Likely pathogenic variants in SHROOM3 for CFM patients from Chinese, European, and Hispanic ancestries
| Chromosome position (hg38) | SHROOM3 cHGVS NM_020859.4 | SHROOM3 pHGVS | AlphaMissense prediction | Domain | Model | Populations |
|---|---|---|---|---|---|---|
| Chr 4: 76,555,619 | c. 179G > T | p.(Gly60Val) | Pathogenic | PDZ | eQTL-P | GMKF |
| Chr 4: 76,555,718 | c. 278C > T | p.(Ser93Phe) | Ambiguous | PDZ | eQTL-P | CCFM |
| Chr 4: 76,555,759 | c. 319C > T | p.(Arg107Cys) | Ambiguous | PDZ | CCFM | |
| Chr 4: 76,555,760 | c. 320G > A | p.(Arg107His) | Ambiguous | PDZ | CCFM | |
| Chr 4: 76,730,823 | c. 475C > T | p.(Arg159Ter) | FaceBase | |||
| Chr 4: 76,739,581 | c. 1408G > C | p.(Val470Leu) | Ambiguous | CCFM | ||
| Chr 4: 76,740,538 | c. 2365G > A | p.(Glu789Lys) | Pathogenic | eQTL-P | CCFM | |
| Chr 4: 76,741,361 | c. 3188G > C | p.(Arg1063Pro) | Ambiguous | ASD1 | eQTL-P | GMKF |
| Chr 4: 76,741,475 | c. 3302_3347del | p.(Ala1102ArgfsTer23) | eQTL-P | CCFM | ||
| Chr 4: 76,741,847 | c. 3674T > C | p.(Leu1225Pro) | Pathogenic | CCFM | ||
| Chr 4: 76,741,904 | c. 3731C > T | p.(Pro1244Leu) | Ambiguous | CCFM | ||
| Chr 4: 76,755,001 | c. 4518C > G | p.(Asp1506Glu) | Ambiguous | GMKF | ||
| Chr 4: 76,770,802 | c. 5526C > G | p.(Asp1842Glu) | Ambiguous | ASD2 | CCFM | |
| Chr 4: 76,770,821 | c. 5545C > T | p.(Leu1849Phe) | Pathogenic | ASD2 | eQTL-P | CCFM |
| Chr 4: 76,778,885 | c. 5699G > T | p.(Arg1900Leu) | Pathogenic | ASD2 | eQTL-P | CCFM |
[i] (Domain) Protein domain; (Populations) the variant identified from Chinese CFM (CCFM) or Gabriella Miller Kids First (GMKF). eQTL-P marks the pathogenic variant in combination with rs10017322, with red mark predicted pathogenic variants.