A patient (KL) with progressive motor neuron disease associated with partial Hex A (αβ) and no Hex B (ββ) activity, synthesized β-chains which only associated with α-chains. To identify the molecular basis of this inability of β-chains to self associate, RNA from cultured fibroblasts was reverse transcribed, the cDNA encoding the β-chain amplified by polymerase chain reaction, subcloned, and sequenced to reveal two types of single missense mutation. The first mutation, (Type I) 619A {black rightwards arrow} G, was paternally inherited and converted a 207lle {black rightwards arrow} Val in a highly conserved region believed to be associated with catalytic activity and activator protein binding. Biochemical evidence for impaired activator protein binding was obtained by purifying Hex A from KL urine and demonstrating a greater than 50% reduction of in vitroGM2hydrolysis compared to normal urinary Hex A. In other cDNA species (Type II), a maternally inherited 1367A {black rightwards arrow} C mutation converted 456Tyr {black rightwards arrow} Ser in another highly conserved region of the β-chain and we propose that this mutation leads to the inability of the β-chains to self associate and thus reach maturity. These same cDNA species contained a second 362A {black rightwards arrow} G mutation which converted 121Lys {black rightwards arrow} Arg, but is apparently a polymorphism since it also occurs in some normal subjects. We propose that the patient is a compound heterozygote in which a combination of no self-association of the mutant β-chains and impaired activator protein binding to α-β(mutant)(Hex A) required for GM2hydrolysis result in total β-Hex B deficiency and slow accumulation of GM2ganglioside, primarily in motor neurons. © 1991 Academic Press, Inc.