Table 1 Summary of the detected variants in the skeletal ciliopathy panel.
From: Unclassifiable short-rib thoracic dysplasia diagnosed using targeted gene panel sequencing
No. | DNA change | Protein change | Inheritance | ClinVer ID | CADD | Polyphen-2 | SIFT | PROVEAN | M-CAP | Frequency (in Japanese population)# | Evaluation of pathogenicity (ACMG/AMP) |
|---|---|---|---|---|---|---|---|---|---|---|---|
1 | DYNC2H1 (NM_001080463.2) c.3404 A > T | p.Glu1135Val | M | SCV005077956 | 24.8 | 0.089 (Benign) | 0.013 (Deleterious) | −5.45 (Deleterious) | 0.096 (Possibly Pathogenic) | — | Likely Pathogenic Previously not reported (PM2, PM3, PP3, PP4) |
2 | DYNC2H1 (NM_001080463.2) c.5682_5683del | p.His1896Tyrfs*9 | P | SCV000788364 | 33.0 | — | — | — | — | 0.00046 | Pathogenic Previously reported (PVS1, PM2, PM3, PP5) |
3 | IFT140 (NM_014714.4) c.3602 G > A | p.Arg1201His | M | 318004 | 22.8 | 0.028 (Benign) | 0.152 (Tolerated) | −0.914 (Neutral) | 0.010 (Likely Benign) | 0.00619 | Uncertain Significant (PM2, BP4) |
4 | IFT122 (NM_018262) c.457 A > C | p.Asn153His | P | — | 25.9 | 0.771 (Possibly damaging) | — | −3.922 (Deleterious) | 0.059 (Possibly Pathogenic) | 0.00230 | Uncertain Significant (PM2, PP3) |
