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. 2021 May 30;13(11):2704. doi: 10.3390/cancers13112704

Table 2.

Potentially pathogenic variants in the Chinese dataset.

ID Gender Age Morphology Gene Chr Location SNP IDS REF VAR Variant
Type		 Protein
Change		 Variant
Impact		 Pathogenecity Prediction a HGMD/
ClinVar		 MAF in Control Datasets Pathway/Process
METASVM METALR CADD gnomAD Exomes EAS b gnomAD Genomes EAS c
1804 M 65 Conventional ATP8B2 1 154317567 A C missense Lys836Gln moderate D D 26.2 1.74 × 10−4 0 Mesoderm commitment
1686 M 64 Conventional LRP2 2 170033035 C T missense Gly3486Glu moderate D D 33 0 0 Sonic Hedgehog
1372 NA NA NA LRP2 2 170062924 rs577943281 T A missense Thr2436Ser moderate D D 22.7 2.90 × 10−4 6.17 × 10−4 Sonic Hedgehog
1964 M 24 Chondroid LRP2 2 170055366 rs755215116 A C missense Ile2836Met moderate D D 24.2 3.66 × 10−3 6.17 × 10−4 Sonic Hedgehog
1442 NA NA NA PDK1 2 173460575 rs745678398 A G structural interaction High 0 0 PI3K/AKT/mTOR
1886 F 62 Conventional TCF7L1 2 85536476 C T missense Thr553Ile moderate D D 23 5.82 × 10−5 0 Mesoderm commitment
1790 M 65 Conventional TCF7L1 2 85531113 rs373770977 G A missense Val252Ile moderate D D 23.4 1.25 × 10−4 0 Mesoderm commitment
1779 M 47 Conventional TCF7L1 2 85536536 rs555810312 C T missense Pro573Leu moderate D D 23.2 4.19 × 10−4 0 Mesoderm commitment
2011 F 7 Conventional TBXT 6 166581010 rs563349798 C G missense Val24Leu moderate D D 29.7 0 0 T super-enhancer
1686 M 64 Conventional EXT1 8 118819501 rs753261171 G A missense Thr613Met moderate D D 33 0 0 Mesoderm commitment
776 M 54 Conventional SUFU 10 104309738 C T structural interaction High 5.80 × 10−5 0 Sonic Hedgehog
1921 M 57 Conventional EXT2 11 44193231 rs767085143 A G missense Asn448Ser moderate D D 24.3 2.90 × 10−4 0 Mesoderm commitment
1372 NA NA NA COL2A1 12 48369322 rs995646562 C T missense Ala1222Thr moderate D D 24.1 0 0 Notochord development
1909 M 26 Conventional COL2A1 12 48372528 G T missense Pro916His moderate D D 25 0 0 Notochord development
1936 F 71 Conventional TSC2 16 2134572 rs45517338 C G missense Pro1450Arg moderate D D 25.8 2.35 × 10−4 0 PI3K/AKT/mTOR
1417 M 59 Conventional TSC2 16 2134572 rs45517338 C G missense Pro1450Arg moderate D D 25.8 2.35 × 10−4 0 PI3K/AKT/mTOR
1979 M 59 Chondroid TSC2 16 2121610 rs45509392 G A missense Asp647Asn moderate D D 32 DM 5.80 × 10−4 0 PI3K/AKT/mTOR
1570 M 24 Chondroid TSC2 16 2121610 rs45509392 G A missense Asp647Asn moderate D D 32 DM 5.80 × 10−4 0 PI3K/AKT/mTOR
462 F 62 Conventional TSC2 16 2121610 rs45509392 G A missense Asp647Asn moderate D D 32 DM 5.80 × 10−4 0 PI3K/AKT/mTOR
1084 NA NA NA ACACA 17 35549102 rs772483773 C T missense Val1449Met moderate D D 25.2 6.96 × 10−4 6.17 × 10−4 Mesoderm commitment

Chr, chromosome; REF, reference allele; VAR, variant allele; Freq, frequency; MAF, minor allele frequency; T, tolerant; D, deleterious; P, pathogenic; DM, disease-causing mutation. a Pathogenicity prediction for missense variants based on in silico algorithms, METALR and METASVM, which are ensemble prediction scores that incorporate results from nine algorithms and allele frequency. CADD was also applied. b,c Genome Aggregation Database (gnomAD) exomes and genomes, respectively, in East Asian population. Structural interaction: variants that impact the internal interactions of the resulting polypeptide structure.