Table 1. Number of different single nucleotide variants and gene constraints in human transglutaminase genes.
Gene | Synonymous | Non-synonymous | Loss-of-Function | n_mis | exp_mis | mis_z | GDI | GDI-Phred I |
---|---|---|---|---|---|---|---|---|
F13a | 120 | 283 | 22 | 252 | 269.8 | 0.53 | 4254.7 | 12.9 |
TGM1 | 163 | 320 | 19 | 314 | 349.2 | 0.92 | 277.2 | 3.5 |
TGM2 | 148 | 272 | 29 | 270 | 290.5 | 0.59 | 240.6 | 3.3 |
TGM3 | 144 | 313 | 20 | 304 | 271.9 | -0.95 | 1529.8 | 7.2 |
TGM4 | 121 | 279 | 39 | 264 | 232.6 | -1.0 | 3544.7 | 11.4 |
TGM5 | 95 | 273 | 40 | 261 | 255.9 | -0.15 | 2224.6 | 8.6 |
TGM6 | 136 | 336 | 39 | 320 | 287.7 | -0.92 | 764.5 | 5.4 |
TGM7 | 91 | 293 | 28 | 283 | 263.3 | -0.59 | 698.4 | 5.2 |
Number of synonymous, non-synonymous and LOF variants were determined based on data available in ExAC database. The n_mis, and exp_mis scores [11], and GDI and GDI-Phred I values [21] were taken from datasets published previously. See methods section for brief description and ref. [11] and [21] for detailed explanation of calculations and determination of the scores. Frameshift mutations, splice acceptor, splice donor, stop gained are included under LOF category. Definition of values and scores shown in the table is as follows. The n_mis scores: number of rare (minor allele frequency (MAF) <0.1%) missense variants found in ExAC r0.3 database. The exp_mis scores: depth adjusted number of expected rare (MAF <0.1%) missense variants. The mis_z scores: corrected missense z scores. The z score is a constraint metric to contrast observed and expected number of variants per gene [11]. The number of nsSNVs in columns 3 and 5 differ because for mis_z score calculation only nsSNVs with MAF < 0.1% are taken into account (n_mis, column 5). GDI is a metric used to score accumulated mutational damage on human genes [21]. GDI-Phred I: the GDI ranking of the gene relative to all other human genes.