Table 2. Pathogenicity prediction analyses of the three novel CSF1R variants identified in this study.
| Patient 1 | Patient 2 | Patient 4 | |
|---|---|---|---|
| Genome location | |||
| Position | 149441075 | 149435682 | 150056217 |
| CSF1R exon/intron | Exon 13 | Exon 19 | Intron 17–18 |
| Variant effect | |||
| Base change | c.1837G>T | c.2461T>C | c.2442+2_2442+3dupT |
| Amino acid change | p.V613L | p.W821R | NA |
| Domain | Tyrosine kinase domain | Tyrosine kinase domain | NA |
| Population allele frequency | |||
| Genome Aggregation Database | NR | NR | NR |
| 1000 Genomes Project | NR | NR | NR |
| Exome Aggregation Consortium | NR | NR | NR |
| Functional prediction | |||
| Polyphen2 | Probably damaging | Probably damaging | NA |
| SIFT | Damaging | Damaging | NA |
| Mutation Taster | Disease-causing | Disease-causing | NA |
| LRT | Deleterious | Deleterious | NA |
| General prediction | |||
| CADD Phred score | 31 | 28.1 | NA |
| ACMG/AMP criteria | Likely pathogenic | Likely pathogenic | Uncertain significance |
ACMG/AMP, American College of Medical Genetics and Genomics and Association for Molecular Pathology; CADD, combined annotation-dependent depletion; CSF1R, colony-stimulating factor 1 receptor (NM_ 005211.3); LRT, likelihood ratio test; NA, not available; NR, not reported; Polyphen2, Polymorphism Phenotyping v2; SIFT, sorting intolerant from tolerant.