Table 3. Unexpected detection of cases with biallelic mutations in genes irrelevant to metabolite abnormalities.
| Sample ID | Metabolites (Level; RR or cut-off) | Gene | NT alteration | AA alteration | Conventional criteria | ACMG category | Status* | Zygosity | Disease name | |
|---|---|---|---|---|---|---|---|---|---|---|
| Abnormal | Relevant | |||||||||
| IMD_35 | C0 (4.06; cut-off 7) | Cit (10.9; RR 2-55), Arg (16.8; RR 0–67) Gln (103; RR 0–300) | OTC | c.298+5G>C | NA | KP | LP | Known | Hom | OTC deficiency |
| IMD_36 | C0 (6.599, cut-off 7) | Glu (258; RR 0–805), C4 (0.23; RR 0–1.2), C6 (0.024; RR 0–0.5), C8 (0.007, RR 0–0.35), C10 (0.023 RR 0–0.5), C12 (0.033; RR 0–0.6), C18 (0.416; RR 0–2.13) | ETFB | c.155insT | p.P52fs | EP | LP | Novel | Hom | GA Type II |
| IMD_132 | Gal (14.8; RR: less than 13) | Arg (1.162; RR 0–67.3), Orn (47.565; RR 0–175) | SLC7A7 | c.498T>G | p.I166M | EP | VUS | Novel | Hom | LPI |
| IMD_162 | C5 (1.909; RR: less than 0.81) | Arg (3.353; RR 0–67.31), Orn (34.551; RR 0–175) | SLC7A7 | c.498T>G | p.I166M | EP | VUS | Novel | Hom | LPI |
| IMD_205 | TSH (12.7; RR: less than 12) | Phe (29.4; RR 0–130), Tyr (34.268; RR 0–299), Phe/Tyr (0.858; RR 0–2.5) | PAH | c.721C>T | p.R241C | KP | LP | Known | ComHet | PKU |
| PAH | c.442-1G>A | NA | KP | P | Known | |||||
| IMD_214 | Gal (21.4; RR: less than 13) | TSH (3.2; RR; less than 12), FT4 (1.8; RR; less than 0.8) | DUOX2 | c.3239T>C | p.I1080T | KP | LP | Known | ComHet | CH |
| DUOX2 | c.2678A>G | p.N893S | EP | VUS | Novel | |||||
| IMD_216 | Gal (13.5; RR: less than 13) | TSH (2.5; RR; less than 12), FT4 (2.3; RR; less than 0.8) | DUOX2 | c.617G>T | p.G206V | KP | VUS | Known | ComHet | CH |
| c.4232G>A | p.C1411Y | KP | VUS | Known | ||||||
| IMD_234 | Gal (27.7; RR: less than 13) | Cit (11.4; RR 2-55), Arg (14.7; RR 0–67), Gln (32; RR 0–300) | OTC | c.298+5G>C | NA | KP | LP | Known | Hom | OTC deficiency |
| IMD_237 | FT4 (0.2; RR less than 0.8) | C3 (0.4; RR 0.2-5) | PCCB | c.1283C>T | p.T428I | KP | LP | Known | ComHet | PA |
| PCCB | c.1316A>G | p.Y439C | KP | LP | Known | |||||
| IMD_243 | FT4 (0.6; RR less than 0.8) | Arg (9.5; RR 0-67.3), Orn (36; RR 0-175) | SLC7A7 | c.498T>G | p.I166M | EP | VUS | Novel | Hom | LPI |
Reference sequences of OTC, ETFB, HAL, SLC7A7, PAH, DUOX2, and PCCB were NM_000531.5, NM_001014763, NM_001258333, NM_001126105, NM_000277, NM_014080, and NM_000532, respectively. The metabolites units of TSH and FT4 were mU/L, ng/dL, ng/mL, respectively. The unit of the other metabolites was µmol/L.
*The mutation status was assessed based on the Human Genome Mutation Database (DM) or ClinVar (pathogenic) databases.
Abbreviations: AA, amino acid; NT, nucleotide; KP, known pathogenic; EP, expected pathogenic based on population frequency, in silico prediction, and mutation type (loss of function mutations); P, pathogenic; LP, likely pathogenic; VUS, variant of unknown significance; RR, reference range; Gal, galactose; TSH, thyroid-stimulating hormone; FT4, free thyroxine; Cit, citrulline; Arg, arginine; Gln, glutamine; Glu, glutamate; Orn, ornithine; Phe, phenylalanine; Tyr, tyrosine; NA, not applicable; Het, heterozygous; ComHet, compound heterozygous; Hom, homozygous; OTC deficiency, Ornithine carbamoyltransferase deficiency; LPI, Lysinuric protein intolerance; CH, Congenital hypothyroidism; PA, Propionic academia, GA type II, Glutaric acidemia type II; PKU, Phenylketonuria.