Table 3.
Call for disorders based on nucleotide sequence variations detected by next-generation sequencing
| Patient # | Gene | Variants | Variant type | Variant call | Heredity1 |
|---|---|---|---|---|---|
| Known single nucleotide variant (SNV) | |||||
| 37 | FGFR3 | (Gly382Arg (c.1138G > A, het) | rs28931614 | Yes | AD |
| 71 | PAH | p.Arg243Gln (c.728G > A) | rs62508588 | Yes | AR |
| 71 | PAH | c.442-1G > A | rs62514907 | Yes | AR |
| 83 | RB1 | c.1215 + 1G > A | rs587776783 | Yes | AD |
| 89 | SOS1 | p.Arg552Gly(c.1654A > G) | rs137852814 | Yes | AD |
| 102 | WT1 | p.Arg462Trp(c.1384 C > T, het) | rs121907900 | Yes | AD |
| Introduction of stop codon (nonsense mutation) | |||||
| 1 | ABCA12 | p.Arg2482*(c.7444 C > T) | stop | Yes | AR |
| 1 | ABCA12 | p.Arg1950*(c.5848 C > T) | stop | Yes | AR |
| 46 | GCH1 | p.Glu242*(c.724 G > , het) | stop | Yes | AD |
| 56 | JAG1 | p.Tyr434* (c.1302 C > A, het) | stop | Yes | AD |
| 62 | NF1 | p.Gln554*(c.1660C > T) | stop | Yes | AD |
| 84 | RB1 | p.Arg272* (c.814 A > T, het) | stop | Yes | AD |
| Insertion and deletion (indel) | |||||
| 34 | FBN1 | c.1698_1712del15(exon13, het) | ins | Yes | AD |
| 55 | JAG1 | c.1 720 + 1dupG(intron13, het) | del | Yes | AD |
| 100 | VPS33B | c.740_741delAT(exon10,het) | del | Yes | AR |
| 100 | VPS33B | c.403 + 2 T > A(intron6,het) | ins | Yes | AR |
| Single nucleotide variant (SNV) without public records | |||||
| 10 | ARSA | p.Cys493Ser (c.1478G > C,het) | SNV | Yes | AR |
| 10 | ARSA | p.Asp411Gly (c.1232A > G,het) | SNV | Yes | AR |
| 24 | COL1A2 | c.595-1G > C | SNV | Yes | AD |
| 26 | COMP | p.Asp376His (c.1126 G > C,het) | SNV | Yes | AD |
| 54 | IVD | p.Ala29Thr (c.85G > A,het) | SNV | Yes | AR |
| 77 | PKHD1 | p.Leu2665Pro(c.7994T > C) | SNV | Yes | AR |
| 77 | PKHD1 | p.Val836Ala(c.2333G > T) | SNV | Yes | AR |
| 97 | TSC2 | p.Gly1204Arg(c.3610G > C, het) | SNV | Yes | AD |
| Variant with high frequency among healthy people 2 | |||||
| 39 | GALC | p.Ile562Thr(c.1685T > C, homo) | SNV | No | x 27% |
| 47 | GJB2 | p.Gly114Glu | SNV | No | x 5% |
| 47 | GJB2 | p.Val27Ile | SNV | No | x 8% |
| Big deletion | |||||
| 7 | PRODH | 1 copy del | gene del | Yes | AR |
| 7 | PRODH | p.Leu441Pro | SNV | Yes | AR |
| 15 | BTK | del. Exon6~10 (both copies) | partial del | Yes | 2 copies |
| 29 | DMD | exon2~exon7 duplication | partial dup | Yes | AD |
| 60 | MECP2 | MECP2 duplication | gene dup | Yes | AD |
1Heredity = basis for calling disorders; AD = autosomal dominant inheritance; AR = autosomal recessive inheritance, x = No call. Bold indicates a patient with a disorder resulting from composite heterozygotes, phasing issue not resolved but regarded as trans; 2Disease call was unsuccessful due to a high frequency of alleles among healthy populations.