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Genotypic and phenotypic spectrum of anophthalmia/microphthalmia in families from Khyber Pakhtunkhwa, Pakistan

Journal of Human Genetics volume 70, pages 565–575 (2025)Cite this article

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Abstract

Anophthalmia/microphthalmia (A/M) are rare congenital ocular malformations involving the absence or underdevelopment of the eyes, and they display considerable clinical and genetic heterogeneity. Establishing a genetic diagnosis for A/M is critical because it facilitates early intervention, informed genetic counseling, and the prevention of disease transmission in high-risk families. This study explored the genotypic and phenotypic landscape of A/M in 10 Pakistani families meeting specific criteria: confirmed A/M phenotype, residence in Khyber Pakhtunkhwa, no prior genetic testing, and informed consent. Whole-exome sequencing (WES) and segregation analysis in families identified a novel missense variant in SMOC1 (c.406T>G, p.Cys136Gly) in a family with Waardenburg anophthalmia syndrome (WAS). Additionally, causative variants in VSX2 (c.598C>T, p.Arg200Ter) and ALDH1A3 (c.172dup, p.Glu58GlyfsTer5) were detected, potentially representing founder variants in the Pashtun ethnic group. Moreover, a likely pathogenic variant in FOXE3 (c.145G>T, p.Gly49Ter) and a variant of uncertain significance in STRA6 (c.1399C>T, p.Arg467Cys), which exhibited incomplete penetrance, were also identified. In addition, segregation analysis of the causal genetic variants in the 5 families revealed a carrier frequency of 60.86% among the phenotypically unaffected family members. Notably, the average size of autozygous regions among probands was substantial (282.62 Mb), indicating a high degree of consanguinity and familial relatedness due to endogamous practices. However, no causative variants were identified in five families, each with a single affected member, with unilateral A/M in the majority of cases. These findings support the value of genetic diagnostics in reproductive counseling and highlight the utility of broader genomic approaches to improve diagnostic outcomes in unresolved cases.

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Fig. 1: Clinical spectrum of A/M phenotypes observed among the investigated families.
Fig. 2: Pedigree, genetic findings, and autozygosity analysis in Families 1, 2, and 4.
Fig. 3: Pedigree, genetic findings, and autozygosity analysis in Family 3 and 5.
Fig. 4: Autozygosity analysis in unresolved families without identified causal variants.

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Data availability

The datasets generated and/or analyzed during the current study are available in the ClinVar repository, with the accession numbers i.e. SCV005901551, SCV005901552, SCV005901553, SCV005901554 and SCV005901555.

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Acknowledgements

The authors would like to thank the patients and their family members for participating in the study.

Funding

This study was supported by the Kohat University of Science & Technology by a PYP start-up grant from the National University of Singapore and the Ministry of Education, Singapore (T2EP30122-0015).

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Authors and Affiliations

  1. Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology, Kohat, Khyber Pakhtunkhwa, Pakistan

    Muhammad Dawood, Niamat Khan & Shamim Saleha

  2. Department of Biological Sciences, National University of Singapore, Singapore, Singapore

    Xinran Ji & Shifeng Xue

  3. Department of Ophthalmology, KMU Institute of Medical Sciences KIMS, Kohat, Khyber Pakhtunkhwa, Pakistan

    Irfan U. Shah

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  1. Muhammad Dawood
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  3. Irfan U. Shah
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  6. Shamim Saleha
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Contributions

Clinical data collection, sample collation, and analysis: MD, IUS, and SS; Genetic testing and data analysis: MD, XJ, NK, SX, and SS; Manuscript writing: MD and NK; Manuscript revision; SX and SS; Study supervision and coordination: NK and SS. All authors read and approved the final manuscript.

Corresponding author

Correspondence to Shamim Saleha.

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The authors declare no competing interests

Ethical approval and consent to participate

The study was approved by the Ethical Committee of Kohat University of Science and Technology (REF:/KUST/Ethical Committee/1050) and IRB of National University of Singapore (N-20-054E). The study was conducted in accordance with the Declaration of Helsinki. Informed written consent was obtained from the participating members of the families and the parents of the minor children.

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Dawood, M., Ji, X., Shah, I.U. et al. Genotypic and phenotypic spectrum of anophthalmia/microphthalmia in families from Khyber Pakhtunkhwa, Pakistan. J Hum Genet 70, 565–575 (2025). https://doi.org/10.1038/s10038-025-01382-6

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