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

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 B6J^c
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.

ISSN: 1474-760X