Table 2.
Overview results of WES in Family A
| Chr. | Genomic DNA | Ref. | Aberration | Reads | Variation readsa | Gene | Messenger RNA | Protein | PhyloP | Confirmedb | Segregationc | CADD | SIFT | MutationTaster | Polyphen2 | Allele frequency in gnomAD |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Compound heterozygous variants | ||||||||||||||||
| 1 | 235628968 | Dup AA | 273 | 57 (21%) | B3GALNT2 | c.822_823dup | p.Ile276Leufs*26 | 3.624 | Yes | Yes | - | - | - | - | 0.0002057 | |
| 1 | 235621948 | G | A | 100 | 30 (30%) | B3GALNT2 | c.988C > T | p.Arg330Cys | 1.708 | Yes | Yes | 29.3 | Deleterious (score: 0) | Disease causing (p value: 1) | Probably damaging (score: 1.000) | 0.00001234 |
| 12 | 101016068 | G | A | . | 37 (36%) | GAS2L3 | c.664G > A | p.Glu222Lys | 5.61 | Yes | Nod | 27.6 | Deleterious (score: 0.03) | Disease causing (p value: 1) | Possibly damaging (score: 0.563) | 0.001949 |
| 12 | 101016071 | G | A | . | 38 (37%) | GAS2L3 | c.667G > A | p.Asp223Asn | 5.61 | Yes | Nod | 24.8 | Deleterious (score: 0.02) | Disease causing (p value: 1) | Benign (score: 0.392) | 0.001956 |
| Variants in known intellectual disability genes | ||||||||||||||||
| 1 | 27105725 | A | G | . | 10 (45%) | ARID1A | c.5336A > G | p.Glu1779Gly | 0.69 | Yes | Noe | 13.65 | Deleterious (score: 0.03) | Disease causing (p value: 0.689) | Possibly damaging (score: 0.483) | 0 |
aVariation reads: number of variant reads (% of total reads)
bVariant confirmed in proband by Sanger sequencing
cSegregation of confirmed variant with phenotype in respective family
dThe variants in GAS2L3 were both inherited from the (healthy) mother
eThe single confirmed variant in ARID1A was inherited from the (healthy) mother and was not present in the affected brother of the proband