Table 3 Sequence variants of interest identified in our cohort
Family | DLD-1 | DLD-5 | DLD-6 | DLD-11 | DLD-12 | DLD-13 | |||
|---|---|---|---|---|---|---|---|---|---|
Individual | II:2 | II:3 | II:1 | II:1 | II:2 | II:3 | II:2 | II:2 | |
Gene | IQSEC2 | DDX47 | SOX30 | PPP2R2C | ZNF292 | ARID4A | |||
Sequence variants identified | Genomic coordinates (GRCh37/hg19) | NC_000023.11: g.53238184T > C | NC_000012.12: g.12,823,958 C > A | NC_000005.10: g.157,651,130 C > T | NC_000004.12: g.6,378,573 C > T | NC_000006.12: g.87259789_87259790del | NC_000014.9: g.58351207dup | ||
cDNA | NM_001111125.3: c.3238 A > G | NM_016355.4: c.839 C > A | NM_178424.2: c.949G > A | NM_020416.4: c.169-1G > A | NM_015021.3: c.6160-6161del | NM_002892.4: c.1539dup | |||
Predicted protein | p.(Ile1080Val) | p.(Ala280Asp) | p.(Val317Met) | p.? | p.(Glu2054LysfsTer14) | p.(Glu514ArgfsTer3) | |||
Status | Homozygous | Heterozygous | Heterozygous | Heterozygous | Heterozygous | Heterozygous | |||
Inheritance | Maternal | Paternal | de novo | Maternal | de novo | de novo | |||
Exon | 12 | 8 | 1 | intron 2 | 8 | 16 | |||
Frequency in population databases | gnomAD v2 AF | 0 | 0 | 0 | 0 | 0 | 0 | ||
gnomAD v4 AF | 0 | 0.000001590 | 0 | 0 | 0.000001246 | 0 | |||
deCAF AF | 0 | 0 | 0 | 0 | 0 | 0 | |||
All of Us AF | 0.000002 | 0 | 0 | 0 | 0.000004 | 0 | |||
in silico predictions of deleteriousness | PHRED-like scaled CADD score | 20 | 27 | 25 | 34 | 33 | NA | ||
REVEL score | 0.063 | 0.511 | 0.482 | NA | NA | NA | |||
MISTIC score | 0.32 | 0.32 | 0.71 | NA | NA | NA | |||
Gene constraint scores | gnomAD v2 LOEUF score | 0.13 | 0.98 | 0.23 | 0.38 | 0.14 | 0.14 | ||
gnomAD v2 missense Z score | 5.19 | 0.39 | 0.78 | 3.53 | 1.41 | 1.45 | |||
ACMG classification | 3 | NA | NA | NA | 5 | NA | |||