ESM-variants (ESM-1v zero-shot variant scoring)

Applies Meta FAIR's ESM-1v protein language model to zero-shot missense variant effect scoring, deployed as a public tool.

Unsigned

Overview

esm-variants applies Meta FAIR's ESM-1v protein language model (Meier et al., "Language models enable zero-shot prediction of the effects of mutations on protein function", 2021) to zero-shot missense variant-effect scoring on human protein-coding variants, developed by the Ntranos lab. It is deployed as a public tool (huggingface.co/spaces/ntranoslab/esm_variants) and is distinct from the base ESM-2 model already catalogued in this registry (`data/models/esm2.json`): esm-variants is a purpose-built variant-scoring application layer over the earlier ESM-1v checkpoints, not a standalone foundation model.

**Marginal call, stated plainly**: this entry is a real, fetchable, distinct variant-effect-prediction tool, but it is a thin wrapper/application over an existing base model (ESM-1v) rather than a standalone genomic or protein foundation model in its own right, so it is catalogued here as a marginal fit rather than a clean one.

**Licence note**: this repository carries its own `LICENSE` file, confirmed directly (MIT, copyright Nadav Brandes and Vasilis Ntranos, 2023) -- resolving the licence uncertainty an earlier research pass flagged, rather than relying on the underlying `facebookresearch/esm` repository's separate MIT licence.

**Registry note on `model_card_uri`**: the esm-variants tool itself publishes no separate model card. This points instead to the Hugging Face model card of the underlying ESM-1v checkpoint (`facebook/esm1v_t33_650M_UR90S_1`) it applies for zero-shot scoring, not a GA4GH Genomic AI Model Card v0.6.0-formatted document (no model has yet published one, since it is a newly drafted specification). The primary source repository for the scoring tool itself remains `github.com/ntranoslab/esm-variants`.

Details

Licence: MIT
Version: ESM-1v zero-shot scoring (Meier et al. 2021)
Category: Variant effect prediction
Homepage: https://huggingface.co/spaces/ntranoslab/esm_variants
Repository: https://github.com/ntranoslab/esm-variants
Maintainers: Susheel Varma (@susheel, GA4GH AI Workstream / Sage Bionetworks)
Keywords: missense-variantvariant-effectprotein-language-modelesm-1vzero-shot

Safety classification

No safety classification has been submitted for this entry.

Model Card

View the full GA4GH Genomic AI Model Card ↗

Hosting: github
Access: https://huggingface.co/spaces/ntranoslab/esm_variants

Mirrored data last synced from the Model Card at 2026-09-08T00:00:00.000Z. See the linked card for the authoritative, live version.

Provenance

Created: 2026-09-08T00:00:00.000Z
Updated: 2026-09-08T00:00:00.000Z
Last verified: 2026-09-08T00:00:00.000Z