"Through him all things were made; without him nothing was made that has been made" (John 1:3 NIV)
πάντα δι’ αὐτοῦ ἐγένετο, καὶ χωρὶς αὐτοῦ ἐγένετο οὐδὲ ἕν. ὃ γέγονεν (SBLGNT)
There is no doubt that ὁ λόγος in John 1:1 is grammatically masculine, but the issue is how one renders the pronoun αὐτοῦ. Most translate in accordance with the pronoun's antecedent, which in this case is masculine: ὁ λόγος. But αὐτός can be rendered "he/she/it" (3rd person singular). It is like qui est in Exodus 3:14 (Latin Vulgate). Some try to make the construction, "she who is," but in context, one should translate "He who is" and certainly not "it that is."