Table 5.
Novel, Rare, and Potentially Etiologic Variants Observed in Sequenced Genes.
| Part A: Variants Observed in Cases and Some Parents but Not in Controls | ||||
|---|---|---|---|---|
| HGVS | HGVp | Total No. of Cases with Variant | Subphenotype of Cases with Variant | Segregation Analyses |
| ARHGAP29 | ||||
| c.341-30T>A | NA | 1 | NSCL | NA |
| c.511-107T>C | NA | 2 | NSCLP and NSCPO | NA |
| c.967A>G | p.Asn323Asp | 1 | NSCL | Absent in father |
| c.1277delAinsTA | p.Lys426IlefsTer6 | 1 | NSCLP | Absent in mother |
| c.1281+4A>G | NA | 1 | NSCLP | Observed in clinically unaffected mother |
| PAX7 | ||||
| c.1227G>A | p.Leu409Leu | 1 | NSCL | NA |
| Part B: Bioinformatics-Predicted Effects of Potentially Pathogenic Variants | ||||
| HGVS | Polyphen-2 | SIFT | Human Splice Finder | RegulomeDB |
| ARHGAP29 | ||||
| c.341-30T>A | NA | NA | Alteration of ESS site | NA |
| c.511-107T>C | NA | NA | Alteration of ESS site and creation of new ESE site | NA |
| c.967A>G | Benign | Deleterious | NA | NA |
| c.1277delAinsTA | NA | NA | NA | NA |
| c.1281+4A>G | NA | NA | Alteration of wildtype donor site | NA |
| PAX7 | ||||
| c.1227G>A | Benign | Tolerated | Alteration of an ESE site | NA |
All analyses were based on genome assembly number GRCh37/hg19, 2009 (http://genome.ucsc.edu).
ESE, exonic splicing enhancer; ESS, exonic splicing silencer; NA, not applicable; NSCLP, nonsyndromic cleft lip and palate; NSCL, nonsyndromic cleft lip only; NSCPO, nonsyndromic cleft palate only.