Table 3.
Overview of IKZF2 variants
| Family | Variant GRCh37 (hg19) NM_001387220.1 |
Effect on protein NP_001374149.1 | GnomAD minor allele frequency (%) | Variant classificationa | CADD_ PHRED |
SIFT | PolyPhen-2 | Mutation Taster |
|---|---|---|---|---|---|---|---|---|
| W16-0482 | Chr2:g.213914526T > G c.485A > C | p.(His162Pro) | 0.0004/0.003 (other/non-Finnish European) |
Likely pathogenic (PS2_supp, PS3_supp, PM2, PP3) |
24.6 | 0.00 | 0.998 | Deleterious |
| W22-1907 | Chr2:g.213914502C > T c.509G > A | p.(Cys170Tyr) | – |
Likely pathogenic (PS3_supp, PM2, PP1_mod, PP3) |
29.4 | 0.01 | 0.998 | Deleterious |
| W22-2757 | Chr2:g.213914577C > A c.434G > T | p.(Cys145Phe) | – |
Unknown significance (PS3_supp, PM2, PP1, PP3) |
32.0 | 0.86 | 0.998 | Deleterious |
aVariant classification was performed using the American College of Medical Genetics and Genomics Standards and Guidelines (Oza et al. 2018; Richards et al. 2015). CADD, Combined Annotation Dependent Depletion, threshold value ≥ 15 (Kircher et al. 2014); GnomAD, Genome Aggregation Database (version 2.1.1), total population exome frequency / maximum exome frequency (corresponding population); MutationTaster, threshold value ‘deleterious’ (Schwarz et al. 2014); PolyPhen-2, Polymorphism Phenotyping v2, threshold value ≥ 0.450 (Adzhubei et al. 2010); SIFT, Sorting Intolerant From Tolerant, threshold value ≤ 0.05 (Ng and Henikoff 2001); –, not present in database