Table 1.
Rare and novel sequence variants found by Sanger Sequencing and their respective bioinformatic analysis
| Exonic DNA variants | ||||||||
| Gene | Patient | DNA change (Location) | Freq. | Protein change | Bioinformatic analysis | |||
| PolyPhen 2 | SIFT | HSF | Mutation taster | |||||
| CCDC39 | 3 (He) | c.233G > A (exon 3) | 0.56 % | p.R78H | Benign (s = 0.004) | Tolerated (s = 0.28) | No effect on Splice | P (p = 0.90) |
| 1 (He) | c.2540A > G (exon 18) | New variant | p.E847G | Benign (s = 0.165) | Tolerated (s = 0.06) | ESE (wt: 72.9 -mt: 82.9) | Disease causing ( p = 0.69) | |
| CCDC40 | 4 (He) | c.2682G > A (exon 16) | 0.61 % | P (=) | – | – | No effect on Splice | P (p = 0.90) |
| Intronic DNA variants | ||||||||
| Gene | Patient | DNA change (Location) | Freq. | Bioinformatic analysis | ||||
| Splice Algorithms | Mutation taster | |||||||
| CCDC40 | 3 (He) | c.2620-92C > T (Intron 15) | New variant | No effect on Splice | P (p = 0.9) | |||
| DNAH5 | 3 (Ho) | c.1537-102 T > A (Intron11) | ND | No effect on Splice | P (p = 0.9) | |||
| 4 (Ho) | c.1537-100_1537-99delTT (Intron 11) | ND | ||||||
| 1 (He) | ||||||||
| 1–4 (He) | c.3835-3delT | 0.1 % | ↓ ASS | Disease causing ( p = 1) | ||||
| (intron24) | nt:92.6 – mt:89.1 (SpliceSiteFinder-like) | |||||||
| nt:12.8 – mt:10.4 (MaxEntScan) | ||||||||
| nt:11.9 – mt:9.8 (GeneSplicer) | ||||||||
| nt:85.8– mt:85.3 (HSF) | ||||||||
| 3 (He) | c.5882 + 133A > G (Intron 35) | New variant | No effect on Splice | P (p = 0.9) | ||||
| 2 (Ho) 4,5 (He) | c.7408-84_7408-83delAT (intron 44) | ND | ||||||
| 1 (He) | c.10282-81delT (Intron60) | ND | ||||||
| 3 (He) | c.10872 + 84 T > C (Intron63) | ND | ||||||
| 3 (He) | c.11570 + 124G > C (Intron67) | New variant | ||||||
| DNAH1 | 1 (He) | c.81 + 61A > G | 0.3 % | ↑ ASS | Disease causing ( P = 0.98) | |||
| (Intron2) | wt:54.03/ mt:82.97; nt: 83.19(HSF) | |||||||
Human Splice Finder (HSF): http://www.umd.be/HSF/; PolyPhen-2: http://genetics.bwh.harvard.edu/pph2/; SIFT: http://sift.jcvi.org; and the MutationTaster: http://www.mutationtaster.org/. Scores higher than 0.5 in Polyphen are considered damaging and in SIFT scores less than 0.05 are considered deleterious. In MutationTaster a probability (p) closer to 1 indicates a high confidence in the prediction. At bold are the variants with predict pathogenic impact
Freq. Frequency within control population (based on Exome variant server and SNP database from NCBI), He Heterozygous, Ho Homozygous, ND Variant listed in databases but with undetermined frequency on population, RArginine, HHistidine, EGlutamic acid, GGlycine, sscore, pprobability, PPolymorphism, ASS Acceptor Splice Site, wt reference score (i.e., the score of non-mutated sequence), mt mutant score (i.e., the score of mutated sequence), nt native splice site (i.e., normally occurring splice site), ESE Exonic Splice Enhancer