Table 1 Rare variants extracted from the exome sequencing data of patient IV-4 and primer sequences for the respective variants
Gene | Chr | OMIM | GenBank | cDNA change | Amino acid change | Genotype | dbSNP | MAF (gnomAD) | MAF South Asian (gnomAD) | PROVEAN | SIFT | Polyphen2 | Mutation Taster | Segregation | Primer Sequence with melting temperature |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
PSPH | 7 | 172,480 | NM_004577.3 | c.398A > G | p.Arg133Ser | Homozygous | rs148469975 | 7.08e-5 | 0 | Deleterious | Damaging | Probably Damaging | Disease Causing | No | 56.2 °C-F-5′-CCAGGCAGTATACCTTGTCA-3′ 55.4 °C-F-5′-TAGATACCAAAGCTAGGACAGG-3′ |
CHCHD2 | 7 | 616,244 | NM_016139.2 | c.418G > A | p.Val140Met | Homozygous | NA | 0 | 0 | Neutral | Tolerated | Probably Damaging | Disease Causing | No | 60.2 °C-F-5′-AGCATCTGGTGCTAGTTCCATT-3′ 58.6 °C-F-5′-GGCCCAGTTGTTAGGAGTTAAT-3′ |
BNC2 | 9 | 608,669 | NM_017637.5 | c.2860G > A | p.Ala954Thr | Homozygous | rs763487720 | 8.13e-5 | 0.0006781 | Neutral | Tolerated | Benign | Disease Causing | No | 59.4 °C-F-5′-TGCCAACATAAACCTACATCGT-3′ 59.5 °C-R-5′-TCCCCTTGTTGCTGTACATTT-3′ |
SLC24A4 | 14 | 609,840 | NM_153646.3 | c.1192C > T | p.Gln398* | Homozygous | NA | 0 | 0 | NA | NA | NA | NA | Yes | 55.5 °C-F-5′-CATGCAAATGTAAGTGACCA-3′ 54.6 °C-R-5′-AGCTCTAACCCACAGTTCAG-3′ |