HOXD13-Related Disorders via the HOXD13 Gene

Pathogenic variants in HOXD13 cause the related autosomal dominant disorders synpolydactyly 1, ysndactyly type V, brachydactyly type D, and brachydactyly type E.

Syndactyly is the joining of digits caused by the fusion of bones or connective tissue and synpolydactyly (SPD) is the presence of both syndactyly and polydactyly, extra digits or toes. Using the Temtamy-McKusick syndactyly classification system, SPD is classified as syndactyly Type 2, characterized by mesoaxial fusion of fingers 3/4 including an extra mesoaxial finger (Malik. 2012. PubMed ID: 22333904). The toe synpolydactyly involves a post-axial extra toe and the fusion of digits 4/5/6 (Malik et al. 2006. PubMed ID: 16712704).

Patients with brachydactyly have short fingers or toes relative to the length of other long bones. Brachydactyly type D is characterized by short and broad distal phalanges of the thumbs and big toes, while in type E, the brachydactyly involves shortening of the metatarsal and metacarpal bones (Temtamy and Aglan. 2008. PubMed ID: 18554391). These distal limb malformations may be isolated or part of a syndrome such as Greig cephalopolysyndactyly syndrome or Rubinstein-Taybi syndrome 1.

While syndactyly and polydactyly are each common limb malformations with estimated birth prevalences of 0.03-0.1% and 0.03-0.36%, respectively (Malik. 2012. PubMed ID: 22333904, Umair et al. 2018. PubMed ID: 30459804), SPD is rare with an undocumented prevalence. Most types of isolated brachydactyly are rare; however, type D is quite common with a prevalence of ~2%. There are over 200 genetic syndromes that include brachydactyly as a clinical manifestation, exhibiting a complete spectrum of penetrance (Temtamy and Aglan. 2008. PubMed ID: 18554391).

HOXD13 testing can identify the underlying genetic etiology of congenital polydactyly, syndactyly, or polysyndactyly, thereby providing a diagnostic answer to families. Identification of a clinically significant HOXD13 variant allows for the testing of family members as well as prenatal testing.

HOXD13-associated disorders follow an autosomal dominant pattern of inheritance. Like other homeobox transcription factors, HOXD13 is involved in embryonic pattern formation. It is located in the 5’ end of the cluster of HOX genes on chromosome 2 and so is expressed later in development during terminal limb formation (Krumlauf 1994. PubMed ID: 7913880). HOXD13 has been cited as a non-essential gene for growth of human tissue culture cells (Online Gene Essentiality).

HOXD13 pathogenic variants were originally identified via their role in synpolydactyly pathogenesis, and HOXD13 is the primary SPD-associated gene (SPD1). Genotype-phenotype correlation is documented albeit with exceptions. Pathogenic HOXD13 variants have high yet incomplete penetrance, and both a wide spectrum of severity and marked phenotypic variability exist within and between families (Malik et al. 2006. PubMed ID: 16712704), although de novo variants have been reported. HOXD13 variants are also associated with synpolydactyly and hypospadias in males (Tuzel et al. 2007. PubMed ID: 17656229) and VACTERL (Garcia-Barcelo et al. 2008. PubMed ID: 19006232).

The protein domain location and type of HOXD13 variant correlates with phenotype, and duplications in the 15-residue polyalanine tract in the first exon are the most common cause of classical synpolydactyly, with frequent expansions between 7-14 additional alanines (Brison et al. 2012. PubMedID: 21782042). Unlike repeat expansion disorders with genetic anticipation, the polyalanine repeats are mitotically stable, and expansions are caused by unequal crossing-over between different alanine codons (Warren. 1997. PubMed ID: 9005557). Severity and penetrance correlate with expansion size and rare homozygotes have a more severe presentation. Mice with Hoxd13 polyalanine expansions also exhibit SPD with an evident dominant-negative mechanism, with nearby Hox genes impacted much more than Hoxd13 itself (Bruneau et al. 2001. PubMedID: 11543619). Polyalanine tract expansions have also been reported in patients with syndactyly type V. Recently, polyalanine tract contractions with losses of 4 or 7 residues were identified.

Pathogenic HOXD13 variants may also localize in the homeodomain. Missense variants in the homeodomain cause brachydactyly D and brachydactyly E. Truncating variants in the homeodomain have been reported in two families with an atypical foot SPD characterized by bilateral polydactyly of the second metatarsals (Goodman et al. 1998. PubMed ID: 9758628, Kan et al. 2003. PubMed ID: 12900906). Speculated haploinsufficiency in these patients is supported by the presence of distal limb malformations in patients with a 2q31.3 microdeletion including the HOXD13 gene (Dimitrov et al. 2011. PubMed ID: 21068127).

Approximately 2.5-3% of patients with congenital limb malformations have pathogenic HOXD13 variants (Furniss et al. 2009. PubMedID: 19429598). HOXD13 deletion is rare, and the percentage of patients with HOXD13 copy number variants is not known. Regarding patients with isolated synpolydactyly, HOXD13 is one of three loci known to have causative variants. The other two loci are the FBLN1 gene (SPD2; Bohlega et al. 2014. PubMed ID:24084572) and a region identified by linkage analysis at 14q11.2-q12 (Malik et al. 2006. PubMed ID: 16712704). HOXD13 pathogenic variants are the most common known cause of isolated SPD, and are identified in the majority of cases with known genetic etiology. Expansion of the polyalanine tract in exon 1 is the primary mechanism of disease.

This test is performed using Next-Generation sequencing with additional Sanger sequencing as necessary.

This test provides full coverage of all coding exons of the HOXD13 gene plus 10 bases flanking noncoding DNA in all available transcripts in addition to non-coding regions in which pathogenic variants have been identified at PreventionGenetics or reported elsewhere. We define full coverage as ≥20X NGS reads or Sanger sequencing. PGnome panels typically provide slightly increased coverage over the PGxome equivalent. PGnome sequencing panels have the added benefit of additional analysis and reporting of deep intronic regions (where applicable).

Dependent on the sequencing backbone selected for this testing, discounted reflex testing to any other similar backbone-based test is available (i.e., PGxome panel to whole PGxome; PGnome panel to whole PGnome).