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Novel variants in STAG2 and PKD1 associate with multiple congenital malformations and autosomal dominant polycystic kidney disease in a Chinese family: A case report and literature review

  • Authors:
    • Qi Yang
    • Qiang Zhang
    • Sheng Yi
    • Xunzhao Zhou
    • Yiyan Ruan
    • Shujie Zhang
    • Shang Yi
    • Qinle Zhang
    • Zailng Qin
    • Jingsi Luo
  • View Affiliations / Copyright

    Affiliations: Guangxi Key Laboratory of Reproductive Health and Birth Defects Prevention, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, Guangxi Zhuang Autonomous Region 530023, P.R. China, Department of Pediatric Neurology, Guangxi Clinical Research Center for Pediatric Diseases, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, Guangxi Zhuang Autonomous Region 530023, P.R. China
    Copyright: © Yang et al. This is an open access article distributed under the terms of Creative Commons Attribution License.
  • Article Number: 62
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    Published online on: December 30, 2025
       https://doi.org/10.3892/etm.2025.13057
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Abstract

Cohesinopathies are rare multisystem disorders caused by defects in the cohesin complex, which is critical for chromosome segregation, DNA repair, replication, heterochromatin formation and gene transcription regulation. Stromal antigen 2 (STAG2), a key cohesin component, is linked to neurodevelopmental disorders such as X‑linked holoprosencephaly 13 and Mullegama‑Klein‑Martinez syndrome (MKMS). Polycystic kidney disease (PKD), particularly autosomal dominant PKD (ADPKD), is characterized by renal cysts and is commonly associated with variants in the PKD1 gene. In the present study, a Chinese family was enrolled, which included an infant diagnosed with MKMS and familial PKD. Trio whole‑exome sequencing (trio‑WES) was performed to identify a heterozygous in‑frame deletion variant in STAG2 [NM_001042750.2:c.1775_1777del, p.(Pro592del)] and a heterozygous frameshift variant in PKD1 [NM_001009944.3:c.8985delC, p.(Ser2996fs*78)] in the proband. The STAG2 variant [c.1775_1777del, p.(Pro592del)] was confirmed by Sanger sequencing to be absent in other family members and was therefore de novo. By contrast, the PKD1 variant [c.8985delC, p.(Ser2996fs*78)] was identified in the mother, aunt and grandmother of the proband. The proband exhibited clinical features consistent with STAG2‑related disorders, including seizures, global developmental delay, short stature, microcephaly, hypotonia, dysmorphic features, incomplete cleft palate, micrognathia, spina bifida occulta and duplication of the middle phalanx of the third finger on the left hand. Comparative analysis of the present patient and previously reported cases with STAG2 variants suggested that intellectual disability, brain abnormalities, dysmorphic features and skeletal anomalies are the core clinical features of STAG2‑related disorders. Furthermore, familial PKD was observed in the proband, mother, aunt and grandmother, confirming an autosomal dominant inheritance pattern associated with the PKD1 variant. In summary, the present report identified a novel de novo STAG2 variant associated with multisystem congenital malformations and a novel familial PKD1 variant causing ADPKD, expanding the genetic and phenotypic spectrum of these disorders. The present findings highlight the utility of WES in diagnosing complex genetic conditions.
View Figures

Figure 1

Clinical and genetic features. (A)
Pedigree chart of the family of the proband with
Mullegama-Klein-Martinez syndrome and familial polycystic kidney
disease. The pedigree depicts the segregation of both the STAG2
(shown in black) and PKD1 (shown in blue) variants within the
family. (B) Facial appearance of the proband (Ⅲ-1) at the age of 4
months, showing microcephaly (head circumference of 39 cm, <-1
SD), narrow forehead, saddle nose, large ears, micrognathia and
microstomia. (C) The Sanger sequencing chromatograms illustrate the
presence of a novel heterozygous STAG2 variant
[NM_001042750.2:c.1775_1777del, p.(Pro592del)] and a novel
heterozygous frameshift PKD1 variant [NM_001009944.3:
c.8985delC, p.(Ser2996fs*78)] in the proband. (D) The spectrum of
STAG2 pathogenic variants. The red variant is the novel
variant identified in the present study. STAG, stromal antigen;
SCD, stromalin conservative domain; HEAT_SCC3-SA, cohesin subunit
SCC3/SA, HEAT-repeats domain.

Figure 2

Three-dimensional molecular structure
modeling of the STAG2 protein. (A) The crystal structure of the WT
STAG2 shows that the Pro592 residue is located in the region
composed of α-helices. (B) The Pro592del variant results in the
disruption of α-helices. WT, wild-type; STAG2, stromal antigen
2.
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Copy and paste a formatted citation
Spandidos Publications style
Yang Q, Zhang Q, Yi S, Zhou X, Ruan Y, Zhang S, Yi S, Zhang Q, Qin Z, Luo J, Luo J, et al: Novel variants in <em>STAG2</em> and <em>PKD1</em> associate with multiple congenital malformations and autosomal dominant polycystic kidney disease in a Chinese family: A case report and literature review. Exp Ther Med 31: 62, 2026.
APA
Yang, Q., Zhang, Q., Yi, S., Zhou, X., Ruan, Y., Zhang, S. ... Luo, J. (2026). Novel variants in <em>STAG2</em> and <em>PKD1</em> associate with multiple congenital malformations and autosomal dominant polycystic kidney disease in a Chinese family: A case report and literature review. Experimental and Therapeutic Medicine, 31, 62. https://doi.org/10.3892/etm.2025.13057
MLA
Yang, Q., Zhang, Q., Yi, S., Zhou, X., Ruan, Y., Zhang, S., Yi, S., Zhang, Q., Qin, Z., Luo, J."Novel variants in <em>STAG2</em> and <em>PKD1</em> associate with multiple congenital malformations and autosomal dominant polycystic kidney disease in a Chinese family: A case report and literature review". Experimental and Therapeutic Medicine 31.3 (2026): 62.
Chicago
Yang, Q., Zhang, Q., Yi, S., Zhou, X., Ruan, Y., Zhang, S., Yi, S., Zhang, Q., Qin, Z., Luo, J."Novel variants in <em>STAG2</em> and <em>PKD1</em> associate with multiple congenital malformations and autosomal dominant polycystic kidney disease in a Chinese family: A case report and literature review". Experimental and Therapeutic Medicine 31, no. 3 (2026): 62. https://doi.org/10.3892/etm.2025.13057
Copy and paste a formatted citation
x
Spandidos Publications style
Yang Q, Zhang Q, Yi S, Zhou X, Ruan Y, Zhang S, Yi S, Zhang Q, Qin Z, Luo J, Luo J, et al: Novel variants in <em>STAG2</em> and <em>PKD1</em> associate with multiple congenital malformations and autosomal dominant polycystic kidney disease in a Chinese family: A case report and literature review. Exp Ther Med 31: 62, 2026.
APA
Yang, Q., Zhang, Q., Yi, S., Zhou, X., Ruan, Y., Zhang, S. ... Luo, J. (2026). Novel variants in <em>STAG2</em> and <em>PKD1</em> associate with multiple congenital malformations and autosomal dominant polycystic kidney disease in a Chinese family: A case report and literature review. Experimental and Therapeutic Medicine, 31, 62. https://doi.org/10.3892/etm.2025.13057
MLA
Yang, Q., Zhang, Q., Yi, S., Zhou, X., Ruan, Y., Zhang, S., Yi, S., Zhang, Q., Qin, Z., Luo, J."Novel variants in <em>STAG2</em> and <em>PKD1</em> associate with multiple congenital malformations and autosomal dominant polycystic kidney disease in a Chinese family: A case report and literature review". Experimental and Therapeutic Medicine 31.3 (2026): 62.
Chicago
Yang, Q., Zhang, Q., Yi, S., Zhou, X., Ruan, Y., Zhang, S., Yi, S., Zhang, Q., Qin, Z., Luo, J."Novel variants in <em>STAG2</em> and <em>PKD1</em> associate with multiple congenital malformations and autosomal dominant polycystic kidney disease in a Chinese family: A case report and literature review". Experimental and Therapeutic Medicine 31, no. 3 (2026): 62. https://doi.org/10.3892/etm.2025.13057
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