TABLE 1.
SATB2 variants found in individuals with SATB2-associated syndrome previously reported and from this study (numbering is according to the cDNA sequence (GenBank entry NM_015265.3)
| Variant type | Position | DNA variant | Predicted effect on protein |
Unrelated families in our cohort |
Unrelated families in the literature |
Variant reference (dbSNP, ClinVar) |
References |
|---|---|---|---|---|---|---|---|
| Nonsense | Exon 3 | c.124G>T | p.Gly42* | 1 | RCV000486598.1; rs1064793947 | Zarate et al. (1993); Zarate, Smith-Hicks et al. (2018) | |
| Exon 4 | c.346G>T | p.Gly116* | 1 | Zarate, Smith-Hicks et al. (2018); Scott et al. (2018) | |||
| Exon 5 | c.390T>A | p.Tyr130* | 1 | Bengani et al. (2017); Zarate, Smith-Hicks et al. (2018) | |||
| Exon 6 | c.505C>T | p.Gln169* | 1 | Zarate, Smith-Hicks et al. (2018); Scott et al. (2018) | |||
| Exon 7 | c.688A>T | p.Lys230* | 1 | Vissers et al. (2017) | |||
| Exon 8 | c.715C>T | p.Arg239* | 3 | 3 | RCV000002627.6; RCV000256175.2; rs137853127 | Leoyklang et al. (2007); This study | |
| Exon 8 | c.748C>T | p.Gln250* | 1 | RCV000708552.1 | Zarate et al. (2017) | ||
| Exon 8 | c.847C>T | p.Arg283* | 2 | 4 | RCV000190685.3; RCV000254800.2; RCV000686152.1; rs797044874 | Zarate et al. (2017); Kikuiri et al. (2018); This study | |
| Exon 8 | c.868C>T | p.Gln290* | 2 | RCV000413829.1; RCV000624904.1; rs1057518496 | This study | ||
| Exon 8 | c.988C>T | p.Gln330* | 1 | This study | |||
| Exon 8 | c.997C>T | p.Gln333* | 1 | RCV000599413.1 | This study | ||
| Exon 8 | c.1135C>T | p.Gln379* | 1 | This study | |||
| Exon 8 | c.1171C>T | p.Gln391* | 1 | RCV000708554.1 | Zarate, Smith-Hicks et al. (2018); Scott et al. (2018) | ||
| Exon 9 | c.1255C>T | p.Gln419* | 1 | Zarate et al. (1993); Zarate, Smith-Hicks et al. (2018); Scott et al. (2018) | |||
| Exon 9 | c.1285C>T | p.Arg429* | 1 | 3 | RCV000307104.1; rs886041847 | Bengani et al. (2017); This study | |
| Exon 9 | c.1375C>T | p.Arg459* | 1 | 4 | RCV000625170, RCV000680089.2, RCV000719613.1 | Bengani et al. (2017); This study; This study | |
| Exon 10 | c.1495A>T | p.Lys499* | 1 | RCV000224980.1; rs878853163 | Zarate, Smith-Hicks et al. (2018); Bowling et al. (2017); Scott et al. (2018) | ||
| Exon 12 | c.1756C>T | p.Gln586* | 1 | This study | |||
| Exon 12 | c.2074G>T | p.Glu692* | 1 | RCV000708559.1 | Bengani et al. (2017) | ||
| Missense | Exon 4 | c.185T>A | p.Val62Asp | 1 | RCV000479021.1; rs1064796649 | Zarate, Smith-Hicks et al. (2018) | |
| Exon 4 | c.257T>G | p.Leu86Arg | 1 | This Study | |||
| Exon 4 | c.287T>G | p.Leu96Arg | 1 | RCV000485845.1; rs1064795247 | Zarate, Smith-Hicks et al. (2018) | ||
| Exon 4 | c.346G>C┼ | p.Gly116Arg | 1 | RCV000494383.1; rs1131691672 | Zarate et al. (1993); Zarate, Smith-Hicks et al. (2018) | ||
| Exon 5 | c.392T>A | p.Val131Glu | 1 | RCV000485195.1; rs1064794638 | Zarate, Smith-Hicks et al. (2018) | ||
| Exon 8 | c.760C>T | p.His254Tyr | 1 | This study | |||
| Exon 8 | c.983C>A | p.Ala328Asp | 1 | Farwell et al. (2015) | |||
| Exon 8 | c.1102G>T | p.Val368Phe | 1 | This study | |||
| Exon 8 | c.1136A>C | p.Gln379Pro | 1 | This study | |||
| Exon 8 | c.1142T>G | p.Val381Gly | 1 | RCV000708553.1 | Rauch et al. (2012) | ||
| Exon 8 | c.1157C>T | p.Ala386Val | 1 | Bengani et al. (2017); Zarate, Smith-Hicks et al. (2018) | |||
| Exon 8 | c.1165C>T | p.Arg389Cys | 5 | 5 | RCV000430827.1; RCV000623230.1; RCV000656508.2; rs1057521083 | Bengani et al. (2017); This study | |
| Exon 8 | c.1166G>T | p.Arg389Leu | 1 | 1 | Bengani et al. (2017); This study | ||
| Exon 8 | c.1169C>T | p.Thr390Ile | 1 | 1 | RCV000199456.1; rs863224917 | Zarate, Smith-Hicks et al. (2018); Zarate, Steinraths et al. (2018); This study | |
| Exon 9 | c.1174G>C | p.Gly392Arg | 1 | Zarate, Smith-Hicks et al. (2018); Zarate, Steinraths et al. (2018) | |||
| Exon 9 | c.1175G>A | p.Gly392Glu | 1 | RCV000489186.1; rs1085308028 | This study | ||
| Exon 9 | c.1181T>C | p.Leu394Ser | 1 | Bengani et al. (2017) | |||
| Exon 9 | c.1186G>C | p.Glu396Gln | 1 | RCV000708555.1 | Lee et al. (2016) | ||
| Exon 9 | c.1196G>A | p.Arg399His | 2 | 2 | RCV000413401.1; rs1057518190 | Bengani et al. (2017); Zarate, Smith-Hicks et al. (2018); Scott et al. (2018); This study | |
| Exon 9 | c.1196G>T | p.Arg399Leu | 2 | This study | |||
| Exon 9 | c.1196G>C | p.Arg399Pro | 1 | SCV000847591.1; rs1057518190 | Zarate, Smith-Hicks et al. (2018); Zarate, Steinraths et al. (2018) | ||
| Exon 9 | c.1204G>A | p.Glu402Lys | 1 | Bengani et al. (2017); Zarate, Smith-Hicks et al. (2018) | |||
| Exon 9 | c.1253T>G | p.Met418Arg | 1 | This study | |||
| Exon 9 | c.1286G>A | p.Arg429Gln | 1 | 3 | RCV000300452.2; RCV000708556.1; rs886041516 | Zarate et al. (1993); Zarate, Smith-Hicks et al. (2018); This study | |
| Exon 10 | c.1541A>G | p.Gln514Arg | 1 | This study | |||
| Exon 11 | c.1543G>A | p.Gly515Ser | 1 | SCV000778507.1 | Bengani et al. (2017) | ||
| Exon 11 | c.1554T>G | p.Cys518Trp | 1 | This study | |||
| Exon 11 | c.1564C>T | p.Arg522Cys | 1 | This study | |||
| Exon 11 | c.1696G>A | p.Glu566Lys | 1 | RCV000482629.1; RCV000656509.1; rs1064795530 | Bengani et al. (2017) | ||
| Exon 12 | c.1903G>T | p.Asp635Tyr | 1 | This study | |||
| Exon 12 | c.1964C>T | p.Pro655Leu | 1 | RCV000502290.1 | Zarate et al. (1993); Zarate, Smith-Hicks et al. (2018) | ||
| Frameshift | Exon 3 | c.9_16del | p.Arg4Glufs*68 | 1 | This study | ||
| Exon 3 | c.19dupA | p.Ser7Lysfs*68 | 1 | RCV000519084.1; RCV000709933.1; | This study | ||
| Exon 4 | c.245_263del | p.Ala82Glyfs*30 | 1 | This study | |||
| Exon 4 | c.334delG | p.Ala112Profs*6 | 1 | This study | |||
| Exon 5 | c.400delG | p.Ala134Hisfs*17 | 1 | Zarate et al. (1993); Zarate, Smith-Hicks et al. (2018) | |||
| Exon 6 | c.482delA | p.Lys161Serfs*19 | 1 | RCV000479959.1; rs1064793820 | Zarate et al. (1993); Zarate, Smith-Hicks et al. (2018) | ||
| Exon 6 | c.583dupT | p.Cys195Leufs*14 | 1 | Zarate et al. (1993); Bengani et al. (2017); Zarate, Smith-Hicks et al. (2018); Zarate, Steinraths et al. (2018) | |||
| Exon 6 | c.594_595delCC | p.Gln199Glufs*9 | 1 | Bengani et al. (2017) | |||
| Exon 8 | c.808_809delCA | p.Gln270Valfs*33 | 1 | RCV000623347.1 | Zarate, Smith-Hicks et al. (2018); Scott et al. (2018) | ||
| Exon 8 | c.816delT | p.His273Thrfs*21 | 1 | Zarate et al. (1993); Zarate, Smith-Hicks et al. (2018) | |||
| Exon 8 | c.832delC | p.His278Thrfs*16 | 1 | This study | |||
| Exon 8 | c.1131_1132delGT | p.Ser378Profs*18 | 1 | RCV000209866.1; rs875989830 | Zarate, Smith-Hicks et al. (2018) | ||
| Exon 8 | c.1132_1133insAC | p.Ser378Tyrfs*36 | 1 | This study | |||
| Exon 9 | c.1196delG | p.Arg399Leufs*14 | 1 | RCV000624362.1 | This study | ||
| Exon 9 | c.1203dupA | p.Glu402Argfs*35 | 1 | Bengani et al. (2017) | |||
| Exon 9 | c.1311_1314dupG-GAG | p.Arg439Glyfs*38 | 1 | SCV000845949.1 | Zarate, Smith-Hicks et al. (2018) | ||
| Exon 10 | c.1478_1479delAG | p.Gln493Argfs*19 | 1 | Kikuiri et al. (2018) | |||
| Exon 10 | c.1498delG Mosaic | p.Val500Cysfs*46 | 1 | This study | |||
| Exon 10 | c.1511_1512in-sCAAGCCT | p.Phe505Lysfs*10 | 1 | This study | |||
| Exon 10 | c.1515delT | p.Phe505Leufs*41 | 1 | RCV000255520.1; rs886039740 | Zarate, Smith-Hicks et al. (2018); Scott et al. (2018) | ||
| Exon 11 | c.1574delA | p.Glu525Glyfs*21 | 1 | Bengani et al. (2017) | |||
| Exon 11 | c.1592dupA | p.Asn531Lysfs*21 | 1 | RCV000533352.1 | Zarate, Smith-Hicks et al. (2018) | ||
| Exon 11 | c.1627delC | p.Arg543Alafs*3 | 1 | RCV000496200.1; rs1135401803 | Cherot et al. (2018) | ||
| Exon 11 | c.1639_1642de-linsTTT | p.Leu547Phefs*77 | 1 | This study | |||
| Exon 11 | c.1645delC | p.Gln549Serfs*75 | 1 | Bengani et al. (2017) | |||
| Exon 11 | c.1657delG | p.Asp553Metfs*71 | 1 | This study | |||
| Exon 11 | c.1728delT | p.Glu577Serfs*47 | 1 | Zarate et al. (1993); Zarate, Smith-Hicks et al. (2018) | |||
| Exon 12 | c.1945dupT | p.Ser649Phefs*40 | 1 | SCV000837674.1 | Zarate et al. (2017); Zarate, Smith-Hicks et al. (2018) | ||
| Exon 12 | c.1972_1973delAC | p.Thr658Hisfs*30 | 1 | Zarate, Smith-Hicks et al. (2018) | |||
| Exon 12 | c.2005dupC | p.His669Profs*20 | 1 | Zarate, Smith-Hicks et al. (2018); Zarate, Steinraths et al. (2018) | |||
| Exon 12 | c.2018dupA | p.His673Glnfs*16 | 1 | RCV000708558.1 | Boone et al. (2016) | ||
| Exon 12 | c.2028delG | p.Glu678Serfs*18 | 1 | Zarate, Smith-Hicks et al. (2018) | |||
| In-frame insertion | Exon 8 | c.929_930in-sTTGTAAGGCAAC | p.Q310delinsHis CysLysAlaThr | 1 | Gilissen et al. (2014) | ||
| Splice | Exon 4 | c.346+2T>G | p.? | 1 | SCV000837664.1 | Zarate et al. (2017) | |
| Exon 5 | c.473+1delG | p.? | 1 | RCV000598568.1 | This study | ||
| Exon 7 | c.598-2A>G | p.? | 1 | Bengani et al. (2017) | |||
| Exon 8 | c.1173+2T>C | p.? | 1 | Bengani et al. (2017) | |||
| Exon 9 | c.1174-2A>G | p.? | 1 | Zarate, Smith-Hicks et al. (2018); Scott et al. (2018) | |||
| Exon 12 | c.1741-1G>A | p.? | 1 | Kikuiri et al. (2018) | |||
| Translocation | t(2;11) cis regulatory | c.? | p.? | 1 | Rainger et al. (2014) | ||
| t(2;3) cis regulatory | c.? | p.? | 1 | Rainger et al. (2014) | |||
| t(2;7) intron 3 | c.? | p.? | 1 | Brewer et al. (1999) | |||
| t(2:14) intron 10 | c.? | p.? | 1 | Tegay et al. (2009) | |||
| t(2;10) Intron 8-to 11 | c.? | p.? | 1 | Baptista et al. (2008) | |||
| t(2;6) | c.? | p.? | 1 | Talkowski et al. (2012) |
┼
This variant is also predicted to affect splicing if not resulting in a missense substitution.