{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,22]],"date-time":"2026-10-22T17:41:42Z","timestamp":1792690902623,"version":"4.5.0"},"reference-count":31,"publisher":"Springer Science and Business Media LLC","issue":"11","license":[{"start":{"date-parts":[[2026,7,23]],"date-time":"2026-07-23T00:00:00Z","timestamp":1784764800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2026,7,23]],"date-time":"2026-07-23T00:00:00Z","timestamp":1784764800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Sci. China Life Sci."],"published-print":{"date-parts":[[2026,11]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>\n                    Hypospadias is one of the most common birth defects in China and a key feature of differences in sex development (DSD), yet its genetic etiology remains largely unresolved. Current diagnostic approaches using DSD-targeted gene panels have a low rate of definitive diagnoses (5.5%), highlighting the need for more comprehensive genetic investigation. In this study, we performed next-generation sequencing (NGS) on the largest trio-based cohort of hypospadias to date, comprising 106 pediatric cases and their parents (92 trios). We achieved a definitive genetic diagnosis in 6.6% of patients, identifying pathogenic variants in canonical DSD genes such as\n                    <jats:italic>AR, NR5A1<\/jats:italic>\n                    and\n                    <jats:italic>WT1<\/jats:italic>\n                    . By incorporating a broader spectrum of potentially clinically significant variants, we increased the overall genetic identification rate to 33.0% (35\/106). Strikingly, trio analysis uncovered a significant burden of\n                    <jats:italic>de novo<\/jats:italic>\n                    loss-of-function (LoF) variants (2.2-fold enrichment,\n                    <jats:italic>P<\/jats:italic>\n                    =0.001), primarily driven by variants in genes associated with ciliopathies (10.35-fold,\n                    <jats:italic>P<\/jats:italic>\n                    =0.016), a previously underappreciated gene class in hypospadias. Furthermore, we identified and functionally validated two high-confidence risk genes,\n                    <jats:italic>PRKCZ<\/jats:italic>\n                    and\n                    <jats:italic>HRNR<\/jats:italic>\n                    , based on recurrent\n                    <jats:italic>de novo<\/jats:italic>\n                    variants. Functional assays confirmed that these variants disrupt key biological mechanisms, including cell proliferation, migration, and androgen signaling. Our large-scale trio approach substantially expands the genetic landscape of hypospadias, demonstrates the critical value of trio-based sequencing for improving diagnostic yield, and decisively implicates ciliary genes in its pathogenesis.\n                  <\/jats:p>","DOI":"10.1007\/s11427-025-3253-3","type":"journal-article","created":{"date-parts":[[2026,8,12]],"date-time":"2026-08-12T08:34:51Z","timestamp":1786523691000},"page":"4091-4102","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["The genetic landscape of hypospadias: clinical insights into inherited and de novo risk factors"],"prefix":"10.1007","volume":"69","author":[{"given":"Yanqin","family":"You","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yingliu","family":"Luo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Honghui","family":"Zhou","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qiaowei","family":"Liang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jingjie","family":"Xue","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhuo","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yaowang","family":"Zhao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tianqu","family":"He","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kexin","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hongyan","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhongzhong","family":"Chen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lingqian","family":"Wu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,7,23]]},"reference":[{"key":"3253_CR1","doi-asserted-by":"publisher","first-page":"e2103856118","DOI":"10.1073\/pnas.2103856118","volume":"118","author":"CM Amato","year":"2021","unstructured":"Amato, C.M., and Yao, H.H.C. (2021). Developmental and sexual dimorphic atlas of the prenatal mouse external genitalia at the single-cell level. Proc Natl Acad Sci USA 118, e2103856118.","journal-title":"Proc Natl Acad Sci USA"},{"key":"3253_CR2","doi-asserted-by":"publisher","first-page":"516","DOI":"10.1016\/j.eururo.2021.01.006","volume":"79","author":"LS Baskin","year":"2021","unstructured":"Baskin, L.S. (2021). New insights into hypospadias: next-generation sequencing reveals potential genetic factors in male urethral development. Eur Urol 79, 516\u2013518.","journal-title":"Eur Urol"},{"key":"3253_CR3","first-page":"673","volume":"12","author":"J Chang","year":"2020","unstructured":"Chang, J., Wang, S., and Zheng, Z. (2020). Etiology of hypospadias: a comparative review of genetic factors and developmental processes between human and animal models. Res Rep Urol 12, 673\u2013686.","journal-title":"Res Rep Urol"},{"key":"3253_CR4","doi-asserted-by":"publisher","first-page":"1993","DOI":"10.1016\/j.scib.2023.08.005","volume":"68","author":"Z Chen","year":"2023","unstructured":"Chen, Z., Gao, Y., Lu, L., Li, N., Liu, P., Peng, R., Liu, L., Huang, H., Fu, Q., Hong, H., et al. (2023a). Rare loss-of-function variants reveal threshold and multifactorial inheritance of dextrocardia. Sci Bull 68, 1993\u20131998.","journal-title":"Sci Bull"},{"key":"3253_CR5","doi-asserted-by":"publisher","first-page":"106663","DOI":"10.1016\/j.isci.2023.106663","volume":"26","author":"Z Chen","year":"2023","unstructured":"Chen, Z., Lei, Y., Finnell, R.H., Ding, Y., Su, Z., Wang, Y., Xie, H., and Chen, F. (2023b). Whole-exome sequencing study of hypospadias. iScience 26, 106663.","journal-title":"iScience"},{"key":"3253_CR6","doi-asserted-by":"publisher","first-page":"71","DOI":"10.5582\/irdr.2023.01024","volume":"12","author":"Z Chen","year":"2023","unstructured":"Chen, Z., Li, P., Lyu, Y., Wang, Y., Gao, K., Wang, J., Lan, F., and Chen, F. (2023c). Molecular genetics and general management of androgen insensitivity syndrome. Intractable Rare Dis Res 12, 71\u201377.","journal-title":"Intractable Rare Dis Res"},{"key":"3253_CR7","doi-asserted-by":"publisher","first-page":"196","DOI":"10.1186\/s12920-019-0642-0","volume":"12","author":"Z Chen","year":"2019","unstructured":"Chen, Z., Lin, X., Lei, Y., Chen, H., Finnell, R.H., Wang, Y., Xu, J., Lu, D., Xie, H., and Chen, F. (2019). Genome-wide association study in Chinese cohort identifies one novel hypospadias risk associated locus at 12q13.13. BMC Med Genomics 12, 196.","journal-title":"BMC Med Genomics"},{"key":"3253_CR8","doi-asserted-by":"publisher","first-page":"318","DOI":"10.5582\/bst.2023.01160","volume":"17","author":"Z Chen","year":"2023","unstructured":"Chen, Z., Wang, Y., Lan, F., Li, S., and Wang, J. (2023d). An expanded view of infertility: the challenge of the changing profiling of major birth defects in China. Biosci Trends 17, 318\u2013321.","journal-title":"Biosci Trends"},{"key":"3253_CR9","doi-asserted-by":"publisher","first-page":"112","DOI":"10.1111\/j.1399-0004.2007.00821.x","volume":"72","author":"A Delahaye","year":"2007","unstructured":"Delahaye, A., Sznajer, Y., Lyonnet, S., Elmaleh-Berg\u00e8s, M., Delpierre, I., Audollent, S., Wiener-Vacher, S., Mansbach, A., Amiel, J., Baumann, C., et al. (2007). Familial CHARGE syndrome because of CHD7 mutation: clinical intra- and interfamilial variability. Clin Genet 72, 112\u2013121.","journal-title":"Clin Genet"},{"key":"3253_CR10","doi-asserted-by":"publisher","first-page":"2125","DOI":"10.1093\/hmg\/ddu733","volume":"24","author":"C Dong","year":"2015","unstructured":"Dong, C., Wei, P., Jian, X., Gibbs, R., Boerwinkle, E., Wang, K., and Liu, X. (2015). Comparison and integration of deleteriousness prediction methods for nonsynonymous SNVs in whole exome sequencing studies. Hum Mol Genet 24, 2125\u20132137.","journal-title":"Hum Mol Genet"},{"key":"3253_CR11","doi-asserted-by":"publisher","first-page":"507","DOI":"10.1016\/j.eururo.2020.12.036","volume":"79","author":"V Ea","year":"2021","unstructured":"Ea, V., Bergougnoux, A., Philibert, P., Servant-Fauconnet, N., Faure, A., Breaud, J., Gaspari, L., Sultan, C., Paris, F., and Kalfa, N. (2021). How far should we explore hypospadias? Next-generation sequencing applied to a large cohort of hypospadiac patients. Eur Urol 79, 507\u2013515.","journal-title":"Eur Urol"},{"key":"3253_CR12","doi-asserted-by":"publisher","first-page":"302","DOI":"10.1016\/j.neuron.2018.06.019","volume":"99","author":"CG Furey","year":"2018","unstructured":"Furey, C.G., Choi, J., Jin, S.C., Zeng, X., Timberlake, A.T., Nelson-Williams, C., Mansuri, M.S., Lu, Q., Duran, D., Panchagnula, S., et al. (2018). De novo mutation in genes regulating neural stem cell fate in human congenital hydrocephalus. Neuron 99, 302\u2013314.e4.","journal-title":"Neuron"},{"key":"3253_CR13","doi-asserted-by":"publisher","first-page":"122","DOI":"10.1111\/cge.13432","volume":"95","author":"N Kalfa","year":"2019","unstructured":"Kalfa, N., Gaspari, L., Ollivier, M., Philibert, P., Bergougnoux, A., Paris, F., and Sultan, C. (2019). Molecular genetics of hypospadias and cryptorchidism recent developments. Clin Genet 95, 122\u2013131.","journal-title":"Clin Genet"},{"key":"3253_CR14","doi-asserted-by":"publisher","first-page":"e61824","DOI":"10.1371\/journal.pone.0061824","volume":"8","author":"N Kalfa","year":"2013","unstructured":"Kalfa, N., Philibert, P., Werner, R., Audran, F., Bashamboo, A., Lehors, H., Haddad, M., Guys, J.M., Reynaud, R., Alessandrini, P., et al. (2013). Minor hypospadias: the \u201ctip of the iceberg\u201d of the partial androgen insensitivity syndrome. PLoS One 8, e61824.","journal-title":"PLoS One"},{"key":"3253_CR15","doi-asserted-by":"publisher","first-page":"e1008810","DOI":"10.1371\/journal.pgen.1008810","volume":"16","author":"A Kothandapani","year":"2020","unstructured":"Kothandapani, A., Lewis, S.R., Noel, J.L., Zacharski, A., Krellwitz, K., Baines, A., Winske, S., Vezina, C.M., Kaftanovskaya, E.M., Agoulnik, A.I., et al. (2020). GLI3 resides at the intersection of hedgehog and androgen action to promote male sex differentiation. PLoS Genet 16, e1008810.","journal-title":"PLoS Genet"},{"key":"3253_CR16","doi-asserted-by":"publisher","first-page":"582","DOI":"10.1038\/ng.3303","volume":"47","author":"N Krumm","year":"2015","unstructured":"Krumm, N., Turner, T.N., Baker, C., Vives, L., Mohajeri, K., Witherspoon, K., Raja, A., Coe, B.P., Stessman, H.A., He, Z.X., et al. (2015). Excess of rare, inherited truncating mutations in autism. Nat Genet 47, 582\u2013588.","journal-title":"Nat Genet"},{"key":"3253_CR17","doi-asserted-by":"publisher","first-page":"1832","DOI":"10.1093\/eurheartj\/ehac112","volume":"43","author":"AK Lucas-Herald","year":"2022","unstructured":"Lucas-Herald, A.K., Montezano, A.C., Alves-Lopes, R., Haddow, L., Alimussina, M., O\u2019Toole, S., Flett, M., Lee, B., Amjad, S.B., Steven, M., et al. (2022). Vascular dysfunction and increased cardiovascular risk in hypospadias. Eur Heart J 43, 1832\u20131845.","journal-title":"Eur Heart J"},{"key":"3253_CR18","doi-asserted-by":"publisher","first-page":"e735","DOI":"10.1210\/clinem\/dgad525","volume":"109","author":"AK Lucas-Herald","year":"2024","unstructured":"Lucas-Herald, A.K., Montezano, A.C., Alves-Lopes, R., Haddow, L., O\u2019Toole, S., Flett, M., Lee, B., Amjad, S.B., Steven, M., McNeilly, J., et al. (2024). Effects of sex hormones on vascular reactivity in boys with hypospadias. J Clin Endocrinol Metab 109, e735\u2013e744.","journal-title":"J Clin Endocrinol Metab"},{"key":"3253_CR19","doi-asserted-by":"publisher","first-page":"1376","DOI":"10.1111\/andr.13229","volume":"10","author":"L Phillips","year":"2022","unstructured":"Phillips, L., Lundholm, C., Kvist, U., Almqvist, C., Nordenskj\u00f6ld, A., and Skarin Nordenvall, A. (2022). Increased androgen-related comorbidity in adolescents and adults born with hypospadias: a population-based study. Andrology 10, 1376\u20131386.","journal-title":"Andrology"},{"key":"3253_CR20","doi-asserted-by":"publisher","first-page":"533","DOI":"10.1038\/nrm.2017.60","volume":"18","author":"JF Reiter","year":"2017","unstructured":"Reiter, J.F., and Leroux, M.R. (2017). Genes and molecular pathways underpinning ciliopathies. Nat Rev Mol Cell Biol 18, 533\u2013547.","journal-title":"Nat Rev Mol Cell Biol"},{"key":"3253_CR21","doi-asserted-by":"publisher","first-page":"34","DOI":"10.1111\/cge.12401","volume":"87","author":"M Roifman","year":"2015","unstructured":"Roifman, M., Marcelis, C.L.M., Paton, T., Marshall, C., Silver, R., Lohr, J.L., Yntema, H. G., Venselaar, H., Kayserili, H., van Bon, B., et al. (2015). De novo WNT5A-associated autosomal dominant Robinow syndrome suggests specificity of genotype and phenotype. Clin Genet 87, 34\u201341.","journal-title":"Clin Genet"},{"key":"3253_CR22","doi-asserted-by":"publisher","first-page":"944","DOI":"10.1038\/ng.3050","volume":"46","author":"KE Samocha","year":"2014","unstructured":"Samocha, K.E., Robinson, E.B., Sanders, S.J., Stevens, C., Sabo, A., McGrath, L.M., Kosmicki, J.A., Rehnstr\u00f6m, K., Mallick, S., Kirby, A., et al. (2014). A framework for the interpretation of de novo mutation in human disease. Nat Genet 46, 944\u2013950.","journal-title":"Nat Genet"},{"key":"3253_CR23","doi-asserted-by":"publisher","first-page":"109041","DOI":"10.1016\/j.steroids.2022.109041","volume":"184","author":"W Shaomei","year":"2022","unstructured":"Shaomei, W., Yongbin, P., Daiyue, Y., Zhaorong, H., Huirong, Y., Nan, L., Huanbin, L., Yuzhu, L., and Kai, W. (2022). Whole exome sequencing applied to 42 Han Chinese patients with posterior hypospadias. Steroids 184, 109041.","journal-title":"Steroids"},{"key":"3253_CR24","doi-asserted-by":"publisher","first-page":"2089","DOI":"10.1093\/cvr\/cvad059","volume":"119","author":"A Stathopoulou","year":"2023","unstructured":"Stathopoulou, A., Wang, P., Thellier, C., Kelly, R.G., Zheng, D., and Scambler, P.J. (2023). CHARGE syndrome-associated CHD7 acts at ISL1-regulated enhancers to modulate second heart field gene expression. Cardiovasc Res 119, 2089\u20132105.","journal-title":"Cardiovasc Res"},{"key":"3253_CR25","doi-asserted-by":"publisher","first-page":"985","DOI":"10.1016\/j.ajhg.2017.10.006","volume":"101","author":"TY Tan","year":"2017","unstructured":"Tan, T.Y., Gonzaga-Jauregui, C., Bhoj, E.J., Strauss, K.A., Brigatti, K., Puffenberger, E., Li, D., Xie, L.Q., Das, N., Skubas, I., et al. (2017). Monoallelic BMP2 variants predicted to result in haploinsufficiency cause craniofacial, skeletal, and cardiac features overlapping those of 20p12 deletions. Am J Hum Genet 101, 985\u2013994.","journal-title":"Am J Hum Genet"},{"key":"3253_CR26","doi-asserted-by":"publisher","first-page":"e164","DOI":"10.1093\/nar\/gkq603","volume":"38","author":"K Wang","year":"2010","unstructured":"Wang, K., Li, M., and Hakonarson, H. (2010). ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res 38, e164.","journal-title":"Nucleic Acids Res"},{"key":"3253_CR27","first-page":"7.25.1","volume":"87","author":"JS Ware","year":"2015","unstructured":"Ware, J.S., Samocha, K.E., Homsy, J., and Daly, M.J. (2015). Interpreting de novo variation in human disease using denovolyzeR. Curr Protoc Hum Genet 87, 7.25.1\u20137.25.15.","journal-title":"Curr Protoc Hum Genet"},{"key":"3253_CR28","doi-asserted-by":"publisher","first-page":"1375","DOI":"10.1093\/bioinformatics\/btu839","volume":"31","author":"Q Wei","year":"2015","unstructured":"Wei, Q., Zhan, X., Zhong, X., Liu, Y., Han, Y., Chen, W., and Li, B. (2015). A Bayesian framework for de novo mutation calling in parents-offspring trios. Bioinformatics 31, 1375\u20131381.","journal-title":"Bioinformatics"},{"key":"3253_CR29","doi-asserted-by":"publisher","first-page":"e827","DOI":"10.1002\/mgg3.827","volume":"7","author":"W Zhang","year":"2019","unstructured":"Zhang, W., Shi, J., Zhang, C., Jiang, X., Wang, J., Wang, W., Wang, D., Ni, J., Chen, L., Lu, W., et al. (2019). Identification of gene variants in 130 Han Chinese patients with hypospadias by targeted next-generation sequencing. Mol Gen Gen Med 7, e827.","journal-title":"Mol Gen Gen Med"},{"key":"3253_CR30","doi-asserted-by":"publisher","first-page":"100953","DOI":"10.1016\/j.xcrm.2023.100953","volume":"4","author":"R Zhao","year":"2023","unstructured":"Zhao, R., Cao, L., Gu, W.J., Li, L., Chen, Z.Z., Xiang, J., Zhou, Z.Y., Xu, B., Zang, W.D., Zhou, X.Y., et al. (2023). Gestational palmitic acid suppresses embryonic GATA-binding protein 4 signaling and causes congenital heart disease. Cell Rep Med 4, 100953.","journal-title":"Cell Rep Med"},{"key":"3253_CR31","doi-asserted-by":"publisher","first-page":"E7194","DOI":"10.1073\/pnas.1515981112","volume":"112","author":"Z Zheng","year":"2015","unstructured":"Zheng, Z., Armfield, B.A., and Cohn, M.J. (2015). Timing of androgen receptor disruption and estrogen exposure underlies a spectrum of congenital penile anomalies. Proc Natl Acad Sci USA 112, E7194\u2013E7203.","journal-title":"Proc Natl Acad Sci USA"}],"container-title":["Science China Life Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s11427-025-3253-3.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1007\/s11427-025-3253-3","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s11427-025-3253-3.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,10,22]],"date-time":"2026-10-22T17:02:51Z","timestamp":1792688571000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/article\/10.1007\/s11427-025-3253-3"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,7,23]]},"references-count":31,"journal-issue":{"issue":"11","published-print":{"date-parts":[[2026,11]]}},"alternative-id":["3253"],"URL":"https:\/\/doi.org\/10.1007\/s11427-025-3253-3","relation":{},"ISSN":["1674-7305","1869-1889"],"issn-type":[{"value":"1674-7305","type":"print"},{"value":"1869-1889","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,7,23]]},"assertion":[{"value":"6 October 2025","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"8 February 2026","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"23 July 2026","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare that they have no conflict of Interest. This study received approval from the Institutional Review Board (NO. 2022-1-47), and written Informed consent was obtained from the parents of all participants.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Compliance and ethics"}}]}}