S-adenosyl-L-methionine-dependent methyltransferase that mediates N(3)-methylcytidine modification of residue 32 of the tRNA anticodon loop of tRNA(Thr)(UGU) and tRNA(Arg)(CCU) (PubMed:28655767, PubMed:34268557). N(3)-methylcytidine methylation by METTL2A requires the N6-threonylcarbamoylation of tRNA (t6A37) by the EKC/KEOPS complex as prerequisite (PubMed:34268557). {ECO:0000269|PubMed:28655767, ECO:0000269|PubMed:34268557}. This is the function of ENSG00000087995 (METTL2A, methyltransferase 2A, tRNA N3-cytidine).