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Table 3 Comparison of predicted effects of SNPs and SVs that might contribute to the phenotypic differences between C57BL/6N and C57BL/6J.a

From: A comparative phenotypic and genomic analysis of C57BL/6J and C57BL/6N mouse strains

Protein coding gene C57BL/6J amino acid C57BL/6N amino acid SNP is private to: PROVEAN prediction (score)b MP terms B6J versus B6N2 B6N versus B6Jc
Adcy5 Valine (V) Methionine (M) B6N Tolerated
Impaired coordination_MP:0001405 NR P
      Hypoactivity_MP:0001402 NR P
Pmch Isoleucine (I) Threonine (T) B6N Tolerated (0.493) Decreased circulating glucose level_MP:0005560 NR A
      Abnormal glucose tolerance_MP:0005291 NR A
      Increased oxygen consumption_MP:0005289 NR P
Pdzk1 Asparagine (N) Aspartic Acid (D) B6J Tolerated (0.95) Increased circulating cholesterol level_MP:0001556 A NR
Nlrp12 Lysine
B6J Tolerated (0.781) Abnormal type IV hypersensitivity reaction_MP:0002534 P NR
Crb1 - - B6N - Photosensitivity_MP:0001999 NR P
      Abnormal ocular fundus morphology_MP:0002864 NR P
      Retinal degeneration_MP:0001326 NR P
      Abnormal retinal morphology_MP:0001325 NR P
      Abnormal retinal photoreceptor layer_MP:0003728 NR P
Chl1 - - B6J - Abnormal learning/memory_ MP:0001449 A NR
      Abnormal spatial working memory_MP:0008428 A NR
Rptor - - B6J - Increased lean body mass_MP:0003960 P NR
      Increased oxygen consumption_MP:0005289 A NR
      Hypoactivity_MP:0001402 A NR
      Decreased circulating glucose level_MP:0005560 P NR
      Improved glucose tolerance_MP:0005292 A NR
Nnt - - B6J - Impaired glucose tolerance_MP:0005293 P NR
  1. Abbreviations: A, phenotype absent; MP, Mammalian Phenotype; NP, Single-nucleotide polymorphism; NR, not relevant; P, phenotype present; PROVEAN, Protein Variation Effect Analyzer; SOP, Standard operating procedure; SV, structural variant.
  2. aWe have identified variant genes that show homozygote knockout phenotypes with associated MP terms that were assessed in the phenotyping pipeline, and compared these phenotypes to those seen between N and J.
  3. bThreshold for intolerance is -2.3.
  4. cThese columns indicate the direction of the phenotype effect that might be seen given the assignment of a SNP or SV as private to B6J or B6N. Only one direction will be relevant and comparable with the effects of the knockout mutation.