Table 1.
Predicted Pathogenicity and Allele Frequencies of SPATA5 Variants
| Amino Acid Change | Chromosome 4 Coordinates | Nucleotide Change | SIFT | PROVEAN | PolyPhen-2 | MutationTaster | MetaSVM | CADD Phred |
Allele Frequency |
|||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ExAC | 1000 Genomes | EVS | XomeDx | |||||||||
| p.Arg84Gln | 123848876G>A | c.251G>A | tolerated (0.111) | neutral (−0.653) | possibly damaging (0.849) | disease causing (0.39392) | deleterious (0.88398) | 22.30 | 0.00004118 | 0 | 0 | 0.0003 |
| p.Ser90Ile | 123848894G>T | c.269G>T | damaging (0.001) | neutral (−2.020) | possibly damaging (0.873) | disease causing (0.34117) | deleterious (0.86851) | 17.76 | 0 | 0 | 0 | 0.0001 |
| p.Ala100Thr | 123850204G>A | c.298G>A | damaging (0.002) | neutral (−2.020) | damaging (0.960) | disease causing (0.997) | deleterious (0.90678) | 27.60 | 0 | 0 | 0 | 0.0001 |
| p.Arg186∗ | 123855302C>T | c.556C>T | NA | NA | NA | disease causing (0.70825) | NA | 37.00 | 0 | 0 | 0 | 0.0001 |
| p.Thr330del | 123855735_123855737del | c.989_991del | NA | deleterious (−4.557) | damaging | disease causing | unknown | 22.40 | 0.0001334 | 0 | 0 | 0 |
| p.Ser448Leu | 123859289C>T | c.1343C>T | damaging (0.001) | deleterious (−4.648) | possibly damaging (0.672) | disease causing (0.35151) | deleterious (0.97264) | 24.40 | 0.00002471 | 0 | 0 | 0.0001 |
| p.Asn525Thrfs∗20 | 123868503_123868507del | c.1574_1578delATGCT | NA | NA | NA | NA | NA | NA | 0 | 0 | 0 | 0.0001 |
| p.Arg529Gln | 123868515G>A | c.1586G>A | damaging (0.000) | deleterious (−3.731) | damaging (0.985) | disease causing (0.70825) | deleterious (0.99505) | 34.00 | 0.00002471 | 0 | 0 | 0.0001 |
| p.Tyr559∗ | 123868606C>A | c.1677C>A | NA | NA | damaging | disease causing | unknown | 37.00 | 0 | 0 | 0 | 0 |
| NA | 123868644G>A | c.1714+1G>A | NA | NA | unknown | disease causing (1.000) | unknown | 16.40 | 0.0001341 | 0 | 0.00015378 | 0 |
| p.Trp626Cys | 123949349G>C | c.1878G>C | damaging (0.000) | deleterious (−12.091) | damaging (0.946) | disease causing (0.40733) | deleterious (0.99215) | 21.90 | 0 | 0 | 0 | 0 |
| p.Asp628Gly | 123949354A>G | c.1883A>G | damaging (0.001) | deleterious (−6.762) | damaging (0.97) | disease causing (0.70825) | deleterious (0.99139) | 32.00 | 0.00003295 | 0 | 0 | 0.0001 |
| p.Arg784Gln | 124177181G>A | c.2351G>A | damaging (0.001) | deleterious (−3.835) | damaging (0.971) | disease causing (0.40733) | deleterious (0.99177) | 21.80 | 0 | 0 | 0 | 0.0001 |
| p.Ile788Serfs∗47 | 124177192_124177201del | c.2362_2371delATTGATAGAA | NA | NA | NA | NA | NA | NA | 0 | 0 | 0 | 0.0001 |
| p.Ala844Val | 124235068C>T | c.2531C>T | tolerated (0.085) | deleterious (−3.512) | possibly damaging (0.723) | disease causing (0.3652) | deleterious (0.95928) | 24.80 | 0 | 0 | 0 | 0.0001 |
The following abbreviation is used: NA, not applicable.