110: Rare coding variants implicate STAG1 and ZNF136 in schizophrenia

Chick SL et al et al., Nature Communications - Largest exome-sequencing meta-analysis to date (28,898 cases, 103,041 controls, 3,444 trios) identifies STAG1 and ZNF136 at exome-wide significance and six additional genes at FDR<5%, highlighting roles for chromatin organisation and GABAergic signalling. Key terms: schizophrenia, rare coding variants, STAG1, SLC6A1, whole-exome sequencing.

Study Highlights:
The authors generated a new exome-sequenced case-control sample (4,650 cases, 5,719 controls) and meta-analysed published data for a total of 28,898 cases, 103,041 controls and 3,444 trios. They report exome-wide significant enrichment of rare PTVs and damaging missense variants in STAG1 and PTVs in ZNF136, plus six genes at FDR<5% including SLC6A1 and KLC1. SLC6A1 and KLC1 associations are driven by damaging missense variants, and STAG1 and KLC1 overlap loci from schizophrenia GWAS. Several implicated genes show pleiotropic rare-variant enrichment in developmental disorders, autism and epilepsy.

Conclusion:
STAG1 and ZNF136 are implicated in schizophrenia at exome-wide significance and six additional genes at FDR<5%, supporting disrupted chromatin organisation and altered GABAergic/neural transport pathways in disease etiology.

Music:
Enjoy the music based on this article at the end of the episode.

Article title:
Whole-exome sequencing analysis identifies risk genes for schizophrenia

First author:
Chick SL et al

Journal:
Nature Communications

DOI:
10.1038/s41467-025-62429-y

Reference:
Chick SL et al., Whole-exome sequencing analysis identifies risk genes for schizophrenia. Nature Communications (2025). DOI: 10.1038/s41467-025-62429-y

License:
This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/

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Episode link: https://basebybase.com/episodes/whole-exome-sequencing-identifies-new-schizophrenia-risk-genes

QC:
This episode was checked against the original article PDF and publication metadata for the episode release published on 2025-08-18.

QC Scope:
- article metadata and core scientific claims from the narration
- excludes analogies, intro/outro, and music
- transcript coverage: Audited transcript sections covering study design and sample, gene discoveries (STAG1, ZNF136; six additional genes), mechanistic biology (cohesin/chromatin, GABA signaling), convergence with common-variant signals, NRXN1 CNV locus, pleiotropy, and limitations.
- transcript topics: Study design and new exome sequencing sample; Gene discovery: STAG1 and ZNF136 (exome-wide); Six additional genes at FDR<5%: SLC6A1, PCLO, ZMYND11, BSCL2, KLC1, CGREF1; Damaging missense variants driving SLC6A1 and KLC1 (MPC > 2); Convergence of rare- and common-variant signals at STAG1 and KLC1; NRXN1 PTV enrichment and CNV locus overlap

QC Summary:
- factual score: 10/10
- metadata score: 10/10
- supported core claims: 7
- claims flagged for review: 0
- metadata checks passed: 4
- metadata issues found: 0

Metadata Audited:
- article_doi
- article_title
- article_journal
- license

Factual Items Audited:
- STAG1 exome-wide significance for rare PTVs and damaging missense (MPC>2)
- ZNF136 exome-wide significance for rare PTVs
- Six additional genes at FDR<5%: SLC6A1, PCLO, ZMYND11, BSCL2, KLC1, CGREF1
- SLC6A1 and KLC1 associations driven by damaging missense variants (MPC>2) alone
- NRXN1 PTV enrichment observed at a CNV locus
- Convergence of rare-variant and common-variant signals at STAG1 and KLC1

QC result: Pass.