Table 3.
In silico prediction scores of clinical pathogenicity for UMOD variants
| Family | Nucleotide change | GnomAD_ genomes_AF | CLIN_SIG | PolyPhen-2 | SIFT | MetaSVM | M-CAP | LRT | GERP++_RS | CADD_ PHRED |
|---|---|---|---|---|---|---|---|---|---|---|
| FGJD | c.944G>T | 0 | NA | D | D | D | D | D | 4.64 | 32 |
| FGIT | c.605G>C | 0 | NA | D | D | D | D | D | 5.13 | 32 |
| FGDC FGJF |
c.317G>T | 0 | Likely pathogenic | D | D | D | D | D | 5.45 | 28 |
| FGCM FGCO FGGR |
c.278_289delins CCGCCTCCT |
0 | Pathogenic | NA | NA | NA | NA | NA | NA | 20.4 |
| FGLV | c.235C>G | 0 | NA | NA | NA | NA | NA | NA | NA | 0.566 |
| G48055 (control) | c.1743_1744 delinsTG |
0 | NA | NA | NA | NA | NA | NA | NA | NA |
CLIN_SIG, Clinvar database annotation signature; D, deleterious; GnomAD_genomes_AF, variant frequency in GnomAD database; NA, not applicable.
Prediction tools for predicting deleteriousness of single nucleotide variants or insertion/deletion variants: PolyPhen-2, Polymorphism Phenotyping v2; SIFT, Sorting Tolerant From Intolerant; M-CAP, Mendelian Clinically Applicable Pathogenicity; LRT, likelihood ratio test; GERP++RS, Genomic Evolutionary Rate Profiling rejected substitution; and CADD, Combined Annotation Dependent Depletion.