diff --git a/src/api/routers/map.py b/src/api/routers/map.py
index 8577263..7c173c3 100644
--- a/src/api/routers/map.py
+++ b/src/api/routers/map.py
@@ -49,6 +49,14 @@ async def map_scoreset(urn: str) -> ScoresetMapping:
         msg = f"Unable to acquire resource from MaveDB: {e}"
         raise HTTPException(status_code=500, detail=msg) from e
 
+    if not records:
+        return JSONResponse(
+            content=ScoresetMapping(
+                metadata=metadata,
+                error_message="Score set contains no variants to map",
+            ).model_dump(exclude_none=True)
+        )
+
     try:
         alignment_result = align(metadata, True)
     except BlatNotFoundError as e:
diff --git a/src/dcd_mapping/main.py b/src/dcd_mapping/main.py
index a51fb82..f0048bc 100644
--- a/src/dcd_mapping/main.py
+++ b/src/dcd_mapping/main.py
@@ -321,6 +321,20 @@ async def map_scoreset_urn(
         _logger.critical(msg)
         click.echo(f"Error: {msg}")
         raise e
+
+    if not records:
+        _emit_info("Score set contains no variants to map", silent, logging.ERROR)
+        final_output = write_scoreset_mapping_to_json(
+            urn,
+            ScoresetMapping(
+                metadata=metadata,
+                error_message="Score set contains no variants to map",
+            ),
+            output_path,
+        )
+        _emit_info(f"Score set mapping output saved to: {final_output}.", silent)
+        return
+
     await map_scoreset(
         metadata, records, output_path, vrs_version, prefer_genomic, silent
     )