diff --git a/Lib/fontTools/subset/__init__.py b/Lib/fontTools/subset/__init__.py
index 8d196ac07..ebd99728f 100644
--- a/Lib/fontTools/subset/__init__.py
+++ b/Lib/fontTools/subset/__init__.py
@@ -1790,11 +1790,14 @@ def subset_glyphs(self, s):
 	return bool(self.variations)
 
 def _remap_index_map(s, varidx_map, table_map):
-	map = {k:varidx_map[v] for k,v in table_map.mapping.items()}
+	map_ = {k:varidx_map[v] for k,v in table_map.mapping.items()}
+	# Emptied glyphs are remapped to:
+	# if GID <= last retained GID, 0/0: delta set for 0/0 is expected to exist & zeros compress well
+	# if GID > last retained GID, major/minor of the last retained glyph: will be optimized out by table compiler
 	last_idx = varidx_map[table_map.mapping[s.last_retained_glyph]]
 	for g,i in s.reverseEmptiedGlyphMap.items():
-		map[g] = last_idx if i > s.last_retained_order else 0
-	return map
+		map_[g] = last_idx if i > s.last_retained_order else 0
+	return map_
 
 @_add_method(ttLib.getTableClass('HVAR'))
 def subset_glyphs(self, s):
diff --git a/Lib/fontTools/varLib/varStore.py b/Lib/fontTools/varLib/varStore.py
index 64e227853..e6609a689 100644
--- a/Lib/fontTools/varLib/varStore.py
+++ b/Lib/fontTools/varLib/varStore.py
@@ -218,9 +218,8 @@ def VarStore_subset_varidxes(self, varIdxes, optimize=True, retainFirstMap=False
 		items = data.Item
 		newItems = []
 		if major == 0 and retainFirstMap:
-			zeros = [0] * len(items[0])
 			for minor in range(len(items)):
-				newItems.append(items[minor] if minor in usedMinors else zeros)
+				newItems.append(items[minor] if minor in usedMinors else [0] * len(items[minor]))
 				varDataMap[minor] = minor
 		else:
 			for minor in sorted(usedMinors):