Table 2.
Homozygote and Compound Heterozygote Genotypes of Damaging and/or Disruptive Variants Observed in Schizophrenia Cases
| Gene | Haplotype | Variant | Transcript | Effect | SIFT | PolyPhen | ClinVar | MAF |
|---|---|---|---|---|---|---|---|---|
| AGA | Paternal | 4:178360811-G>T | ENST00000264595 | L105I | Tolerated (0.06) | probably_damaging(0.954) | Benign | 0.012 |
| Maternal | (Homozygous) | |||||||
| FH | Paternal | 1:241669398-T>C | ENST00000366560 | Y270C | Deleterious (0.03) | benign(0.243) | Uncertain significance | 0.0003 |
| Maternal | (Homozygous) | |||||||
| LRP2 | Paternal | 2:170042245-T>C | ENST00000263816 | N3205D | probably_damaging(0.999) | Absent | 0.00002 | |
| Maternal | (Homozygous) | |||||||
| MCPH1 | Paternal | 8:6371240-C>G | ENST00000325203 | L386F | Tolerated (0.15) | probably_damaging(0.972) | Absent | 0.003 |
| Maternal | (Homozygous) | |||||||
| MTRR | Paternal | 5:7885945-A>G | ENST00000264668 | I372M | Deleterious (0.03) | benign(0.208) | Absent | 0.0003 |
| Maternal | (Homozygous) | |||||||
| PCCB | Paternal | 3:136002730-C>T | ENST00000469217 | P219S | deleterious_ low_confidence (0.01) | probably_damaging(0.998) | Uncertain significance | 0.007 |
| Maternal | (Homozygous) | |||||||
| RELN | Paternal | 7:103234828-G>C | ENST00000428762 | I1217M | Deleterious (0) | possibly_damaging(0.643) | Conflicting interpretations of pathogenicity: Likely benign3 or Uncertain significance3 | 0.004 |
| Maternal | 7:103138569-G>A | ENST00000428762 | T2933I | Deleterious (0.01) | possibly_damaging(0.493) | Likely benign | 0.0002 | |
| SCN3A | Paternal | 2:165950891-C>T | ENST00000283254 | R1510H | Deleterious (0.01) | probably_damaging(0.977) | Absent | 0.000008 |
| Maternal | 2:166003301-G>A | ENST00000283254 | S540F | Deleterious (0.04) | probably_damaging(0.986) | Likely benign | 0.002 | |
| SLX4 | Paternal | 16:3639713-G>A | ENST00000294008 | S1309F | Deleterious (0.01) | probably_damaging(0.962) | Uncertain significance | 0.0004 |
| Maternal | (Homozygous) |
For the compound heterozygotes, both the paternal and maternal allele are listed or else the genotype is noted to be homozygous. A transcript is given for which the stated SIFT and PolyPhen annotations were output. Also, shown are the ClinVar entry and minor allele frequency (MAF) in non-Finnish Europeans.