diff --git a/alembic/versions/15c40c367731_index_functional_classification_variant_.py b/alembic/versions/15c40c367731_index_functional_classification_variant_.py
new file mode 100644
index 00000000..773a5ed9
--- /dev/null
+++ b/alembic/versions/15c40c367731_index_functional_classification_variant_.py
@@ -0,0 +1,38 @@
+"""index functional classification variant fk
+
+variant_id is only the trailing column of score_calibration_functional_classification_variants'
+composite primary key, so Postgres has no index it can use to look up rows by variant_id alone.
+Every Variant delete (including the per-variant cascade when a score set is deleted) forces a
+sequential scan of this table to enforce that FK, which dominates the delete for any score set
+with a nontrivial number of variants. See mavedb-api#677 ("unpublished score set deletion often
+fails").
+
+Built CONCURRENTLY, outside a transaction, so this doesn't hold an exclusive lock on the table for
+the build's duration.
+
+Revision ID: 15c40c367731
+Revises: c4b18d0f7a92
+Create Date: 2026-09-21 11:19:39.396343
+
+"""
+
+from alembic import op
+
+# revision identifiers, used by Alembic.
+revision = "15c40c367731"
+down_revision = "c4b18d0f7a92"
+branch_labels = None
+depends_on = None
+
+INDEX_NAME = "ix_score_calib_func_classification_variants_variant_id"
+TABLE_NAME = "score_calibration_functional_classification_variants"
+
+
+def upgrade():
+    with op.get_context().autocommit_block():
+        op.execute(f"CREATE INDEX CONCURRENTLY IF NOT EXISTS {INDEX_NAME} ON {TABLE_NAME} (variant_id)")
+
+
+def downgrade():
+    with op.get_context().autocommit_block():
+        op.execute(f"DROP INDEX CONCURRENTLY IF EXISTS {INDEX_NAME}")
diff --git a/src/mavedb/models/score_calibration_functional_classification_variant_association.py b/src/mavedb/models/score_calibration_functional_classification_variant_association.py
index 61f074bd..e9475f79 100644
--- a/src/mavedb/models/score_calibration_functional_classification_variant_association.py
+++ b/src/mavedb/models/score_calibration_functional_classification_variant_association.py
@@ -1,6 +1,6 @@
 """SQLAlchemy association table for variants belonging to functional classifications."""
 
-from sqlalchemy import Column, ForeignKey, Table
+from sqlalchemy import Column, ForeignKey, Index, Table
 
 from mavedb.db.base import Base
 
@@ -11,4 +11,5 @@
         "functional_classification_id", ForeignKey("score_calibration_functional_classifications.id"), primary_key=True
     ),
     Column("variant_id", ForeignKey("variants.id"), primary_key=True),
+    Index("ix_score_calib_func_classification_variants_variant_id", "variant_id"),
 )