Table 3.
TOR2A variants reported by NCBI’s ClinVar and PubMed.
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| VARIANT(ACCESSION) | PROTEIN CHANGE | CONDITION (NUMBER OF PROBANDS) | CLINICAL SIGNIFICANCE | gnomAD V3.1.2 (ALLELE FREQUENCY) | CADDPHRED-SCALED | MetaLR | REVEL | REF. |
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| c.194T>C (SCV003669886.1) |
p. Leu65Pro | Inborn genetic disease (N = 1) |
Uncertain significance | – | 31.0 | 0.2864 | 0.664 | [14] |
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| c.247C>T (SCV003546031.1) |
p. Pro83Ser | Inborn genetic disease (N = 1) |
Uncertain significance | 2/152200 | 28.3 | 0.2573 | 0.376 | |
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| c.338G>A (SCV003885945.1) |
p. Gly113Asp | Inborn genetic disease (N = 1) |
Uncertain significance | – | 31.0 | 0.02109 | 0.024 | |
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| c.423T>A (SCV003950745.1) |
p. Asp141Glu | Inborn genetic disease (N = 1) |
Uncertain significance | 2/152214 | 16.1 | 0.04569 | 0.031 | |
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| c.463C>T (SCV003757814.1) |
p. Arg155Cys | Inborn genetic disease (N = 1) |
Uncertain significance | 2/152230 | 24.5 | 0.3835 | 0.281 | |
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| c.553T>C (SCV003661212.1) |
p. Tyr185His | Inborn genetic disease (N = 1) |
Uncertain significance | – | 23.5 | 0.0976 | 0.182 | |
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| c.62T>C (SCV003534402.1) |
p.Val21Ala | Inborn genetic disease (N = 1) |
Uncertain significance | 3/152194 | 14.8 | 0.1089 | 0.0540 | |
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| c.734A>G (SCV003566928.1) |
p.Asn245Ser | Inborn genetic disease (N = 1) |
Uncertain significance | 1/231144 | 7.8 | 0.0521 | 0.040 | |
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| c.737C>T (SCV003615110.1) |
p.Ser246Leu | Inborn genetic disease (N = 1) |
Uncertain significance | 2/152226 | 26.0 | 0.4321 | 0.563 | |
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| c.766G>A (SCV004004774.1) |
p. Ala256Thr | Inborn genetic disease (N = 1) |
Uncertain significance | 6/276576 | 21.2 | 0.1399 | 0.089 | |
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| c.785C>G (SCV003708033.1) |
p. Pro262Arg | Inborn genetic disease (N = 1) |
Uncertain significance | 4/152198 | 27.3 | 0.5009 | 0.809 | |
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| c.805C>T (SCV003951769.1) |
p. Arg269Trp | Inborn genetic disease (N = 1) |
Uncertain significance | 7/279546 | 26.5 | 0.3993 | 0.172 | |
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| c.907C>A (SCV001041175.1) |
p. Gln303Lys | Inborn genetic disease (N = 1) |
Uncertain significance | 67/152230 | 17.1 | 0.0676 | 0.146 | |
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| c.925G>A (SCV003551979.1) |
p. Gly309Ser | Inborn genetic disease (N = 1) |
Uncertain significance | 9/152230 | 27.1 | 0.5849 | 0.813 | |
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| c.937G>A (SCV003529445.1) |
p. Val313Met | Inborn genetic disease (N = 1) |
Uncertain significance | 6/152246 | 25.4 | 0.5539 | 0.658 | |
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| c.568C>T (NM_001085347.3) |
p.Arg190Cys | BSP/BSP+ (N = 3, one pedigree) | Likely pathogenic | 5/152188 | 29.2 | 0.548 | 0.5 | [11] |
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| c.593+31G>C (NM_001085347.2) |
p. Trp208Cys | BSP | Benign | 97582/ 152038 | 0.203 | 0.000 | 0.0320 | [13] |
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| c.-42G>A (NM_130459.3) |
NA | BSP/BSP+ (N = 6) | Benign | 12139/152166 | 12.2 | – | – | [12] |
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| c.277_288dup (NM_001085347.3) | p.Gly93_Gly96dup | BSP/BSP+ (N = 1 homozygote) | Uncertain significance | 11/152226 | 21.5 | – | – | |
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| c.418–51T>G (NM_001085347.3) |
NA | BSP/BSP+ (N = 35), Controls (N = 40) | Benign | 98659/151956 | 10.3 | – | – | |
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| c.555C>T (NM_001085347.3) |
p.Tyr185= | BSP/BSP+ (N = 1), Controls (N = 0) | Uncertain significance | 9/152204 | 0.382 | – | – | |
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| c.593+36del (NM_001085347.3) c.629del (NM_130459.4) |
NA p.Gly210AlafsTer60 |
BSP/BSP+ (N = 1), Controls (N = 0) | Uncertain significance | 3/152204 | 0.81 | – | – | |
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| c.594–46C>T (NM_001085347.3) |
NA | BSP/BSP+ (N=23 heterozygotes, 6 homozygotes), Controls (18 heterozygotes, 8 homozygotes) | Benign | 18456/152198 | 0.252 | – | – | |
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| c.721+32A>G (NM_001085347.3) |
NA | BSP/BSP+ (N=35 heterozygotes, 9 homozygotes), Controls (48 heterozygotes, 24 homozygotes) | Benign | 101903/152022 | 4.89 | – | – | |
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| c.721+52G>A (NM_001085347.3) |
NA | BSP/BSP+ (N = 10), Controls (N = 12) | Benign | 25185/152088 | 7.55 | – | – | |
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| c.594–59C>T (NM_001085347.3) | NA | BSP/BSP+ (N = 1), Controls (N = 0) | Uncertain significance | 7/152224 | 0.154 | – | – | |
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| c.721+83C>T (NM_001085347.3) |
NA | BSP/BSP+ (N = 1), Controls (N = 0) | Uncertain significance | – | 1.89 | – | – | |
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| c.594-55C>A (NM_001085347.3) |
NA | BSP/BSP+ (N = 1), Controls (N = 0) | Uncertain significance | 28/152228 | 6.55 | – | – | |
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| c.*28del (NM_001085347.3) |
NA | BSP/BSP+ (N = 9), Controls (N = 8) | Benign | 387/152220 | 0.128 | – | – | |
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| c.*125A>G (NM_001085347.3) |
N/A | BSP/BSP+ (N = 1), Controls (N = 1) | Uncertain significance | 1/152222 | 5.65 | NA | NA | |
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| c.786G>A (NM_001085347.3) |
p.Pro262= | BSP/BSP+ (N = 1), Controls (N = 1) | Benign | 83/152120 | 0.572 | 0.0614 | 0.0440 | |
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