Developmental genomics of congenital limb malformations: further indication of allelic series in association with gene dosage effects that contribute to the variability of phenotypes

Genetic heterogeneity, reduced penetrance and variable expressivity, the latter including asymmetric body axis plane presentations, have all been described in families with congenital limb malformations (CLM). Both interfamilial and intrafamilial heterogeneity highlight the complexity of the underlying genetic pathogenesis of these developmental anomalies. Family-based genomics by exome sequencing (ES) and rare variant analyses combined with whole-genome array-based comparative genomic hybridization, were implemented to investigate 18 families with limb birth defects. Eleven of 18 (61%) families revealed explanatory variants including 7 single nucleotide variant alleles and 3 copy number variants (CNVs), at previously reported ‘disease trait associated loci’: BHLHA9 , GLI3, HOXD cluster, HOXD13, NPR2 and WNT10B. Breakpoint junction analyses for all three CNV alleles revealed mutational signatures consistent with microhomology-mediated break-induced replication (MMBIR); a mechanism facilitated by Alu/Alu -mediated rearrangement. Of note, homozygous duplication of BHLHA9 was observed in one Turkish kindred and represents a novel contributory genetic mechanism to Gollop-Wolfgang Complex (MIM %228250); wherein triplication of the locus has been reported in one family from Japan [i.e., 4n = 2n + 2n versus 4n = 3n + 1n allelic configurations]. In conclusion , genes acting on limb patterning are sensitive to a gene dosage effect and are often associated with an allelic series. We extend an allele-specific gene dosage model to potentially assist, in an adjuvant way, interpretations of interconnections among an allelic series, clinical severity, and reduced penetrance of the BHLHA9 -related CLM spectrum. Duan et al. implemented family-based genomics and rare variant analyses in 18 families with CLMs. The result highlighted that allelic series and gene dosage effects contribute to the variability of phenotypes. The allele-specific gene dosage model explains observations of the BHLHA9-related CLM spectrum including the Gollop Wolfgang Complex (MIM %228250)