Isolated brachydactyly type E can be caused by HOXD13 nonsense mutation: case report

Brachydactyly type E (BDE; MIM#113300) is characterized by shortening of the metacarpal, metatarsal, and often phalangeal bones, and predominantly affects postaxial ray(s) of the limb. BDE may occur as an isolated trait or as part of a syndrome. Isolated BDE is rare and in the majority of cases has unknown genetic background. Originally, molecular cause of isolated BDE has been unravelled in 2 families and shown to result from heterozygous missense mutations in the homeodomain of the HOXD13 gene product. Since the initial paper, HOXD13 mutation has never been reported in a patient manifesting isolated BDE. In this paper, we report on a Polish family exhibiting isolated BDE caused by a nonsense heterozygous HOXD13 mutation. We investigated a Polish female proband and her father, both affected by isolated BDE, in whom we identified a nonsense heterozygous mutation c.820C>T(p.R274X) in the HOXD13 gene. So far, only two missense HOXD13 mutations (p.S308C and p.I314L), localized within the homeodomain of the HOXD13 transcription factor were associated with BDE. Both changes were supposed to alter DNA binding affinity of the protein. The variant p.R274X identified in our proband is the third HOXD13 mutation, and the first truncating (nonsense) mutation reported to result in typical isolated BDE. Our case stands for the first evidence that truncating HOXD13 mutations can produce isolated BDE. Background Brachydactyly type E (BDE; MIM#113300) is characterized by shortening of the metacarpal, metatarsal, and often phalangeal bones, and predominantly affects postaxial ray(s) of the limb (1). In most cases BDE is syndromic and occurs within the clinical spectrum of Turner syndrome, Albright hereditary osteodystrophy (AHO; MIM#103580) or 2q37 deletion (1). Isolated BDE is rare and in the majority of cases has unknown genetic background. Originally, molecular cause of isolated BDE has been unravelled in 2 families and shown to result from heterozygous missense mutations in the homeodomain of the HOXD13 gene product (2). Missense variants affecting other residues of the C-terminal HOXD13 homeodomain may also give raise to different limb phenotypes such as synpolydactyly (SPD; MIM#186000) or syndactyly type 5 (MIM#186300), whereas expansion of the N-terminal HOXD13 polyalanine tract usually results in SPD (3-6). Recently, Klopocki et al. (7) described causative alterations (microdeletion and point mutations) in the PTHLH gene in five unrelated families affected by isolated BDE. Since the initial paper of Johnson et al. from 2003 (2), HOXD13 mutation has never been reported in a patient manifesting isolated BDE. In addition, only 3 out of 12 annotated HOXD13 mutations resulted in a premature termination of the protein synthesis. Thus, genotype-phenotype correlation for truncating HOXD13 variants remains poorly known. In this paper, we relate on a Polish family exhibiting isolated BDE caused by a nonsense heterozygous HOXD13 mutation. Case presentation We investigated a Polish female proband and her father, both affected by isolated BDE. Skeletal manifestations of the proband (Fig. 1A & 1D) comprised shortening of the V th right metacarpal, bilateral shortening and broadening of the I st metacarpals, and bilateral shortening of the middle phalanges of V th fingers with clinodactyly. Feet of the proband were clinically inconspicuous. The proband’s father (Fig. 1B & 1C) manifested shortening of the V th fingers and toes most probably due to shortened V th metacarpals and metatarsal (no X-ray available). Both patients had normal stature and normal psychomotor development. Genomic DNA was extracted from peripheral blood leukocytes according to saltingout method (8). The entire coding sequence of the HOXD13 gene (GenBank NM_000523.3) was amplified in PCR reactions and directly sequenced using dye-terminator chemistry. Primer sequences are available upon request. The proband and her father carried a nonsense heterozygous mutation c.820C>T(p.R274X) in the HOXD13 gene (Fig. 1E). Presence of this mutation was excluded in 196 ethnically matched control chromosomes. So far, only two missense HOXD13 mutations (p.S308C and p.I314L), localized within the homeodomain of the HOXD13 transcription factor were associated with BDE (2). Both changes were supposed to alter DNA binding affinity of the protein (2). The variant p.R274X identified in our proband is the third HOXD13 mutation, and the first truncating (nonsense) mutation reported to result in typical isolated BDE. The mutant HOXD13 protein synthesized in the proband is predicted to lack the entire homeodomain sequence and most probably cannot bind to DNA. All three previously described truncating HOXD13 mutations were frameshifts and produced a phenotype referred to as "SPD with foot anomalies" (MIM#186000), in which classic SPD was accompanied by supernumerary digit between I st II nd and often IV th -V th metatarsals (9-10). Conclusions Our case stands for the first evidence that HOXD13 mutations that introduce premature stop codon can produce isolated BDE. Consent Written informed consent was obtained from the patient for publication of this case report and any accompanying images. A copy of the written consent is available for review by the Editor-in-Chief of this journal. Competing interests The authors have no competing interests to declare. Authors' contributions AJ consulted the family, conceived the manuscript AS performed molecular testing of the patients and controls LK consulted the family of interest ALB critically revised the manuscript Acknowledgements and fundingThis work was supported by a grant from the Polish Ministry of Science and HigherEducation (495/N-NIEMCY/2009/0). References1. Schwabe GC, Mundlos S. Genetics of congenital hand anomalies. Handchir.Mikrochir Plast Chir 2004, 36(2-3):85-97.2. Johnson D, Kan S, Oldridge M, Trembath RC, Roche P, Esnouf RM, Giele H, WilkieAOM. Missense mutations in the homeodomain of HOXD13 are associated withbrachydactyly types D and E. Am J Hum Genet 2003, 72:984-997.3. Debeer P, Bacchelli C, Scambler PJ, De Smet L, Fryns JP, Goodman FR. Severe digital abnormalities in a patient heterozygous for both a novel missensemutation in HOXD13 and a polyalanine tract expansion in HOXA13. J Med Genet 2002, 39:852-856.4. Muragaki Y, Mundlos S, Upton J, Olsen BR. Altered growth and branchingpatterns in synpolydactyly caused by mutations in HOXD13. Science 1996, 272(5261):548-551.5. Goodman FR, Mundlos S, Muragaki Y, Donnai D, Giovannucci-Uzielli ML, Lapi E,Majewski F, McGaughran J, McKeown C, Reardon W, Upton J, Winter RM, OlsenBR, Scambler PJ. Synpolydactyly phenotypes correlate with size of expansions inHOXD13 polyalanine tract. Proc Natl Acad Sci 1997, 94(14):7458-7463.6. Zhao X, Sun M, Zhao J, Leyva JA, Zhu H, Yang W, Zeng X, Ao Y, Liu Q, Liu G, LoWHY, Jabs EW, Amzel LM, Shan X, Zhang X. Mutations in HOXD13 underlie syndactyly type V and a novel brachydactyly-syndactyly syndrome. Am J Hum Genet 2007, 80(2):361-371.7. Klopocki E, Hennig BP, Dathe K, Koll R, de Ravel T, Baten E, Blom E, Gillerot Y,Weigel JF, Kruger G, Hiort O, Seemann P, Mundlos S. Deletion and pointmutations of PTHLH cause brachydactyly type E. Am J Hum Genet 2010,86(3):434-439. 8. Lahiri DK, Bye S, Nurnberger JI, Jr., Hodes ME, Crisp M. A non-organic and nonenzymatic extraction method gives higher yields of genomic DNA from whole-blood samples than do nine other methods tested. J Biochem Biophys Methods 1992, 25(4):193-205.9. Goodman FR, Giovannucci-Uzielli ML, Hall C, Reardon W, Winter R, Scambler P. Deletions in HOXD13 segregate with an identical, novel foot malformation intwo unrelated families. Am J Hum Genet 1998, 63(4):992-1000.10. Kan S, Johnson D, Giele H, Wilkie AOM. An acceptor splice site mutation in HOXD13 results in variable hand, but consistent foot malformations. Am J Med Genet 2003, 121A:69-74. LegendsFigure 1. A Brachydactyly type E (BDE) in the proband characterized by shortened Vth fingers, B & C clinical picture of BDE (shortened Vthfingers and toes) in the proband'sfather, D X-ray of the proband's hands showing shortening of the Vthright metacarpal,bilateral shortening and broadening of the Istmetacarpals, and bilateral shortening of themiddle phalanges of Vthfingers (skeletal abnormalities are indicated by the white arrows),E Chromatogram picture showing the c.820C>T(p.R274X) HOXD13 mutation.