Table 3

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

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

(-1.712)

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

(K)

Arginine

(A)

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


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.

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.

bThreshold for intolerance is -2.3.

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.

Simon et al. Genome Biology 2013 14:R82   doi:10.1186/gb-2013-14-7-r82

Open Data