Table 1 SMPD1 coding variants from the Discovery dataset
gnomAD 2.1.1 East Asian frequency | Case | Control | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|
Position (Hg37) | Amino acid substitution | Exomes | Genomes | No. of heterozygotes | No. of homozygotes | No. of heterozygotes | No. of homozygotes | Pathogenicity prediction | Functional score | |
Rare deleterious variants | chr11.6411889.C.T | p.Gln21Ter | - | - | 0 | 0 | 1 | 0 | Stop-gain | 25.00% (24.90–25.10%) |
chr11.6412063.C.T | p.Arg79Trp | - | - | 1 | 0 | 0 | 0 | Probably damaging | 69.60% (69.30–69.80%) | |
chr11.6413101.C.T | p.Ala269Val | 4.00×10-4 | 6.00×10-4 | 1 | 0 | 2 | 0 | Probably damaging | 98.80% (92.30–105.70%) | |
chr11.6413106.C.A | p.Pro271Thr | - | - | 0 | 0 | 1 | 0 | Damaging | 76.40% (75.30–77.50%) | |
chr11.6413134.A.ACATCCCCG | p.His284SerfsTer18 | - | - | 2 | 0 | 0 | 0 | Frameshift insertion | 5.60% (5.40–5.90%) | |
chr11.6413137.TC.T | p.Ala283HisfsTer16 | - | - | 0 | 0 | 1 | 0 | Frameshift deletion | 9.30% (9.20–9.40%) | |
chr11.6413139.C.A | p.Pro282Thr | 2.00×10-4 | - | 2 | 0 | 0 | 0 | Damaging | 9.70% (9.70–9.70%) | |
chr11.6413142.G.A | p.Ala283Thr | 1.00×10-4 | - | 1 | 0 | 0 | 0 | Damaging | 11.10% (11.00–11.20%) | |
chr11.6413181.C.T | p.Arg296Trp | 5.44×10-5 | - | 3 | 0 | 0 | 0 | Damaging | 87.10% (85.50–88.60%) | |
chr11.6413187.C.G | p.Leu298Val | - | - | 1 | 0 | 0 | 0 | Damaging | 100.90% (99.90–101.80%) | |
chr11.6413235.G.A | p.Val314Met | 0 | 0 | 1 | 0 | 0 | 0 | Damaging | 55.30% (54.80–55.80%) | |
chr11.6413278.G.C | p.Ser328Thr | - | - | 1 | 0 | 0 | 0 | Probably damaging | 34.20% (34.00–34.30%) | |
chr11.6413290.C.G | p.Pro332Arg | 5.60×10-3 | 1.30×10-3 | 69 | 1 | 48 | 0 | Damaging | 30.40% (30.30–30.50%) | |
chr11.6413296.T.C | p.Ile334Thr | 0 | 0 | 0 | 0 | 1 | 0 | Damaging | 78.80% (78.40–79.10%) | |
chr11.6414486.C.T | p.Arg378Cys | 0 | - | 1 | 0 | 0 | 0 | Damaging | 37.10% (36.70–37.60%) | |
chr11.6414487.G.A | p.Arg378His | 2.00×10-4 | 0 | 2 | 0 | 3 | 0 | Damaging | 63.80% (63.60–64.00%) | |
chr11.6414492.A.T | p.Ile380Phe | - | - | 1 | 0 | 0 | 0 | Damaging | 41.00% (40.40–41.50%) | |
chr11.6414543.A.G | p.Asn397Asp | - | - | 0 | 0 | 1 | 0 | Probably damaging | 67.80% (67.30–68.30%) | |
chr11.6414558.G.A | p.Ala402Thr | 0 | - | 1 | 0 | 0 | 0 | Damaging | 64.20% (64.00–64.40%) | |
chr11.6414877.C.T | p.His432Tyr | 5.44×10-5 | - | 1 | 0 | 0 | 0 | Probably damaging | 111.60% (111.40–111.90%) | |
chr11.6414911.G.A | p.Arg443Gln | 4.00×10-4 | 6.00×10-4 | 5 | 0 | 4 | 0 | Damaging | 24.00% (24.00–24.00%) | |
chr11.6415556.T.C | p.Tyr539His | - | - | 0 | 0 | 1 | 0 | Damaging | 10.20% (10.20–10.20%) | |
chr11.6415622.C.T | p.Arg561Cys | 0 | - | 0 | 0 | 1 | 0 | Damaging | 47.50% (47.30–47.80%) | |
chr11.6415712.C.T | p.Arg591Cys | 0 | 0 | 3 | 0 | 1 | 0 | Damaging | 40.60% (40.50–40.60%) | |
chr11.6415730.G.A | p.Ala597Thr | - | - | 2 | 0 | 0 | 0 | Probably damaging | 50.80% (50.70–51.00%) | |
chr11.6415736.C.T | p.Leu599Phe | - | - | 0 | 0 | 1 | 0 | Damaging | 27.90% (27.80–28.10%) | |
chr11.6415746.G.A | p.Arg602His | 0 | - | 1 | 0 | 2 | 0 | Damaging | 29.50% (29.20–29.80%) | |
chr11.6415769.C.T | p.Arg610Cys | 0 | 0 | 0 | 0 | 1 | 0 | Damaging | 73.70% (73.50–73.80%) | |
Rare benign variants | chr11.6411878.G.A | p.Arg17Gln | 1.00×10-4 | - | 3 | 0 | 2 | 0 | NA | 119.60% (118.70–120.60%) |
chr11.6411917.T.G | p.Leu30Arg | - | - | 1 | 0 | 1 | 0 | NA | 77.10% (76.80–77.50%) | |
chr11.6411958.G.C | p.Ala44Pro | 2.00×10-4 | 6.00×10-4 | 0 | 0 | 1 | 0 | Benign | 126.80% (126.30–127.30%) | |
chr11.6412022.C.T | p.Ser65Phe | - | - | 0 | 0 | 1 | 0 | Benign | 99.60% (98.00–101.30%) | |
chr11.6412054.A.C | p.Ile76Leu | - | - | 1 | 0 | 0 | 0 | Benign | 102.20% (101.40–102.90%) | |
chr11.6413089.G.C | p.Gly265Ala | - | - | 2 | 0 | 2 | 0 | Benign | 57.10% (57.00–57.30%) | |
chr11.6413277.A.G | p.Ser328Gly | - | - | 1 | 0 | 0 | 0 | Benign | 82.30% (81.70–82.90%) | |
chr11.6413305.A.G | p.Asn337Ser | 5.44×10-5 | - | 2 | 0 | 0 | 0 | Benign | 51.80% (51.50–52.00%) | |
chr11.6413377.G.A | p.Arg361His | 5.44×10-5 | 0 | 2 | 0 | 1 | 0 | Benign | 68.30% (68.00–68.50%) | |
chr11.6415259.G.A | p.Gly492Ser | 2.00×10-4 | 6.00×10-4 | 0 | 0 | 3 | 0 | Benign | 49.10% (48.60–49.60%) | |
chr11.6415583.C.T | p.Pro548Ser | 5.44×10-5 | - | 0 | 0 | 1 | 0 | Benign | 64.80% (64.50–65.20%) | |
chr11.6415590.C.T | p.Thr550Ile | - | - | 1 | 0 | 0 | 0 | Benign | 60.20% (59.60–60.90%) | |
chr11.6415634.G.A | p.Asp565Asn | 1.00×10-4 | - | 1 | 0 | 1 | 0 | Benign | 105.30% (104.90–105.70%) | |
chr11.6415639.G.T | p.Met566Ile | 2.00×10-4 | - | 1 | 0 | 3 | 0 | Benign | 70.40% (70.30–70.60%) | |
chr11.6415704.C.T | p.Thr588Met | 0.001 | 0.0013 | 9 | 0 | 10 | 0 | Benign | 62.30% (59.30–65.50%) | |
Common variants | chr11.6415463.G.A | p.Gly508Arg | 0.137 | 0.153 | 1,018 | 83 | 1,329 | 115 | Damaging | 55.60% (55.40–55.80%) |
chr11.6415539.C.T | p.Pro533Leu | 0.007 | 0.014 | 76 | 1 | 76 | 0 | Damaging | 72.10% (71.90–72.30%) | |
