Table 5.
Four Nonsynonymous Variants Identified in PTPRO Are Harbored in the Emphysema-Susceptible Population
| Chromosome | BP | Variation Name | Ref | Alt | MAF* | Resistant Count† | Susceptible Count† | AA change | PolyPhen Prediction | SIFT Prediction |
|---|---|---|---|---|---|---|---|---|---|---|
| 12 | 15654574 | rs117540301 | A | G | 0.0078 | 65/0/0 | 62/2/0 | Ile228Val | Probably damaging | Tolerated |
| 12 | 15654578 | C | G | 0.0039 | 65/0/0 | 63/1/0 | Ser229Cys | |||
| 12 | 15654977 | rs141042273 | A | G | 0.0039 | 65/0/0 | 63/1/0 | His362Arg | Benign | Deleterious |
| 12 | 15656846 | rs61754411 | C | G | 0.0310 | 65/0/0 | 56/8/0 | Asn370Lys | Probably damaging | Deleterious |
Definition of abbreviations: Alt = alternate; BP = base pair; MAF = minor allele frequency; PolyPhen = predictions of functional effects of nonsynonymous SNPs by Polymorphism Phenotyping V2 (PolyPhen-2) algorithm; PTPRO = protein tyrosine phosphatase, type O; Ref = reference; SIFT Prediction = predictions of functional effects of nonsynonymous by Sorting Intolerant from Tolerant (SIFT) algorithm; SNP = single-nucleotide polymorphism.
Minor allele frequency in the entire population (129 individuals).
Counts are given as number of individuals homozygous for the reference allele/number of individuals heterozygous/number of individuals homozygous for the alternate allele.