Table 1.
Likely pathogenic rare variants within the FOXI3 gene identified from patients (CFM or Goldenhar syndrome)
| Family ID | Proband ID | Chromosome Position (hg38) | Reference | Alternative | Consequence | FOXI3 cHGVS NM_001135649.3 | FOXI3 pHGVS | In silico predictions | gnomAD_Allele_Frequency (v3.1.2) |
|---|---|---|---|---|---|---|---|---|---|
| EUR04 | EUR04 (SEA15423) | chr2:88452445 | G | GG | frameshift | c.92dupG | p.(Ala32GlyfsTer147) | CADD: 23.0 | absent |
| EUR05 | EUR05 (SEA15566) | chr2:88452231 | A | T | missense | c.305T>A | p.(Phe102Tyr) | CADD: 14.07 SIFT: 0.96 Polyphen2: 0 | absent |
| CHN-S001 | CHN-S001 | chr2:88452164 | CGCGGGCGCGGCGGGCGAG | C | inframe deletion | c.354_371del | p.(Ser119_Ala124del) | CADD: 19.88 | 0.0000199 |
| CHN-S002 | CHN-S002 | chr2:88452097 | G | T | missense | c.439C>A | p.(Pro147Thr) | CADD: 28.3 SIFT: 0 Polyphen2: 1 | absent |
| CHN-S003 | CHN-S003 | chr2:88452030 | C | T | missense | c.506G>A | p.(Ser169Asn) | CADD: 27.4 SIFT: 0 Polyphen2: 0.994 | absent |
| CHN05 | CHN05 | chr2:88451941 | G | A | missense | c.595C>T | p.(Leu199Phe) | CADD: 29.8 SIFT: 0 Polyphen2: 1 | absent |
| EUR03 | EUR03 (SEA15422) | chr2:88448797 | A | G | missense | c.673T>C | p.(Cys225Arg) | CADD: 26.4 SIFT: 0.02 Polyphen2:0.599 | absent |
| EUR02 | EUR02(SEA15533) | chr2:88448770 | A | C | missense | c.700T>G | p.(Phe234Val) | CADD: 29.1 SIFT: 0 Polyphen2: 0.992 | absent |
| F252 | IV: 5 | chr2:88448768 | G | T | missense | c.702C>A | p.(Phe234Leu) | CADD: 26.4 SIFT: 0 Polyphen2: 0.896 | 0.00001314 |
| CHN-S004 | CHN-S004 | chr2:88448767 | G | A | missense | c.703C>T | p.(Arg235Cys) | CADD: 32 SIFT: 0 Polyphen2: 0.998 | absent |
| CHN01 | IV: 8 | chr2:88448764 | G | A | missense | c.706C>T | p.(Arg236Trp) | CADD: 23.9 SIFT: 0.03 Polyphen2: 0.899 | absent |
| CHN-S005 | CHN-S005 | chr2:88448763 | C | T | missense | c.707G>A | p.(Arg236Gln) | CADD: 28.7 SIFT: 0 Polyphen2: 0.899 | 0.00000657 |
| CHN02 | II: 2 | chr2:88448757 | C | T | missense | c.713G>A | p.(Arg238Gln) | CADD: 28.8 SIFT: 0.04 Polyphen2: 1 | absent |
| CHN-S006 | CHN-S006 | chr2:88448757 | C | T | missense | c.713G>A | p.(Arg238Gln) | CADD: 28.8 SIFT: 0.04 Polyphen2: 1 | absent |
| CHN03 | II: 2 | chr2:88448752 | G | A | missense | c.718C>T | p.(Arg240Cys) | CADD: 29.1 SIFT: 0 Polyphen2: 0.993 | absent |
| EUR01 | EUR01 (SEA9213) | chr2:88448752 | G | A | missense | c.718C>T | p.(Arg240Cys) | CADD: 29.1 SIFT: 0 Polyphen2: 0.993 | absent |
| CHN04 | II: 2 | chr2:88448751 | C | T | missense | c.719G>A | p.(Arg240His) | CADD: 28.2 SIFT: 0 Polyphen2: 0.993 | 0.00002628 |
| CHN-S007 | CHN-S007 | chr2:88448406 | G | A | missense | c.1064C>T | p.(Pro355Leu) | CADD: 12.73 SIFT: 0.09 Polyphen2: 0.003 | 0.00002094 |
| CHN-S008 | CHN-S008 | chr2:88448341 | CGGTGCTATTGCT | C | inframe deletion | c.1117_1128del | p.(Ser373_Thr376del) | CADD: 14.11 | 0.00003245 |
| CHN-S009 | CHN-S009 | chr2:88448341 | CGGTGCTATTGCT | C | inframe deletion | c.1117_1128del | p.(Ser373_Thr376del) | CADD: 14.11 | 0.00003245 |
| CHN-S010 | CHN-S010 | chr2:88448227 | G | A | stop gained | c.1243C>T | p.(Arg415Ter) | CADD:38 | 0.000006574 |
| EUR06 | EUR06 (SEA15421) | chr2:87317229-89306982 | + | - | SV deletion | chr2: 87317229-89306982 deletion | / | / | / |