Table 1.
Predicted pathogenicity and allele frequencies of AFF3 de novo missense variants
| Gene | Proband | Chromosome coordinates (GRCh37/hg19) | Nucleotide change | Amino acid change | dbSNP (v.152) | GnomAD allele frequency (v.2.1.1) |
Deleteriousness prediction (score) |
||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| CADD_PHRED (GRCh37-v.1.6) | SIFT (v.4.0.3) | PROVEAN (v.1.1) | PolyPhen2 (v.2.2.2) | Mutation Taster (19.03.21) | |||||||
| AFF3 NM_001025108.1 NP_001020279.1 | 1 | Chr2: 100623276 | c.766C>T | p.Pro256Ala | – | 0 | 26.1 | damaging (0.000) | deleterious (−6.61) | probably damaging (1.000) | disease causing |
| 2 | Chr2: 100623275 | c.767C>T | p.Pro256Leu | – | 0 | 27.4 | damaging (0.000) | deleterious (−8.26) | probably damaging (1.000) | disease causing | |
| 3–6 | Chr2: 100623270 | c.772G>T | p.Ala258Ser | – | 0 | 24.1 | damaging (0.000) | neutral (−2.48) | probably damaging (1.000) | disease causing | |
| 7–12 and Japanese proband17 | Chr2: 100623270 | c.772G>A | p.Ala258Thr | rs1131692272 | 0 | 23.7 | damaging (0.000) | deleterious (−3.30) | probably damaging (1.000) | disease causing | |
| 13 and 14 | Chr2: 100623269 | c.773C>T | p.Ala258Val | – | 0 | 24.1 | damaging (0.000) | deleterious (−3.30) | probably damaging (1.000) | disease causing | |
| 15 | Chr2: 100623263 | c.779T>G | p.Val260Gly | – | 0 | 24.2 | damaging (0.000) | deleterious (−5.85) | probably damaging (1.000) | disease causing | |
SIFT cutoff = 0.05, PROVEAN cutoff = −2.5, and PolyPhen2 cutoff = 0.5.