A 117-kb microdeletion removing HOXD9-HOXD13 and EVX2 causes synpolydactyly

Abstract

Studies in mouse and chick have shown that the 5' HoxD genes play major roles in the development of the limbs and genitalia. In humans, mutations in HOXD13 cause the dominantly inherited limb malformation synpolydactyly (SPD). Haploinsufficiency for the 5' HOXD genes has recently been proposed to underlie the monodactyly and penoscrotal hypoplasia in two children with chromosomal deletions encompassing the entire HOXD cluster. Similar deletions, however, have previously been associated with split-hand/foot malformation (SHFM), including monodactyly. Here we report a father and daughter with SPD who carry a 117-kb microdeletion at the 5' end of the HOXD cluster. By sequencing directly across the deletion breakpoint, we show that this microdeletion removes only HOXD9-HOXD13 and EVX2. We also report a girl with bilateral split foot and a chromosomal deletion that includes the entire HOXD cluster and extends approximately 5 Mb centromeric to it. Our findings indicate that haploinsufficiency for the 5' HOXD genes causes not SHFM but SPD and point to the presence of a novel locus for SHFM in the interval between EVX2 and D2S294. They also suggest that there is a regulatory region, upstream of the HOXD cluster, that is responsible for activating the cluster as a whole.

Figure 1

Haplotype analysis in the two families. A, Relative positions of the 12 polymorphic markers used, with their approximate distances from the tip of the short arm of chromosome 2. D2S294, D2S333, D2S335, D2S326, D2S364, D2S1391, D2S389, and D2S117 are microsatellite repeats spanning a 20.7-cM interval in the vicinity of the HOXD cluster on chromosome 2q31 (Sheffield et al. ; Dib et al. 1996). HOXD10, originally reported as HOX4E (Rosen and Brown 1993), lies in the 3′ UTR of HOXD10. HOXD11 (a TG repeat in the intron of HOXD11), EVX2 (an AG repeat just telomeric to the 5′ UTR of EVX2), and 5′ HOXD (a CA repeat ∼60 kb centromeric to the HOXD cluster) are three new polymorphic markers identified in the present study (details available on request). B and C, Pedigree drawings of families 1 and 2, respectively (blackened symbols represent affected individuals; arrows indicate the probands), and results of haplotype analysis. The bracketed haplotype for individual I.2 from family 1, from whom DNA was not available, was inferred from the results for individuals I.1 and II.1.

Figure 2

Limb abnormalities in the two families. A, Radiograph of both hands of individual III.1 from family 1 at age 2 years, showing complete cutaneous syndactyly between the third and fourth fingers, duplication of all three phalanges of the third fingers, broad third metacarpals, and hypoplastic fifth middle phalanges. B, Radiograph of right foot of individual III.1 from family 1 at age 11 years, showing broad hallux, partial cutaneous syndactyly between the second to fifth toes, fifth-toe brachydactyly, hypoplastic second to fifth middle phalanges, short second to fifth metatarsals, and partial duplication of the base of the second metatarsal in the first web space. C, Radiograph of right foot of individual II.1 from family 1 at age 35 years, showing broad hallux, partial cutaneous syndactyly between the second to fourth toes, fifth-toe brachydactyly, hypoplastic second to fifth middle phalanges, occasional symphalangism between the middle and distal phalanges, and partial duplication of the base of the second metatarsal in the first web space. D, Photograph of right hand of individual II.1 from family 2 at age 10 mo, showing clenched and overlapping fingers. E, Photograph of right foot of individual II.1 from family 2 at age 10 mo, showing severe “lobster-claw” deformity with absence of the middle three rays.

Figure 3

Precise extent of the deletion in family 1. The electropherogram shows the sequence across the deletion breakpoint. The telomeric end of the deletion is located 658 bp downstream of HOXD9. The centromeric end of the deletion is located within a LINE-1 element, ∼5 kb telomeric to the most 5′ known exon of KIAA1715. Inside the deleted segment, the seven highly conserved regions likely to represent regulatory elements are denoted by blue boxes (R1–R7).