Decoding synpolydactyly the genetic landscape of hoxd13 and the hox gene family" A comprehensive review"
DOI:
https://doi.org/10.55627/zoobotanica.003.03.1732Keywords:
Synpolydactyly, Hox gene, mutation, ; polyalanine, duplicationAbstract
Congenital limb malformations are among the most prevalent developmental abnormalities, occurring in approximately one in every 500 live births. These defects are frequently linked to genetic disruptions within the HOX gene family, which plays a pivotal role in embryonic limb patterning. This review comprehensively examines the genetic and molecular basis of synpolydactyly (SPD) a hereditary limb deformity characterized by fusion and duplication of digits focusing on the HOXD13 gene and its association with other HOX genes. Mutations in HOXD13, including polyalanine tract expansions, missense, nonsense, and frameshift mutations, have been identified as major contributors to SPD and related limb malformations. Furthermore, the functional interplay between HOXD13 and other HOX genes (HOXA1, HOXA2, HOXA11, HOXA13, HOXB1, and HOXB13) underlies a spectrum of genetic syndromes affecting limb and organ development. The review highlights the genotype–phenotype correlations, molecular mechanisms of HOXD13 mutations, and their broader implications in developmental and pathological contexts, including genitourinary and oncogenic disorders. Understanding the complex regulation of HOXD13 and its paralogues provide critical insight into congenital limb anomalies and offers a framework for genetic counseling, diagnosis, and potential therapeutic strategies.
References
Akarsu, A. N., Stoilov, I., Yilmaz, E., Sayli, B. S., & Sarfarazi, M. (1996). Genomic structure of the HOXD13 gene: a nine polyalanine duplication causes synpolydactyly in two unrelated families. Human molecular genetics, 5(7), 945-952.
Akker, E. v. d., Fromental-Ramain, C., Graaff, W. d., Le Mouellic, H., Brûlet, P., Chambon, P., & Deschamps, J. (2001). Axial skeletal patterning in mice lacking all paralogous group 8 Hox genes. Development, 128(10), 1911-1921.
Al-Qattan, M. M., Yang, Y., & Kozin, S. H. (2009). Embryology of the upper limb. The Journal of hand surgery, 34(7), 1340-1350.
Alasti, F., Sadeghi, A., Sanati, M. H., Farhadi, M., Stollar, E., Somers, T., & Van Camp, G. (2008). A mutation in HOXA2 is responsible for autosomal-recessive microtia in an Iranian family. The American Journal of Human Genetics, 82(4), 982-991.
Ali, Z., Ullah, S., Ullah, N., Akbar, F., Haq, I. U., Fawad, S., Baig, S. M., & Dahl, N. (2025). Molecular characterization of acromesomelic dysplasia type maroteaux: A homozygous nonsense mutation in NPR2. World Journal of Biology and Biotechnology, 10(2), 7-10.
Appukuttan, B., Gillanders, E., Juo, S.-H., Freas-Lutz, D., Ott, S., Sood, R., Van Auken, A., Bailey-Wilson, J., Wang, X., & Patel, R. J. (1999). Localization of a gene for Duane retraction syndrome to chromosome 2q31. The American Journal of Human Genetics, 65(6), 1639-1646.
Barham, G., & Clarke, N. M. (2008). Genetic regulation of embryological limb development with relation to congenital limb deformity in humans. Journal of children's orthopaedics, 2(1), 1-9.
Bosley, T. M., Alorainy, I. A., Salih, M. A., Aldhalaan, H. M., Abu‐Amero, K. K., Oystreck, D. T., Tischfield, M. A., Engle, E. C., & Erickson, R. P. (2008). The clinical spectrum of homozygous HOXA1 mutations. American Journal of Medical Genetics Part A, 146(10), 1235-1240.
Botti, G., Cillo, C., De Cecio, R., Malzone, M. G., & Cantile, M. (2019). Paralogous HOX13 genes in human cancers. Cancers, 11(5), 699.
Brison, N., Debeer, P., Fantini, S., Oley, C., Zappavigna, V., Luyten, F. P., & Tylzanowski, P. (2012). An N-terminal G11A mutation in HOXD13 causes synpolydactyly and interferes with Gli3R function during limb pre-patterning. Human molecular genetics, 21(11), 2464-2475.
Brison, N., Tylzanowski, P., & Debeer, P. (2012). Limb skeletal malformations–What the HOX is going on? European journal of medical genetics, 55(1), 1-7.
Cantile, M., Scognamiglio, G., Anniciello, A., Farina, M., Gentilcore, G., Santonastaso, C., Fulciniti, F., Cillo, C., Franco, R., & Ascierto, P. A. (2012). Increased HOX C13 expression in metastatic melanoma progression. Journal of translational medicine, 10(1), 91.
Chisaka, O., & Capecchi, M. R. (1991). Regionally restricted developmental defects resulting from targeted disruption of the mouse homeobox gene hox-1.5. Nature, 350(6318), 473-479.
Copeland, J. W., Nasiadka, A., Dietrich, B. H., & Krause, H. M. (1996). Patterning of the Drosophila embryo by a homeodomain-deleted Ftz polypeptide. Nature, 379(6561), 162-165.
Dai, L., Liu, D., Song, M., Xu, X., Xiong, G., Yang, K., Zhang, K., Meng, H., Guo, H., & Bai, Y. (2014). Mutations in the homeodomain of HOXD13 cause syndactyly type 1-c in two Chinese families. PloS one, 9(5), e96192.
Darbellay, F., Bochaton, C., Lopez-Delisle, L., Mascrez, B., Tschopp, P., Delpretti, S., Zakany, J., & Duboule, D. (2019). The constrained architecture of mammalian Hox gene clusters. Proceedings of the National Academy of Sciences, 116(27), 13424-13433.
Debeer, P., Schoenmakers, E., Twal, W., Argraves, W., De Smet, L., Fryns, J.-P., & Van de Ven, W. (2002). The fibulin-1 gene (FBLN1) is disrupted in at (12; 22) associated with a complex type of synpolydactyly. Journal of Medical Genetics, 39(2), 98-104.
Dorshorst, B., Okimoto, R., & Ashwell, C. (2010). Genomic regions associated with dermal hyperpigmentation, polydactyly and other morphological traits in the Silkie chicken. Journal of Heredity, 101(3), 339-350.
Duboc, V., & Logan, M. P. (2009). Building limb morphology through integration of signaling modules. Current opinion in genetics & development, 19(5), 497-503.
Duboule, D., & Morata, G. (1994). Collinearity and functional hierarchy among genes of the homeotic complexes. Trends in Genetics, 10(10), 358-364.
Dunø, M., Hove, H., Kirchhoff, M., Devriendt, K., & Schwartz, M. (2004). Mapping genomic deletions down to the base: a quantitative copy number scanning approach used to characterize and clone the breakpoints of a recurrent 7p14. 2p15. 3 deletions. Human genetics, 115(6), 459-467.
Economides, K. D., & Capecchi, M. R. (2003). Hoxb13 is required for normal differentiation and secretory function of the ventral prostate.
Ewing, C. M., Ray, A. M., Lange, E. M., Zuhlke, K. A., Robbins, C. M., Tembe, W. D., Wiley, K. E., Isaacs, S. D., Johng, D., & Wang, Y. (2012). Germline mutations in HOXB13 and prostate-cancer risk. New England Journal of Medicine, 366(2), 141-149.
Gehring, W. J., Qian, Y. Q., Billeter, M., Furukubo-Tokunaga, K., Schier, A. F., Resendez-Perez, D., Affolter, M., Otting, G., & Wüthrich, K. (1994). Homeodomain-DNA recognition. Cell, 78(2), 211-223.
Goodman, F., Mundlos, S., Muragaki, Y., Donnai, D., Giovannucci-Uzielli, M., Lapi, E., Majewski, F., McGaughran, J., McKeown, C., & Reardon, W. (1997). Synpolydactyly phenotypes correlate with size of expansions in HOXD13 polyalanine tract. Proceedings of the National Academy of Sciences, 94(14), 7458-7463.
Goodman, F. R. (2002). Limb malformations and the human HOX genes. American journal of medical genetics, 112(3), 256-265.
Gordon, C. T., Rodda, F. A., & Farlie, P. G. (2009). The RCAS retroviral expression system in the study of skeletal development. Developmental Dynamics, 238(4), 797-811.
Greer, J. M., & Capecchi, M. R. (2002). Hoxb8 is required for normal grooming behavior in mice. Neuron, 33(1), 23-34.
Guo, R., Fang, X., Mao, H., Sun, B., Zhou, J., An, Y., & Wang, B. (2021). A novel missense variant of HOXD13 caused atypical synpolydactyly by impairing the downstream gene expression and literature review for genotype–phenotype correlations. Frontiers in Genetics, 12, 731278.
Guthrie, S. (2007). Patterning and axon guidance of cranial motor neurons. Nature Reviews Neuroscience, 8(11), 859-871.
Han, J. Y. (2009). Germ cells and transgenesis in chickens. Comparative immunology, microbiology and infectious diseases, 32(2), 61-80.
Holve, S., Friedman, B., Hoyme, H. E., Tarby, T. J., Johnstone, S. J., Erickson, R. P., Clericuzio, C. L., & Cunniff, C. (2003). Athabascan brainstem dysgenesis syndrome. American Journal of Medical Genetics Part A, 120(2), 169-173.
Ibrahim, D. M., Tayebi, N., Knaus, A., Stiege, A. C., Sahebzamani, A., Hecht, J., Mundlos, S., & Spielmann, M. (2016). A homozygous HOXD13 missense mutation causes a severe form of synpolydactyly with metacarpal to carpal transformation. American Journal of Medical Genetics Part A, 170(3), 615-621.
Ingram, J. L., Stodgell, C. J., Hyman, S. L., Figlewicz, D. A., Weitkamp, L. R., & Rodier, P. M. (2000). Discovery of allelic variants of HOXA1 and HOXB1: genetic susceptibility to autism spectrum disorders. Teratology, 62(6), 393-405.
Innis, J. W., Goodman, F. R., Bacchelli, C., Williams, T. M., Mortlock, D. P., Sateesh, P., Scambler, P. J., McKinnon, W., & Guttmacher, A. E. (2002). A HOXA13 allele with a missense mutation in the homeobox and a dinucleotide deletion in the promoter underlies Guttmacher syndrome. Human mutation, 19(5), 573-574.
Jaouadi, H., Theron, A., Norscini, G., Avierinos, J.-F., & Zaffran, S. (2023). Genetic and phenotypic continuum of HOXA genes: A case with double HOXA9/HOXA13 mutations. Molecular Medicine Reports, 27(3), 59.
Jeong, T.-O., Oh, K.-J., Nguyen, N. T. X., Kim, Y.-R., Kim, M. S., Lee, S. D., Ryu, S. B., & Jung, C. (2012). Evaluation of HOXB13 as a molecular marker of recurrent prostate cancer. Molecular Medicine Reports, 5(4), 901-904.
Jin, H., Lin, P., Wang, Q., Mao, F., Cai, Y., & Gong, Y. (2011). Synpolydactyly in a Chinese kindred: mutation detection, prenatal ultrasonographic and molecular diagnosis. Zhonghua yi xue yi Chuan xue za zhi= Zhonghua Yixue Yichuanxue Zazhi= Chinese Journal of Medical Genetics, 28(6), 601-605.
Johnson, D., Kan, S.-h., Oldridge, M., Trembath, R. C., Roche, P., Esnouf, R. M., Giele, H., & Wilkie, O. A. (2003). Missense mutations in the homeodomain of HOXD13 are associated with brachydactyly types D and E. The American Journal of Human Genetics, 72(4), 984-997.
Juárez-Rendón, K. J., Castro-García, M. A., Prada-Ortega, D. G., Rivera, G., Ruíz-Godoy, L. M., Enríquez-Cárcamo, V. I., & Reyes-Lopez, M. A. (2023). Variants Identified in the HOXC13 and HOXD13 Genes Suggest Association with Cervical Cancer in a Cohort of Mexican Women. Genes, 14(2), 358.
Kjaer, K. W., Hansen, L., Eiberg, H., Utkus, A., Skovgaard, L. T., Leicht, P., Opitz, J. M., & Tommerup, N. (2005). A 72‐year‐old Danish puzzle resolved—comparative analysis of phenotypes in families with different‐sized HOXD13 polyalanine expansions. American Journal of Medical Genetics Part A, 138(4), 328-339.
Lebert-Ghali, C.-É., Fournier, M., Kettyle, L., Thompson, A., Sauvageau, G., & Bijl, J. J. (2016). Hoxa cluster genes determine the proliferative activity of adult mouse hematopoietic stem and progenitor cells. Blood, The Journal of the American Society of Hematology, 127(1), 87-90.
Malik, S. (2012). Syndactyly: phenotypes, genetics and current classification. European Journal of Human Genetics, 20(8), 817-824.
Malik, S., Ahmad, W., Grzeschik, K., & Koch, M. (2005). A simple method for characterizing syndactyly in clinical practice. Genetic counseling, 16(3), 229-238.
Malik, S., Girisha, K., Wajid, M., Roy, A. K., Phadke, S. R., Haque, S., Ahmad, W., Koch, M. C., & Grzeschik, K.-H. (2007). Synpolydactyly and HOXD13 polyalanine repeat: addition of 2 alanine residues is without clinical consequences. BMC Medical Genetics, 8(1), 78.
Malik, S., & Grzeschik, K. H. (2008). Synpolydactyly: clinical and molecular advances. Clinical Genetics, 73(2), 113-120.
Mallo, M., & Gridley, T. (1996). Development of the mammalian ear: coordinate regulation of formation of the tympanic ring and the external acoustic meatus. Development, 122(1), 173-179.
Manley, N. R., & Capecchi, M. R. (1995). The role of Hoxa-3 in mouse thymus and thyroid development. Development, 121(7), 1989-2003.
Mann, R. S., Lelli, K. M., & Joshi, R. (2009). Hox specificity: unique roles for cofactors and collaborators. Current topics in developmental biology, 88, 63-101.
Merlob, P., & Grunebaum, M. (1986). Type II syndactyly or synpolydactyly. Journal of Medical Genetics, 23(3), 237-241.
Monks, D. C., Jahangir, A., Shanske, A. L., Samanich, J., Morrow, B. E., & Babcock, M. (2010). Mutational analysis of HOXA2 and SIX2 in a Bronx population with isolated microtia. International journal of pediatric otorhinolaryngology, 74(8), 878-882.
Mortlock, D. P., & Innis, J. W. (1997). Mutation of HOXA13 in hand-foot-genital syndrome. Nature genetics, 15(2), 179-180.
Muragaki, Y., Mundlos, S., Upton, J., & Olsen, B. R. (1996). Altered growth and branching patterns in synpolydactyly caused by mutations in HOXD13. Science, 272(5261), 548-551.
Nowoshilow, S., Schloissnig, S., Fei, J.-F., Dahl, A., Pang, A. W., Pippel, M., Winkler, S., Hastie, A. R., Young, G., & Roscito, J. G. (2018). The axolotl genome and the evolution of key tissue formation regulators. Nature, 554(7690), 50-55.
Nunes, F. D., Almeida, F. C. S. d., Tucci, R., & Sousa, S. C. O. M. d. (2003). Homeobox genes: a molecular link between development and cancer. Pesquisa Odontologica Brasileira, 17, 94-98.
Olson, E., Arnold, H.-H., Rigby, P., & Wold, B. (1996). Know your neighbors: three phenotypes in null mutants of the myogenic bHLH gene MRF4. Cell, 85(1), 1-4.
Petitte, J., Liu, G., & Yang, Z. (2004). Avian pluripotent stem cells. Mechanisms of Development, 121(9), 1159-1168.
Pickering, J., & Towers, M. (2014). Molecular Genetics of Human Congenital Limb Malformations. eLS.
Qian, P., De Kumar, B., He, X. C., Nolte, C., Gogol, M., Ahn, Y., Chen, S., Li, Z., Xu, H., & Perry, J. M. (2018). Retinoid-sensitive epigenetic regulation of the Hoxb cluster maintains normal hematopoiesis and inhibits leukemogenesis. Cell stem cell, 22(5), 740-754. e747.
Ramfrez-Solis, R., Zheng, H., Whiting, J., Krumlauf, R., & Bradley, A. (1993). Hoxb-4 (Hox-2.6) mutant mice show homeotic transformation of a cervical vertebra and defects in the closure of the sternal rudiments. Cell, 73(2), 279-294.
Sarfarazi, M., Akarsu, A. N., & Sayli, B. S. (1995). Localization of the syndactyly type II (synpolydactyly) locus to 2q31 region and identification of tight linkage to HOXD8 intragenic marker. Human molecular genetics, 4(8), 1453-1458.
Sayli, B. S., Akarsu, A. N., Sayli, U., Akhan, O., Ceylaner, S., & Sarfarazi, M. (1995). Large Turkish kindred with syndactyly type II (synpolydactyly). 1. Field investigation, clinical and pedigree data. Journal of Medical Genetics, 32(6), 421-434.
Scott, V., Morgan, E. A., & Stadler, H. S. (2005). Genitourinary functions of Hoxa13 and Hoxd13. Journal of biochemistry, 137(6), 671-676.
Sharma, D., Kim, M. S., & D’Mello, S. R. (2015). Original Research Featured Article. Experimental Biology and Medicine, 240, 242-251.
Small, K. M., & Potter, S. S. (1993). Homeotic transformations and limb defects in Hox A11 mutant mice. Genes & development, 7(12a), 2318-2328.
Teebi, A. S., & Druker, H. A. (2001). Brachycephaly, cutis aplasia congenita, blue sclerae, hypertelorism, polydactyly, hypoplastic nipples, failure to thrive, and developmental delay: a distinct autosomal recessive syndrome? Clinical Dysmorphology, 10(1), 69-70.
Temtamy, S. A., & McKusick, V. A. (1978). The genetics of hand malformations. Birth defects original article series, 14(3), i-619.
Thompson, A. A., & Nguyen, L. T. (2000). Amegakaryocytic thrombocytopenia and radio-ulnar synostosis are associated with HOXA11 mutation. Nature genetics, 26(4), 397-398.
Ventruto, V., Pisciotta, R., Renda, S., Festa, B., Rinaldi, M. M., Stabile, M., Cavaliere, M. L., Esposito, M., & Opitz, J. M. (1983). Multiple skeletal familial abnormalities associated with balanced reciprocal translocation 2; 8 (q32; p13). American journal of medical genetics, 16(4), 589-594.
Vural, H., Avcı, E., Eroğlu, C., Çınar, İ., Yarar, S., & Gündeşlioğlu, Ö. (2020). A novel missense mutation that may be associated with the polydactyly in the HOXD13 gene: Q241H.
Webb, B. D., Shaaban, S., Gaspar, H., Cunha, L. F., Schubert, C. R., Hao, K., Robson, C. D., Chan, W.-M., Andrews, C., & MacKinnon, S. (2012). HOXB1 founder mutation in humans recapitulates the phenotype of Hoxb1−/− mice. The American Journal of Human Genetics, 91(1), 171-179.
Winter, R. M., & Tickle, C. (1993). Syndactylies and polydactylies: embryological overview and suggested classification. European Journal of Human Genetics, 1(1), 96-104.
Xie, P., Yuan, F.-Q., Zhou, H.-H., Li, X., & Liu, Z.-Q. (2021). The molecular genetics related to polydactyly: an updated review. Pharmacogenomics Res Pers, 2-12.
Xin, Q., Li, L., Li, J., Qiu, R., Guo, C., Gong, Y., & Liu, Q. (2012). Eight-alanine duplication in homeobox D13 in a Chinese family with synpolydactyly. Gene, 499(1), 48-51.
Zhao, X., Sun, M., Zhao, J., Leyva, J. A., Zhu, H., Yang, W., Zeng, X., Ao, Y., Liu, Q., & Liu, G. (2007). Mutations in HOXD13 underlie syndactyly type V and a novel brachydactyly-syndactyly syndrome. The American Journal of Human Genetics, 80(2), 361-371.
Zuniga, A., Zeller, R., & Probst, S. (2012). The molecular basis of human congenital limb malformations. Wiley Interdisciplinary Reviews: Developmental Biology, 1(6), 803-822.
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