TABLE 1.
The overview of variants found in the SFRP4 gene available from online tools.
| c.161C>A p.(Ala54Asp) | c.373T>A p.(Cys125Ser) | |
| gDNA level | Chr7(GRCh38):g.379 16377G>T | Chr7(GRCh38):g.379 16165A>T |
| dbSNP rs number | rs758308395 | rs1344808304 |
| Exon | 1 | 1 |
| Protein domain | Frizzled domain | Frizzled domain |
| gnomAD (v2.1.1) | ALL: 0.00080%, NFE: 0.0018% | ALL: 0.00040%, NFE: 0.00090% |
| gnomAD (v3) | – | – |
| SIFT (v6.2.0) | Deleterious (score: 0) | Deleterious (score: 0) |
| PolyPhen-2 (v2) | Probably damaging (score: 1) | Probably damaging (score: 1) |
| CADD Phred | Deleterious (score: 35) | Deleterious (score: 34) |
| DANN (v2014) | Damaging (score: 0.9971) | Damaging (0.9946) |
| FATHMM (dbNSFP v4.0) | Damaging (score: -1.55) | Damaging (score: -3.22) |
| LRT (dbNSFP v4.0) | Damaging (score: 0) | Deleterious (score: 0) |
| DEOGEN2 (dbNSFP v4.0) | Damaging (score: 0.9279) | Damaging (score: 0.9335) |
| EIGEN (dbNSFP v4.0) | Pathogenic (score: 0.995) | Pathogenic (score: 0.8743) |
| MutationTaster (v2013) | Disease causing (accuracy: 1) | Disease causing (accuracy: 1) |
| PROVEAN (dbNSFP v4.0) | Damaging (score: -5.3) | Damaging (score: -8.74) |
| PhastCons100way (dbNSFP v4.0) | Conserved (score: 1) | Conserved (score: 1) |
| PhyloP100way (dbNSFP v4.0) | Conserved (score: 9. 936) | Conserved (score: 7.433) |
| GERP (v2010) | Conserved (score: 4.6199) | Conserved (score: 4.28) |
| mCSM: Protein stability Change (ΔΔG) | Highly destabilizing (-2.641 Kcal/mol) | Highly destabilizing (-2.412 Kcal/mol) |
Variants are designated according to the SFRP4 reference transcript NM_003014.4 and protein NP_003005.2. Online tools used: Alamut® Visual software, Varsome, mCSM. gDNA: genomic DNA.