New SHH and Known SIX3 Variants in a Series of Latin American Patients with Holoprosencephaly

Abstract

Holoprosencephaly (HPE) is the failure of the embryonic forebrain to develop into 2 hemispheres promoting midline cerebral and facial defects. The wide phenotypic variability and causal heterogeneity make genetic counseling difficult. Heterozygous variants with incomplete penetrance and variable expressivity in the SHH, SIX3, ZIC2, and TGIF1 genes explain ∼25% of the known causes of nonchromosomal HPE. We studied these 4 genes and clinically described 27 Latin American families presenting with nonchromosomal HPE. Three new SHH variants and a third known SIX3 likely pathogenic variant found by Sanger sequencing explained 15% of our cases. Genotype-phenotype correlation in these 4 families and published families with identical or similar driver gene, mutated domain, conservation of residue in other species, and the type of variant explain the pathogenicity but not the phenotypic variability. Nine patients, including 2 with SHH pathogenic variants, presented benign variants of the SHH, SIX3, ZIC2, and TGIF1 genes with potential alteration of splicing, a causal proposition in need of further studies. Finding more families with the same SIX3 variant may allow further identification of genetic or environmental modifiers explaining its variable phenotypic expression.

Keywords: Holoprosencephaly; Latin American populations; SHH; SIX3; Synonymous variants; TGIF1; ZIC2.

Fig. 1

The craniofacial aspect of 20 holoprosencephaly (HPE) probands in this series. Patients 2, 3, 9, 23, and 27 are not shown. Patients 8, 13, 24, 25, and 27 with single median maxillary central incisor had no brain defect, and the information was not available for patient 1. Among the HPE group, all the frequent HPE types were diagnosed: 7 alobar HPE in patient 5, 6, 10, 11, 14, 16, and 18; four semilobar in patients 3, 9, 20, and 22; five lobar in patients 4, 12, 17, 21, and 26; and 2 middle interhemispheric variants in patients 2 and 19; in the remaining 2 patients 7 and 23, the HPE type was not further specified. Patient 15 presented only with corpus callosum agenesis. Twelve patients presented with premaxillary agenesis (2, 3, 5, 6, 10, 11, and 14) or cleft lip and palate (1, 4, 7, 16, and 26). Fourteen patients showed the absence of facial cleft (8, 9, 12, 13, 15, 17–22, 24, 25, and 27). Microphthalmia was described in patients 5, 6, 7, 23, and 27.

Fig. 2

a Pedigrees of 4 patients with HPE demonstrating the segregation of different SHH, SIX3, ZIC2 and TGIF1 variants with phenotypes. Black: fully affected. Gray: only microsigns. Black dot: carrier of pathogenic variants. NA: not available for molecular study. b Electropherograms of the 4 pathogenic variants. c Phylogenetic conservation of the amino acid sequence showing the position of the pathogenic variants in red and the conserved sequence in gray.