Table 1.
Likely gene-disruptive events detected in HYDIN/HYDIN2 by MIP-based sequencing of exons in cases and controls
| Paraloga | Variant | Exon | Intron | Protein position | Amino acid | Cases (n = 3483) | Controls (n = 2629) | ||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| n | Freq. | Number genotypedb | n | Freq. | Number genotypedb | ||||||
| Cases only | |||||||||||
| HYDIN2 | splice_donor | - | 66/85 | - | - | 1 | 0.03% | 3431 | 0 | 0.00% | 2604 |
| HYDIN2 | splice_acceptor | - | 53/85 | - | - | 1 | 0.03% | 3432 | 0 | 0.00% | 2599 |
| HYDIN | stop_gained | 48/86 | - | 2690 | Q/* | 1 | 0.03% | 3433 | 0 | 0.00% | 2603 |
| HYDIN2 | stop_gained | 46/86 | - | 2540 | R/* | 1 | 0.03% | 3425 | 0 | 0.00% | 2598 |
| Controls only | |||||||||||
| HYDIN2 | stop_gained | 80/86 | - | 4563 | W/* | 0 | 0.00% | 3429 | 1 | 0.04% | 2599 |
| HYDIN2 | Frameshift | 48/86 | - | 2680 | G/X | 0 | 0.00% | 3427 | 1 | 0.04% | 2598 |
| HYDIN2 | splice_donor | - | 42/85 | - | - | 0 | 0.00% | 3428 | 1 | 0.04% | 2599 |
| HYDIN | splice_donor | - | 29/85 | - | - | 0 | 0.00% | 3434 | 1 | 0.04% | 2603 |
| HYDIN | stop_gained | 11/86 | - | 1330 | R/* | 0 | 0.00% | 3429 | 1 | 0.04% | 2599 |
| Found in both cases and controls | |||||||||||
| HYDIN2 | splice_acceptor | - | 67/85 | - | - | 11 | 0.32% | 3430 | 6 | 0.23% | 2601 |
| HYDIN2 | splice_acceptor | - | 54/85 | - | - | 1 | 0.03% | 3426 | 1 | 0.04% | 2595 |
| HYDIN2 | frameshift | 46/86 | - | 2485 | A/X | 1 | 0.03% | 3428 | 1 | 0.04% | 2600 |
| HYDIN2 | frameshift | 41/86 | - | 2115-2116 | VI/VSX | 11 | 0.32% | 3427 | 10 | 0.38% | 2598 |
| HYDIN2 | splice_donor | - | 28/85 | - | - | 1 | 0.03% | 3430 | 1 | 0.04% | 2600 |
| HYDIN2 | frameshift | 19/86 | - | 2531-2532 | A/X | 1 | 0.03% | 3434 | 1 | 0.04% | 2607 |
| HYDIN2 | splice_acceptor | - | 14/85 | - | - | 4 | 0.12% | 3429 | 2 | 0.08% | 2605 |
We genotyped 3483 probands and 2629 healthy controls from families with autism using a MIP-based genotyping assay that targeted coding exons and at least five flanking intronic nucleotides. LGD variants (frameshift, stop-gain, stop-loss, and splice-site) were called using FreeBayes. Only variants that could be definitively assigned to HYDIN or HYDIN2 based on the presence of an identifying SUN are shown. Variants include those seen only in cases, seen only in controls, and those seen in both cases and controls. Most of the variants seen in HYDIN2 occur outside of the putative coding sequence
aParalog determined by presence of SUN(s) on variant-containing MIP reads; variants identified by MIP reads that did not intersect a SUN could not be assigned. Variants in HYDIN2 are annotated with the exon numbering scheme from HYDIN
bNumber of samples successfully genotyped for this variant (FreeBayes)