Supplementary Table 3.
Variants detected in the 45 cataract genes in the proband
| Gene | Transcript | Variant | Hom/Het | Reads | Mutation type | Gene region | Functional region | rsID* | Frequency in dbSNP† | Frequency in HapMap‡ | Frequency in 1000 genomes§ | Frequency in 1100 exomes|| |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| SLC16A12 | NM_213606 | c.49 T>G | Het | C99/103A;202 | SNV | CDS1 | Missense | rs3740030 | 0.163 | 0.38 | 0.1538 | 0.3641 |
| PITX3 | NM_005029 | c.285 C>T | Het | A25/22G;47 | SNV | CDS2 | Synonymous | rs2281983 | 0.43 | 0 | 0.424 | 0.3795 |
| BEST1 | NM_001139443 | c.39 C>A | Hom | A142;142 | SNV | CDS1 | Synonymous | rs1109748 | 0.075 | 0.547 | 0.1474 | 0.5333 |
| BEST1 | NM_001139443 | c.1428 T>C | Hom | C249/1T;250 | SNV | CDS8 | Synonymous | rs1800009 | 0 | 0 | 0.3553 | 0.7638 |
| JAM3 | NM_032801 | c.978−3 T>C | Het | C106/142T;248 | SNV | Intron7 | Splice | rs610382 | 0.498 | 0.434 | 0.402 | 0.4342 |
| GJA3 | NM_021954 | c.1017 G>A | Het | T41/19C;60 | SNV | CDS1 | Synonymous | rs11617415 | 0.371 | 0 | 0.3736 | 0.1949 |
| GJA3 | NM_021954 | c.895 C>A | Hom | T103;103 | SNV | CDS1 | Missense | rs968566 | 0.966 | 0 | 0.967 | 1 |
| CNBP | NM_001127192 | c.156 C>T | Het | A108/86G | SNV | CDS2 | Synonymous | rs4303883 | 0.381 | 0.277 | 0.2115 | 0.2308 |
| CTDP1 | NM_004715 | c.978 G>A | Het | A127/122G;249 | SNV | CDS7 | Synonymous | rs599554 | 0.326 | 0.175 | 0.283 | 0.1128 |
| CTDP1 | NM_004715 | c.1461 G>A | Het | A54/28G;82 | SNV | CDS8 | Synonymous | rs2126082 | 0.304 | 0 | 0.2756 | 0.1026 |
| CTDP1 | NM_004715 | c.2817 T>C | Hom | C33;33 | SNV | CDS13 | Synonymous | rs626169 | 0.846 | 0.993 | 0.8672 | 0.9949 |
| EPHA2 | NM_004431 | c.2874 C>T | Het | A42/49G;91 | SNV | CDS17 | Synonymous | rs3754334 | 0.355 | 0.226 | 0.326 | 0.241 |
| EPHA2 | NM_004431 | c.1983 C>T | Het | A77/94G;171 | SNV | CDS11 | Synonymous | rs10907223 | 0.267 | 0.206 | 0.2024 | 0.1949 |
| EPHA2 | NM_004431 | c.987 C>T | Het | A27/35G;62 | SNV | CDS5 | Synonymous | rs2230597 | 0.433 | 0.184 | 0.4158 | 0.2564 |
| BFSP1 | NM_001195 | c.1749 A>G | Hom | C250;250 | SNV | CDS8 | Synonymous | rs6080718 | 0 | 0.358 | 0.5403 | 0.4154 |
| BFSP1 | NM_001195 | c.1500 G>A | Het | T109/141C;250 | SNV | CDS8 | Synonymous | rs6136118 | 0.431 | 0.453 | 0.4295 | 0.4615 |
| BFSP1 | NM_001195 | c.1033 G>A | Het | T102/108C;210 | SNV | CDS7 | Missense | rs6080719 | 0.378 | 0.489 | 0.3608 | 0.4564 |
| BFSP1 | NM_001195 | c.90 G>A | Het | T2/3C;5 | SNV | CDS1 | Synonymous | snp105 | 0 | 0 | 0 | 0 |
| ABHD12 | NM_015600 | c.1068 T>C | Hom | G211;211 | SNV | CDS12 | Synonymous | rs10966 | 0.31 | 0 | 0.3581 | 0.516 |
| CRYAA | NM_000394 | c.6 C>T | Hom | T149;149 | SNV | CDS1 | Synonymous | rs872331 | 0.276 | 0.03 | 0.315 | 0.2278 |
| CRYBB3 | NM_004076 | c.337 C>G | Hom | G144;144 | SNV | CDS4 | Missense | rs9608378 | 0.456 | 0.867 | 0.4908 | 0.8718 |
| CRYBB2 | NM_000496 | c.449+9 G>A | Hom | A96;96 | SNV | Intron5 | Splice | rs4049505 | 0 | 0 | 0.6145 | 0.9026 |
| CRYBB2 | NM_000496 | c.483 G>A | Het | A67/79G;146 | SNV | CDS5 | Synonymous | rs8140949 | 0.412 | 0 | 0.3819 | 0.4923 |
| CRYBA4 | NM_001886 | c.171 T>C | Hom | C128;128 | SNV | CDS3 | Synonymous | rs5761637 | 0.844 | 0 | 0.848 | 0.9949 |
| CRYGD | NM_006891 | c.285 A>G | Hom | C249;249 | SNV | CDS3 | Synonymous | rs2305430 | 0.626 | 0.453 | 0.6392 | 0.3846 |
| CRYGD | NM_006891 | c.51 T>C | Het | G37/40A;77 | SNV | CDS2 | Synonymous | rs200375285 | 0 | 0.518 | 0.435 | 0.2974 |
| FYCO1 | NM_024513 | c.3924 C>T | Hom | A194;194 | SNV | CDS13 | Synonymous | rs1463680 | 0.739 | 0.956 | 0.7473 | 0.8114 |
| FYCO1 | NM_024513 | c.2036 C>T | Het | A68/68G;136 | SNV | CDS7 | Missense | rs3796375 | 0.489 | 0.519 | 0.4203 | 0.3808 |
| FYCO1 | NM_024513 | c.1335 G>A | Het | T101/140C;241 | SNV | CDS7 | Synonymous | rs3796376 | 0.315 | 0.562 | 0.3168 | 0.3203 |
| FYCO1 | NM_024513 | c.962 G>C | Het | G60/84C;144 | SNV | CDS7 | Missense | rs3733100 | 0.499 | 0.489 | 0.457 | 0.3879 |
| FYCO1 | NM_024513 | c.749 G>A | Hom | T219;219 | SNV | CDS7 | Missense | rs4683158 | 0 | 1 | 0.8498 | 0.8932 |
| FYCO1 | NM_024513 | c.267 C>A | Hom | T249;249 | SNV | CDS3 | Synonymous | rs4682801 | 0.622 | 1 | 0.6667 | 0.8114 |
| BFSP2 | NM_003571 | c.603 G>A | Het | A84/129G;213 | SNV | CDS3 | Synonymous | rs2276737 | 0.495 | 0.519 | 0.4277 | 0.4513 |
| SLC33A1 | NM_004733 | c.512 A>G | Het | C113/137T;250 | SNV | CDS1 | Missense | rs3804769 | 0.174 | 0.226 | 0.1722 | 0.2278 |
| EYA1 | NM_172058 | c.1755 T>C | Het | G51/42A;93 | SNV | CDS16 | Synonymous | rs10103397 | 0.497 | 0.407 | 0.4267 | 0.388 |
| EYA1 | NM_172058 | c.1278 C>T | Het | A135/115G;250 | SNV | CDS12 | Synonymous | rs4738118 | 0.399 | 0.455 | 0.2811 | 0.4614 |
| EYA1 | NM_172058 | c.813 A>G | Hom | C248;248 | SNV | CDS7 | Synonymous | rs1445398 | 0.034 | 0.224 | 0.0632 | 0.1747 |
| TDRD7 | NM_014290 | c.33 A>G | Hom | G249;249 | SNV | CDS1 | Synonymous | rs1381532 | 0.322 | 0.299 | 0.3114 | 0.2811 |
| TDRD7 | NM_014290 | c.449 T>C | Hom | C243/5T;248 | SNV | CDS3 | Missense | rs2045732 | 0.322 | 0.281 | 0.3114 | 0.2776 |
| NHS | NM_198270 | c.3955 T>C | Het | C128/121T;249 | SNV | CDS6 | Missense | rs3747295 | 0.469 | 0.25 | 0.1374 | 0.1692 |
| MAF | NM_005360 | c.–1637_−1639 delGGC | Het | W34/M14;48 | Deletion | 5-UTR | 5-UTR | _ | No_frequency | Not_in_HapMap | 0 | 0.4744 |
| GJA8 | NM_005267 | c.426_440 delGCTG GA GGGGACCCT | Het | W169/M78;247 | Deletion | CDS1 | CDS | _ | No_frequency | Not_in_HapMap | 0 | 0 |
| RAB3GAP2 | NM_012414 | c.812−6 delT | Het | W67/M68;135 | Deletion | Intron9 | Splice | _ | No_frequency freq | Not_in_HapMap | 0 | 0.3154 |
*NCBI dbSNP ID; †Allele frequency in NCBI dbSNP; ‡Allele frequency in HapMap; §Allele frequency in 1000 genome project; ||Allele frequency in BGI in-house control exomes. dbSNP: Single nucleotide polymorphism database; SNV: Single nucleotide variant; UTR: Untranslated regions; CDS: Coding sequence; BGI: Beijing Genomic Institute.