Table 1.
Genomic findings of heterozygous PHIP variants
| Subject ID | Chromosome | HGVS DNA reference (NM_017934.6) | HGVS protein reference (NP_060404.4) | Variant type (prediction score)a | ACMG/AMP-2015 classification (criteria Met) | dbSNP/dbVar ID | Parent of origin |
|---|---|---|---|---|---|---|---|
| 1 | Chr 6:79713538 (hg19) Chr6:79003821 (hg38) | c.1562A > G | p.(Lys521Arg) | Missense (CADD v1.3: 24) | Likely pathogenic (PS2, PM2, PP3) | Not available | De novo |
| 2 | Chr 6:79752620 (hg19) Chr6:79042903 (hg38) | c.540_541insA | p.(Gly181ArgfsTer12) | Frameshift | Likely pathogenic (PVS1, PM2) | Not available | Paternal |
| 3 | Chr 6:79735299 (hg19) Chr 6:790255582(hg38) | c.860C > A | p.(Ser287Tyr) | Missense (CADD v1.3: 24.8) | Likely pathogenic (PM2, PS2) | rs1085307845 | De novo |
| 4 | Chr 6:79671468 (hg19) Chr 6:78961751 (hg38) | c.3595delG | p.(Val1199Ter) | Nonsense | Pathogenic (PVS1, PS2, PM2) | Not available | De novo |
| 5 | Chr 6:79692625 (hg19) Chr 6:78982908 (hg38) | c.2744_2747del | p.(Lys915SerfsTer15) | Frameshift | Pathogenic (PVS1, PS2, PM2) | Not available | De novo |
| 6 | Chr 6:79679596 (hg19) Chr 6:78969879 (hg38) | c.3161delT | p.(Leu1054Ter) | Nonsense | Pathogenic (PVS1, PS2, PM2) | Not available | De novo |
| 7 | Chr 6:79752561 (hg19) Chr 6:79042844 (hg38) | c.598_599delACinsT | p.(Thr200LeufsTer8) | Frameshift | Likely pathogenic (PVS1, PM2) | rs1554210073 | Unknown (not paternal) |
| 8 | Chr 6:79668186-79668189 (hg19) Chr 6:78958469-78958472 (hg38) | c.3782 + 3_3782 + 6delAAGT | IVS32 + 3_IVS32 + 6delAAGT | Splice site (HSF 3.1: most probably affecting splicing) | Variant of unknown significance (PM2) | rs1131691771 | Unknown (not maternal) |
| 9 | Chr 6:79655778 (hg19) Chr 6:78946061 (hg38) | c.4570delT | p.(Ser1524LeufsTer22) | Frameshift | Likely pathogenic (PVS1, PM2) | Not available | Unknown |
| 10 | Chr 6:79735796 (hg19) Chr6:79026079 (hg38) | c.686C > T | p.(Ser229Leu) | Missense (CADD v1.3: 32) | Likely pathogenic (PM2, PS2) | Not available | De novo |
(HSF) Human Splicing Finder.
aCADD scores were only available for missense variants.