Numbers and ratios of pigment genes were estimated in a sample of young males with color-vision deficiencies, Eighteen were estimated to have a single L pigment gene on the X-chromosome. In most cases, the one L gene was the only X-linked photopigment gene, as has been reported previously for deuteranopes. However four of the boys in this group were estimated to have M pigment genes in addition, to a single L. Sequences of exons 2-4 of the M genes were obtained from two of the subjects whose ratios indicated one L and two M genes. A substitution of cytosine for thymine was found at nucleotide position 1101 (numbering system from Nathans(1)) of both M genes of both males. This mutation interrupts the function of the encoded M photopigments by replacing cysteine with arginine at amino acid position 203. Deuteranopia is often caused by the loss of M genes, bur here we report that it can also be caused by missense mutations that interrupt the function of all M pigments. In these cases, all photoreceptors that would normally be M cones presumably express the defective opsin. With all the M cones disabled, the total number of functional cones would be fewer than normal in these deuteranopic eyes. (C) 2000 John Wiley & Sons, Inc. Col Res Appl, 26, S100-S105, 2001.