140: SOD1 Variant Landscapes: Activity and Abundance Maps

Axakova A et al., The American Journal of Human Genetics - Axakova et al. produced comprehensive missense variant-effect maps for human SOD1 by assaying enzymatic activity in yeast and protein abundance in human HEK293T cells for ~86% of possible missense substitutions. The study links map patterns to sequence-structure-function features, uses kernel-density calibration to provide LLRp evidence for clinical interpretation, and shows the abundance map best discriminates pathogenic variants and supplies new evidence for many VUSs. Data and LLRp-calibrated scores are available on MaveDB and in supplemental DataS2. Key terms: SOD1, missense variants, VAMP-seq, variant-effect map, ALS.

Study Highlights:
The authors measured functional impacts for over 2,600 missense substitutions across SOD1 using multiplexed yeast complementation (total enzymatic activity) and VAMP-seq in HEK293T cells (protein abundance). Abundance and activity maps reveal complementary mechanisms: many deleterious variants reduce abundance (stability) while others impair activity through effects on metal binding, CCS interaction, or the electrostatic loop. The abundance map outperformed tested computational predictors, was calibrated to log-likelihood ratios (LLRp) for ACMG-style use, and provided new evidence for reclassifying 41% of ClinVar SOD1 VUSs. Map scores also correlated with ALS phenotypes such as age of onset and disease duration.

Conclusion:
Large-scale activity and abundance variant-effect maps for SOD1 provide mechanistic insights and calibrated functional evidence that can improve clinical interpretation of missense variants and prioritize individuals for SOD1-directed interventions.

Music:
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Article title:
Landscapes of missense variant impact for human superoxide dismutase 1

First author:
Axakova A

Journal:
The American Journal of Human Genetics

DOI:
10.1016/j.ajhg.2025.08.019

Reference:
Axakova A., Ding M., Cote A.G., et al. Landscapes of missense variant impact for human superoxide dismutase 1. The American Journal of Human Genetics. 2025;112:1–21. https://doi.org/10.1016/j.ajhg.2025.08.019

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/landscapes-of-missense-variant-impact-for-human-superoxide-dismutase-1

QC:
This episode was checked against the original article PDF and publication metadata for the episode release published on 2025-09-17.

QC Scope:
- article metadata and core scientific claims from the narration
- excludes analogies, intro/outro, and music
- transcript coverage: Audited the transcript sections describing saturation mutagenesis of SOD1, yeast enzymatic activity assay, VAMP-seq abundance assay, the resulting variant-effect maps (activity and abundance), structural/MD insights (metal binding, Asn87, Gly128), genotype-phenotype associations, clinical implications, and limitations.
- transcript topics: SOD1 saturation mutagenesis and library generation; Yeast-based total enzymatic activity assay; VAMP-seq abundance assay in HEK293T cells; Variant-effect maps: activity versus abundance quadrants; Metal binding, CCS interactions, and electrostatic loop in SOD1; Second-shell residues (Asn87) and Gly128 dynamics via MD

QC Summary:
- factual score: 10/10
- metadata score: 10/10
- supported core claims: 5
- 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:
- 86% of all possible SOD1 missense variants were assayed in the variant-effect maps (activity and abundance).
- Over 2,000 SOD1 amino acid substitutions were generated via saturation mutagenesis.
- Variant-effect maps cover roughly 2,600 variants with substantial coverage (86% SNV-accessible substitutions detected).
- Two parallel assays were used: a yeast-based total enzymatic activity assay and a human-cell-based abundance assay (VAMP-seq).
- Abundance map outperforms activity map and several computational predictors in pathogenicity discrimination (e.g., AlphaMissense, CPT, ESM-1b, VARITY).
- Abundance scores show genotype–phenotype correlations with ALS features, including age of onset and disease duration; correlations with mouse protein half-life observed.

QC result: Pass.