Final answer:
A base pair substitution mutation in a germ cell line is likely to not affect phenotype if it occurs in a non-coding region of a gene, as such areas usually do not affect the amino acid sequence or functioning of proteins.
Step-by-step explanation:
A base pair substitution mutation in a germ cell line is likely to not affect phenotype if the substitution occurs in a non-coding region of a gene. Mutations in non-coding regions often do not affect the protein sequence or function, unless they influence gene regulation elements such as promotors or enhancers. In contrast, mutations in coding regions may lead to changes in the protein structure through missense or nonsense mutations, while those in regulatory elements like promoters or enhancers can vastly affect gene expression and result in phenotypic changes. Moreover, a change in the third, or 'wobble', base of a codon may still code for the same amino acid due to the redundancy of the genetic code, often making such mutations silent. Neutral mutations also do not result in a change in the phenotype as they involve the substitution of amino acids with chemically similar ones.