Table 2.
Novel PAX3 and T variants in cases with spina bifida, 2006–2010
| Gene/Subgroup | Position | Allelesa, b | Locationc | Predicted impact (Conservation Scoresd) |
Cases (N) |
Inheritance |
|---|---|---|---|---|---|---|
| PAX3 | ||||||
| Non-Hispanic whites | ||||||
| 223164750 | c.-1466T>G | 5' flank | Creates E2F-p107 TFBSe (1, 5.46, 5.93) |
1 | Maternal | |
| 223164053 | c.-719A>G | 5' flank | - (0.02, 0.44, 0.53) |
1 | Unknown | |
| 223163960 | c.-629G>T | Promoter | Disrupts WT1-KTS TFBSe (0, −0.01, 0.28) |
1 | Maternal | |
| 223162055 | c.86 -123T>G | Intron 1 | Creates splice donor site (0, 0.07, −0.64) |
1 | Maternal | |
| 223066035 | c.*211+400C>T | Exon 10a | Non-coding exonic region (0.02, 0.42, 1.49) |
1 | Unknown | |
| 223066039 | c.*211+396delA | Exon 10a | Non-coding exonic region (0.01, 0.49, 0.58) |
1 | Paternal | |
| 223065753 | c.*374_375insGTf | Exon 11 | Creates splice acceptor sitef (0.01, −0.28, −1.37) |
1 | Unknown | |
| 223065002 | c.*1125C>Tf | Exon 11 | Non-coding exonic region (1, 3.87, 5.59) |
1g | Unknown | |
| Other race/ ethnicities | ||||||
| 223163940 | c.-606G>C | Promoter | - (0, −0.19, −1.16) |
1 | Unknown | |
| 223065775 | c.*352G>Af | Exon 11 | Non-coding exonic region (0, 0.61, 2.57) |
1 | Unknown | |
| 223065659 | c.*468C>Af | Exon 11 | Non-coding exonic region (0, −0.15, −2.82) |
1 | Unknown | |
| T | ||||||
| Other race/ ethnicities | ||||||
| 166582137 | c.-499G>T | Promoter | - (0, 0.82, 1.44) |
1 | Unknown | |
Genomic Build 37.2; Group term GRCh37.2
Positions and alleles are listed in reverse orientation (i.e., increasing position number from 3’ to 5’ on the coding strand)
PAX3 exon/intron numbering based on 11 total exons present in 8 alternative transcripts; T exon/intron numbering based on 8 total coding exons in 2 alternative transcripts
Vertebrate evolutionary conservation score from phastCons (range: 0–1), phyloP (range: −12–6), and GERP++ (range: −12–6), respectively, from the conservation track of the UCSC Genome Browser
Transcription factor binding site
Position relative to the stop codon in alternative transcript NM_181458.3
Homozygous variants; all other novel variants were in the heterozygous state