Molecular and clinical analyses of Greig cephalopolysyndactyly and Pallister-Hall syndromes: robust phenotype prediction from the type and position of GLI3 mutations

Abstract

Mutations in the GLI3 zinc-finger transcription factor gene cause Greig cephalopolysyndactyly syndrome (GCPS) and Pallister-Hall syndrome (PHS), which are variable but distinct clinical entities. We hypothesized that GLI3 mutations that predict a truncated functional repressor protein cause PHS and that functional haploinsufficiency of GLI3 causes GCPS. To test these hypotheses, we screened patients with PHS and GCPS for GLI3 mutations. The patient group consisted of 135 individuals: 89 patients with GCPS and 46 patients with PHS. We detected 47 pathological mutations (among 60 probands); when these were combined with previously published mutations, two genotype-phenotype correlations were evident. First, GCPS was caused by many types of alterations, including translocations, large deletions, exonic deletions and duplications, small in-frame deletions, and missense, frameshift/nonsense, and splicing mutations. In contrast, PHS was caused only by frameshift/nonsense and splicing mutations. Second, among the frameshift/nonsense mutations, there was a clear genotype-phenotype correlation. Mutations in the first third of the gene (from open reading frame [ORF] nucleotides [nt] 1-1997) caused GCPS, and mutations in the second third of the gene (from ORF nt 1998-3481) caused primarily PHS. Surprisingly, there were 12 mutations in patients with GCPS in the 3' third of the gene (after ORF nt 3481), and no patients with PHS had mutations in this region. These results demonstrate a robust correlation of genotype and phenotype for GLI3 mutations and strongly support the hypothesis that these two allelic disorders have distinct modes of pathogenesis.

Figure 1

Flow chart showing numbers of patients included in each part of the study. Notice that, for completeness, data for all patients except those with large deletions are included in tables 1 and 2. (Some of the data have been published elsewhere, as noted.)

Figure 2

Type and distribution of GLI3 mutations described for patients with PHS and GCPS. A, Mutation spectrum. No mutations of the following types have been described for patients with PHS: small in-frame deletions (IFD), translocations (Trans), large deletions (L Del), exonic deletions or duplications (Exon), and missense mutations (Miss). The correlation of mutation type and phenotype is statistically significant (P<.0001 [Fisher's 2×2]) when the classes of mutations were dichotomized into frameshift and nonsense (Trunc) versus all other types and when tested against phenotype (PHS vs. GCPS). B, Diagram of the position within the gene of known nonsense, frameshift, and splice-site mutations. Some of the closely spaced mutations have been adjusted for increased visual clarity. Splice-site mutations are shown in red. Black numbers indicate identical mutations, and red numbers indicate multiple mutations in the same splice donor. Data include published mutations (Bianchi et al. ; Tommerup and Nielsen ; Marks et al. ; Pelz et al. ; Wagner et al. ; Pettigrew et al. ; Vortkamp et al. ; Kang et al. ; Radhakrishna et al. , ; Wild et al. ; Williams et al. ; Kalff-Suske et al. , , , ; Friez and Stevenson ; Killoran et al. ; Galasso et al. ; Kroisel et al. ; Elson et al. ; Debeer et al. ; Driess et al. ; Freese et al. ; Johnston et al. ; Kremer et al. ; Turner et al. ; Ng et al. 2004) and the mutations identified in the present study. The colored bars on the protein show the conserved domains of GLI3 as defined elsewhere (Ruppert et al. 1990).