Homozygous deletion of the very low density lipoprotein receptor gene causes autosomal recessive cerebellar hypoplasia with cerebral gyral simplification

Abstract

An autosomal recessive syndrome of nonprogressive cerebellar ataxia and mental retardation is associated with inferior cerebellar hypoplasia and mild cerebral gyral simplification in the Hutterite population. An identity-by-descent mapping approach using eight patients from three interrelated Hutterite families localized the gene for this syndrome to chromosome region 9p24. Haplotype analysis identified familial and ancestral recombination events and refined the minimal region to a 2-Mb interval between markers D9S129 and D9S1871. A 199-kb homozygous deletion encompassing the entire very low density lipoprotein receptor (VLDLR) gene was present in all affected individuals. VLDLR is part of the reelin signaling pathway, which guides neuroblast migration in the cerebral cortex and cerebellum. To our knowledge, this syndrome represents the first human lipoprotein receptor malformation syndrome and the second human disease associated with a reelin pathway defect.

Figure 1

MRI demonstrating characteristic brain malformations seen in patients with DES-H. A, Sagittal T1W. B, Axial T1W. C, Coronal T2W spin echo images showing a small cerebellum in a fluid-filled but normal-sized posterior fossa. The superior half of the vermis is formed, but the inferior half is not. The pons is abnormally small. The cerebral cortex is simplified. Reprinted with permission (Glass et al., in press).

Figure 2

Haplotype analysis of the Hutterite families. Affected individuals are identified by blackened symbols and unaffected family members by unblackened symbols. In family 1, individuals I-2 and I-3 are full siblings. Haplotypes were constructed by visual inspection, with the assumption of a minimal number of recombination events. The marker order was determined from the physical map of the region. For the children in each family, the allele on the left was inherited from the father and the allele on the right from the mother. A patterned bar indicates haplotypes for chromosome 9 markers, a black bar indicates the alleles associated with the DES-H disease allele, and a gray region indicates a region in which a recombinant event occurred. An observed paternal recombination event in unaffected sibling II-3 from family 4 indicates a proximal limit of D9S286 for the DES-H locus. A recombinant defining the distal boundary for the DES-H locus was not identified. The boxed markers correspond to the smallest region of shared homozygosity and the minimal region for the DES-H gene. D9S129 was predicted to be the distal limit, on the basis of inferred ancestral recombination events that resulted in different D9S129 alleles in affected individuals II-1 from family 2 and the siblings II-1 and II-2 from family 4. D9S1871 was predicted to be the proximal limit on the basis of an inferred recombinant in one of the ancestors of the father in family 2, who carried a different allele on the disease chromosome at this locus.

Figure 3

Characterization of the VLDLR deletion. A, STS walking strategy used to identify the deletion boundaries. STSs were scored as “present” or “absent” in the genomic DNA of patients with DES-H. The dashed line represents the deletion. Blackened circles indicate that STSs are present, and unblackened circles indicate that STSs are not present in patient genomic DNA. The distal boundary was narrowed to a 69-kb region 130 kb from VLDLR by use of STSs present in UniSTS; the proximal boundary was estimated to be within the 70-kb region between VLDLR and KCNV2, on the basis of the presence of exon 1 of the KCNV2 gene in genomic DNA of patients, by use of PCR amplification. STSs were then generated using the chromosome 9 genomic contig (GenBank accession number NT_008413) at 10-kb intervals, to walk along the chromosome in both the 69-kb distal and 70-kb proximal regions. Within these 10-kb intervals, STSs were generated every 1 kb (all primer sequences and amplification conditions available on request). The forward primer of the most-proximal STS present in the distal boundary and the reverse primer of the most-distal STS present in the proximal boundary in genomic DNA of patients were used to amplify a 2.6-kb fragment spanning the deletion. Because of the large size of the deletion, these primers could not be used to amplify control DNA; instead, forward and reverse primers of the two flanking STSs for each of the boundary regions were used. B, Sequence of deletion boundaries. The products a, b, and c were sequenced using the ABI PRISM BigDye Terminator v3.1 cycle sequencing kit (Applied Biosystems) and an ABI PRISM 377 automated sequencer. A direct 8-bp repeat (underlined) was present in the sequenced junction fragment of a patient with DES-H (b) and in the 5′ and 3′ flanking sequences of control DNA (a and c). C, Segregation analysis. Genomic DNA from patients and family members was amplified using a three-primer reaction mix, which generated a 784-bp fragment from a normal chromosome and a 440-bp fragment from a chromosome with the VLDLR deletion. Affected individuals are identified by blackened symbols, unaffected family members by unblackened symbols, and carriers by a small blackened circle within the symbol. The 440-bp product was identified in the patients with DES-H, the 784-bp and 440-bp products in carriers, and the 784-bp product in noncarriers. D, Map of the deleted region. The deleted segment was 199 kb in size and contained the entire VLDLR gene and part of LOC401491. KCNV2, which is proximal to VLDLR, was not contained within the deletion.