258Gly) | - | - | - | - |
| EXT-0854 | No | splice region | RAP1GAP2 | NM_015085.5:c.45-20C>T | - | rs1285394067 | - | - | 1.228e-05 |
| EXT-186 | Yes | splice region | ANO7 | NM_001370694.2:c.1561+17C>T | p.? | ||||
| EXT-1223 | No | missense | DPYD | NM_000110.4:c.745A>G | NP_000101.2:p.(Lys249Glu) | - | 25.8 | 0.782 | - |
| EXT-1223 | No | missense | TMEM131 | NM_015348.2:c.32G>T | NP_056163.1:p.(Gly11Val) | ||||
| EXT-0488 | Yes | missense | SLC25A27 | NM_004277.5:c.811A>G | NP_004268.3:p.(Lys271Glu) | - | 26.8 | 0.728 | - |
| EXT-0488 | Yes | missense | PHKA2 | NM_000292.3:c.869G>A | NP_000283.1:p.(Arg290His) | rs186632999 | 26.2 | 0.829 | 1.091e-05 |
| EXT-0687 | Yes | missense | RGS13 | NM_002927.5:c.227G>A | NP_002918.1:p.(Arg76Gln) | rs1359297515 | 13.43 | 0.016 | 7.985e-06 |
| EXT-0687 | Yes | missense | COL19A1 | NM_001858.6:c.3106G>A | NP_001849.2:p.(Val1036Ile) | - | 22.3 | - | - |
| EXT-1403 | No | synonymous | SPEG | NM_005876.5:c.9057C>T | NP_005867.3:p.(His3019His) | rs200656875 | - | - | 0.0001569 |
| EXT-1403 | No | missense | FAM13A | NM_014883.4:c.481C>A | NP_055698.2:p.(Pro161Thr) | - | 25.6 | 0.675 | - |
| EXT-1551 | No | inframe deletion | SPHK2 | NM_001204159.3:c.387_407del | NP_001191088.1:p.(Arg130_Arg136del) | - | - | - | - |
| EXT-1551 | No | splice region | COL4A3 | NM_000091.5:c.3211-15T>A | - | - | - | - | - |
| ROU-682 | Yes | missense | VPS35 | NM_018206.6:c.1874T>C | NP_060676.2:p.(Leu625Pro) | 29.4 | 0.746 | - | |
| ROU-682 | Yes | synonymous | OXTR | NM_000916.4:c.714G>T | NP_000907.2:p.(Ala238Ala) | - | - | - | - |
| ROU-1331 | Yes | in frame delins | MARK4 | NM_001199867.2:c.947_951delinsAT | NP_001186796.1:p.(Gly316_Glu317delinsAsp) | - | - | - | - |
| ROU-1331 | Yes | missense | ABCA12 | NM_173076.3:c.2067C>A | NP_775099.2:p.(Asp689Glu) | - | 16.65 | 0.204 | - |
| ROU-1331 | Yes | synonymous | ACO2 | NM_001098.3:c.1443C>T | NP_001089.1:p.(Asp481Asp) | rs576516374 | - | - | 2.785e-05 |
| ROU-1331 | Yes | missense | MYCT1 | NM_025107.2:c.580C>T | NP_079383.2:p.(Pro194Ser) | rs1034181147 | 1.859 | 0.036 | 3.979e-06 |
| ROU-1322 | Yes | synonymous | ADH7 | NM_001166504.2:c.651C>T | NP_001159976.1:p.(Val217Val) | rs765427932 | - | - | 7.979e-06 |
| ROU-1597 | No | synonymous | MICALL1 | NM_033386.4:c.1473C>T | NP_203744.1:p.(His491His) | rs374402603 | - | - | 0.0002476 |
| ROU-1750 | No | missense | POP1 | NM_001145860.2:c.1252A>G | NP_001139332.1:p.(Thr418Ala) | - | 21.7 | 0.150 | - |
CADD combined annotation dependent depletion score, REVEL rare exome variant ensemble learner score.
*post-zygotic variant; **likely clone-specific variant, somatic (suspected CHIP).