Table 1 Pathogenic and likely pathogenic rare variants in COVID-19-BR cases.
From: Rare genetic variants and severe COVID-19 in previously healthy admixed Latin American adults
Patient | Consequence | GENE | HGVSc | HGVSp | dbSNP | 1KPG | gnomAD | SABE | DNA Brasil Project | CADD | GDI | ACMG | ClinVar | Alphamissense |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
P78, P43, P44, P1266, P148 | missense_variant | PTOV1 | NM_001394010.1:c.20 C > A | NP_001380939.1:p.Ala7Asp | rs563641001 | 0.0094 | 0.0084 | 0.0076 | NA | 20.8 | 5.66 | B | NA | LP |
P21 | missense_variant | HSD17B14 | NM_016246.3:c.184G > T | NP_057330.2:p.Asp62Tyr | rs139987974 | 0.0006 | 0.0012 | 0.0029 | NA | 24.9 | 6.82 | VUS | NA | LP |
P39, P36, P88 | missense_variant | HSD17B14 | NM_016246.3:c.46G > T | NP_057330.2:p.Gly16Trp | rs113246661 | 0.0010 | 0.0040 | 0.0017 | 0.0020 | 24.8 | 6.82 | VUS | NA | LP |
P28, P145* | missense_variant | PRSS50 | NM_013270.5:c.487T > C | NP_037402.1:p.Ser163Pro | rs147316998 | 0.0012 | 0.0032 | 0.0059 | 0.9972 | 22.8 | 5.61 | VUS | NA | LP |
P60, P1208, P146, P153 | missense_variant | RAB25 | NM_020387.4:c.59 A > G | NP_065120.2:p.Glu20Gly | rs61751627 | 0.0036 | 0.0048 | 0.0089 | 0.0069 | 29.7 | 2.18 | B | NA | LP |
P98, P50* | missense_variant | DXO | NM_005510.4:c.880 C > T | NP_005501.2:p.Arg294Cys | rs45534831 | 0.0012 | 0.0033 | 0.0021 | 0.0029 | 31 | 6.43 | VUS | NA | LP |
P1268 | missense_variant | ANAPC4 | NM_013367.3:c.1250T > G | NP_037499.2:p.Phe417Cys | NA | NA | NA | 0.0012 | NA | 29.9 | 5.19 | VUS | NA | LP |
P1263 | missense_variant | EHMT2 | NM_006709.5:c.2161 C > G | NP_006700.3:p.Pro721Ala | NA | NA | NA | NA | 0.0012 | 23.8 | 5.98 | VUS | NA | LP |
P88 | splice_donor_variant | C2 | NM_000063.6:c.841_849 + 19del | - | rs9332736 | 0.0020 | 0.0050 | 0.0055 | NA | 27.0 | 3.08 | P | NA | NA |
P95 | missense_variant | CYP21A2 | NM_000500.9:c.1360 C > T | NP_000491.4:p.Pro454Ser | rs6445 | 0.0018 | 0.0050 | NA | NA | 22.7 | 9.91 | LP | P | NA |
P31 | missense_variant | ATF6B | NM_004381.5:c.1787 C > A | NP_004372.3:p.Ser596Tyr | NA | NA | NA | NA | NA | 28.7 | 2.05 | VUS | NA | LP |
P22 | frameshift_variant | IFNAR1 | NM_000629.3:c.506del | NP_000620.2:p.Ile169ThrfsTer8 | rs770853192 | NA | 0.0002 | NA | NA | 28.5 | 6.56 | P | NA | NA |
P105 | missense_variant | DONSON | NM_017613.4:c.1411G > A | NP_060083.1:p.Glu471Lys | rs140592434 | 0.0006 | 0.0009 | 0.0005 | 0.0005 | 26.4 | 2.45 | B | VUS | LP |
P70 | splice_donor_variant | DONSON | NM_017613.4:c.402 + 1G > C | - | rs762881899 | NA | NA | 0.0004 | NA | 33 | 2.45 | LP | NA | NA |
P157 | missense_variant | ITSN1 | NM_003024.3:c.1301G > A | NP_003015.2:p.Arg434Gln | NA | NA | NA | NA | NA | 25.0 | 4.73 | VUS | NA | LP |
P20 | splice_donor_variant | ITSN1 | NM_003024.3:c.2304 + 1G > A | - | NA | NA | NA | NA | NA | 34 | 4.73 | LP | NA | NA |
P54 | missense_variant | ARHGAP27 | NM_001282290.2:c.1251G > T | NP_001269219.1:p.Trp417Cys | NA | NA | NA | NA | NA | 28.2 | 6.02 | VUS | NA | LP |
P107 | missense_variant | MYL3 | NM_000258.3:c.250G > A | NP_000249.1:p.Gly84Ser | NA | NA | NA | NA | NA | 28.0 | 0.28 | VUS | NA | LP |
P55 | missense_variant | SPHK2 | NM_020126.5:c.245 A > T | NP_064511.2:p.Lys82Ile | NA | NA | NA | NA | NA | 23.6 | 4.37 | VUS | NA | LP |
P104 | missense_variant | AP2A1 | NM_130787.3:c.781 C > T | NP_570603.2:p.Leu261Phe | NA | NA | NA | 0.0004 | NA | 23.6 | 1.89 | VUS | NA | LP |
P46 | missense_variant | KAT7 | NM_007067.5:c.1579 C > T | NP_008998.1:p.Leu527Phe | NA | NA | NA | NA | 0.0040 | 25.6 | 0.93 | VUS | NA | LP |
P63, P1262 | missense_variant | ARHGEF38 | NM_001242729.2:c.728G > A | NP_001229658.1:p.Arg243His | rs57478337 | 0.0054 | 0.0040 | NA | 0.0040 | 28.4 | 8.35 | VUS | NA | LP |
P109 | missense_variant | GSTCD | NM_001370181.1:c.406T > A | NP_001357110.1:p.Cys136Ser | rs61736388 | 0.0038 | 0.0031 | 0.0029 | 0.0025 | 24.2 | 2.03 | B | NA | LP |
P54 | missense_variant | THBS3 | NM_007112.5:c.2740G > T | NP_009043.1:p.Gly914Trp | NA | NA | NA | NA | NA | 29.0 | 6.74 | LP | NA | LP |
P1268 | missense_variant | PKLR | NM_000298.6:c.1456 C > T | NP_000289.1:p.Arg486Trp | rs116100695 | 0.0016 | 0.0027 | 0.0038 | 0.0023 | 32 | 1.91 | P | P | A |
P55 | missense_variant | GON4L | NM_001282860.2:c.4396G > C | NP_001269789.1:p.Asp1466His | NA | NA | NA | NA | NA | 26.1 | 4.06 | VUS | NA | LP |
