Table 2. SUMF1 genetic data for patients 1-3.
| Patient | Ethnicity | Variant (nucleotide) | Variant (protein) | Genotype | gnomAD MAF | In silico predictions † | ClinVar (ID) | ||
|---|---|---|---|---|---|---|---|---|---|
| Revel | AlphaMissense | SpliceAI | |||||||
| 1(GC15080) | Asian Pakistani | c. 290G>T | p.(Gly97Val) | Hom | Absent | Pathogenic (0.928) | Likely pathogenic (0.8002) | Benign (0.01) | Absent |
| c.293T>A | p.(Val98Glu) | Hom | Absent | Uncertain (0.53) | Likely benign (0.1167) | Benign (0) | Absent | ||
| 2 (GC19954) | Caucasian | c.866A>G | p.(Tyr289Cys) | Hom | 0.00001847 | Pathogenic (0.862) | Likely benign (0.299) | Benign (0) | Uncertain significance (1306425) |
| 3 | Caucasian | c.866A>G | p.(Tyr289Cys) | Het | |||||
| c.726-1G>C | - | Het | 0.000003601 | NA | NA | Splice-altering (0.97) | Likely pathogenic (1067238) | ||
†
REVEL is an ensemble score based on 13 individual scores for predicting the pathogenicity of missense variants. AlphaMissense scores can be interpreted as the approximate probability of a variant being clinically pathogenic. SpliceAI delta scores can be interpreted as the probability that the variant affects splicing at any position within a +/-500bp window around it. Scores for REVEL, AlphaMissense and SpliceAl range from 0 to 1, with higher scores indicating a higher probability of the variant being damaging or having a splice altering effect.
Abbreviations: gnomAD, Genome Aggregation Database v4.0.0; Het, heterozygous, Hom, homozygous; MAF, minor allele frequency