We report the molecular cloning of a cDNA encoding a high affinity human glycine transporter. An open reading frame of 1914 nucleotides encodes a 638-amino acid protein that transports glycine in a Na+/Cl(-)-dependent manner. In common with other Na+/Cl(-)-dependent transporters, it possesses 12 putative transmembrane domains, according to its hydropathicity profile. This protein is the human homologue of a glycine transporter previously isolated from rat [glycine transporter type 1b (GlyT-1b)]. In addition to the human GlyT-1b, we also characterized a novel functional isoform produced by alternative splicing. This isoform, GlyT-1c, which is distinct from GlyT-2 recently characterized in rat, contains an additional exon encoding 54 amino acids in the amino-terminal part of GlyT-1b and is mainly expressed in brain. These two isoforms are products of the same gene and are localized on human chromosome 1p31.3, as well as on mouse chromosome 4, close to the locus for the spontaneous mouse neuromuscular mutation clasper. When expressed in COS-7 cells, both the human GlyT-1b and GlyT-1c display a time- and dose-dependent uptake of glycine, which is abolished when either Na+ or Cl- is substituted with other ions. For both GlyT-1b and GlyT-1c the affinities for glycine are similar, with Km values of 70-90 microM, and this uptake is inhibited by sarcosine with similar potencies. In addition to the three transporter isoforms present in the human genome, i.e., GlyT-1a, GlyT-1b, and GlyT-1c, point-mutated variants, which appear to be totally devoid of glycine uptake activity when expressed in COS-7 cells, were obtained by polymerase chain reaction amplification of mRNA from human substantia nigra. These variants point to regions of the glycine transporter that might be important in the processing or transport function of this protein.