Mutations in ZDHHC9, which encodes a palmitoyltransferase of NRAS and HRAS, cause X-linked mental retardation associated with a Marfanoid habitus

Abstract

We have identified one frameshift mutation, one splice-site mutation, and two missense mutations in highly conserved residues in ZDHHC9 at Xq26.1 in 4 of 250 families with X-linked mental retardation (XLMR). In three of the families, the mental retardation phenotype is associated with a Marfanoid habitus, although none of the affected individuals meets the Ghent criteria for Marfan syndrome. ZDHHC9 is a palmitoyltransferase that catalyzes the posttranslational modification of NRAS and HRAS. The degree of palmitoylation determines the temporal and spatial location of these proteins in the plasma membrane and Golgi complex. The finding of mutations in ZDHHC9 suggests that alterations in the concentrations and cellular distribution of target proteins are sufficient to cause disease. This is the first XLMR gene to be reported that encodes a posttranslational modification enzyme, palmitoyltransferase. Furthermore, now that the first palmitoyltransferase that causes mental retardation has been identified, defects in other palmitoylation transferases become good candidates for causing other mental retardation syndromes.

Figure 1.

Pedigrees of families with XLMR and mutations in ZDHHC9. Individuals marked with an asterisk (*) carry the mutant allele in each family. Carrier females who have been shown to be heterozygous for the wild-type allele and the mutation are labeled “het.” Representative sequence chromatograms of wild-type and mutant sequences are shown below each pedigree. n.a. = no sample was available for testing; wt = wild-type sequence.

Figure 2.

a, RT-PCR analysis of the ZDHHC9 gene by use of lymphocyte RNA from an affected male individual in family 602 and an unaffected control. A 547-bp PCR product was identified from cDNA made from control cells containing sequence from exons 2–4, by use of the predicted splice junctions. In family 602, only a 407-bp PCR product was identified. b, Diagram of the cDNA detected in family 602, which included an upstream splice-donor site, resulting in the loss of 140 bp at the terminus of exon 2, and the sequence chromatogram of the novel splicing event, leading to the mutation. c, Effect of the upstream splice-donor site within exon 2 spliced to exon 3. This results in a frameshift and truncated protein p.T11fsX33.

Figure 3.

Sequence alignment of the conserved palmitoyltransferase active site of proteins ZDHHC9, ZDHHC14, and ZDHHC5 in multiple species (Homo sapiens, Canis familiaris, Mus musculus, Gallus gallus, Danio rerio, Xenopus laevis, Tetraodon nigroviridis, Drosophila melanogaster, Caenorhabditis elegans, Neurospora crassa, and Saccharomyces cerevisiae). Sequence alignment was performed using ClustalW. Conserved amino acid residues are highlighted in yellow, and the two missense mutations are identified in red.

Figure 4.

a, Diagrammatic representation of the exon structure of ZDHHC9, with positions of mutations found in families with XLMR. Exons that are translated are indicated by yellow shading. b, Diagrammatic representation of the protein ZDHHC9, with the palmitoyltransferase domain indicated by green shading. The location of the amino acid changes in the protein due to mutations in ZDHHC9 are indicated by arrows. The family numbers are in parentheses.