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Table 5 Summary of the positively selected sites in the col1a1 gene, their clinical relevance, and, the probability of being located within distance "d" from the nearest disease-implicated site.

From: Positive selection neighboring functionally essential sites and disease-implicated regions of mammalian reproductive proteins

Positively selected sites Posterior Probability Human Variant: SNP position Distance (d) Probability of being d
from nearest
disease-implicated site
Genetic code distances between observed character states Clinical Association
195 0.926 197 2 0.04 A-N = 2 G → C mild phenotype
280 0.588 275 5 0.26 A-S = 1; S-T = 1; T-A = 1 G → D OI-II
478 0.959 476 2 0.128 A-S = 1; S-T = 1; T-A = 1 G → R OI-II
784 0.968 776 8 0.396 A-S = 1; S-T = 1; T-A = 1 G → S OI-II
1032 0.535 1025 7 0.364 A-P = 1 G → R OI-II
1063 0.826 1061 2 0.128 N-S = 1 G → D OI-II
   1061 2 0.032 N-S = 1 G → S OI-IV
1149 0.623 1151 2 0.032 A-S = 1 G → S OI-III
   1151 2 0.128 A-S = 1 G → V OI-II
1194 0.675 1195 1 0.076 A-G = 1; G-S = 1; S-A = 1 G → C OI-II mild form
1196 0.972     A-F = 2; F-Y = 1; Y-A = 2   
1316 0.928 1312 4 0.24 K-N = 1; N-P = 2; P-K = 2 W → C OI-II
1456 0.997 1460 4 0.1 C-F = 1; C-L = 2; C-M = 2; F-L = 1; F-M = 2; L-M = 1 P → H dbSNP: rs17853657
  1. The sites under positive selection in the col1a1 protein and their associated posterior probabilities (PP) are shown. The third column shows variant positions (SNPs) as determined using Swiss-Prot human (PO2452) sequence. The fourth and fifth columns show the residue distance "d" of the positively selected site from its nearest genetic variant, and the probability of being located "d" residues from any disease implicated site by random chance alone. The sixth column uses single-letter amino acid symbols to show the genetic code distances between all observed character states at each positively selected site. "Clinical Association" show the replacement substitution at the human variant position and its clinical association with that human variant. OI = Osteolysis imperfecta, OI-I to -IV. The final entry for dbSNP is database entry number rs17853657 and as yet has not been associated with OI although it is in the same domain as the other disease-causing SNPs.
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