diff --git a/src/Storages/MergeTree/KeyCondition.cpp b/src/Storages/MergeTree/KeyCondition.cpp
index 2d57ea40c9c..80f425c3e06 100644
--- a/src/Storages/MergeTree/KeyCondition.cpp
+++ b/src/Storages/MergeTree/KeyCondition.cpp
@@ -2250,9 +2250,11 @@ static BoolMask forAnyHyperrectangle(
         if (left_bounded && right_bounded)
             hyperrectangle[prefix_size] = Range(left_keys[prefix_size], true, right_keys[prefix_size], true);
         else if (left_bounded)
-            hyperrectangle[prefix_size] = Range::createLeftBounded(left_keys[prefix_size], true, data_types[prefix_size]->isNullable());
+            hyperrectangle[prefix_size]
+                = Range::createLeftBounded(left_keys[prefix_size], true, isNullableOrLowCardinalityNullable(data_types[prefix_size]));
         else if (right_bounded)
-            hyperrectangle[prefix_size] = Range::createRightBounded(right_keys[prefix_size], true, data_types[prefix_size]->isNullable());
+            hyperrectangle[prefix_size]
+                = Range::createRightBounded(right_keys[prefix_size], true, isNullableOrLowCardinalityNullable(data_types[prefix_size]));
 
         return callback(hyperrectangle);
     }
@@ -2262,13 +2264,15 @@ static BoolMask forAnyHyperrectangle(
     if (left_bounded && right_bounded)
         hyperrectangle[prefix_size] = Range(left_keys[prefix_size], false, right_keys[prefix_size], false);
     else if (left_bounded)
-        hyperrectangle[prefix_size] = Range::createLeftBounded(left_keys[prefix_size], false, data_types[prefix_size]->isNullable());
+        hyperrectangle[prefix_size]
+            = Range::createLeftBounded(left_keys[prefix_size], false, isNullableOrLowCardinalityNullable(data_types[prefix_size]));
     else if (right_bounded)
-        hyperrectangle[prefix_size] = Range::createRightBounded(right_keys[prefix_size], false, data_types[prefix_size]->isNullable());
+        hyperrectangle[prefix_size]
+            = Range::createRightBounded(right_keys[prefix_size], false, isNullableOrLowCardinalityNullable(data_types[prefix_size]));
 
     for (size_t i = prefix_size + 1; i < key_size; ++i)
     {
-        if (data_types[i]->isNullable())
+        if (isNullableOrLowCardinalityNullable(data_types[i]))
             hyperrectangle[i] = Range::createWholeUniverse();
         else
             hyperrectangle[i] = Range::createWholeUniverseWithoutNull();
@@ -2324,7 +2328,7 @@ BoolMask KeyCondition::checkInRange(
     key_ranges.reserve(used_key_size);
     for (size_t i = 0; i < used_key_size; ++i)
     {
-        if (data_types[i]->isNullable())
+        if (isNullableOrLowCardinalityNullable(data_types[i]))
             key_ranges.push_back(Range::createWholeUniverse());
         else
             key_ranges.push_back(Range::createWholeUniverseWithoutNull());
diff --git a/src/Storages/MergeTree/MergeTreeDataSelectExecutor.cpp b/src/Storages/MergeTree/MergeTreeDataSelectExecutor.cpp
index 345872efddf..cd0a7615762 100644
--- a/src/Storages/MergeTree/MergeTreeDataSelectExecutor.cpp
+++ b/src/Storages/MergeTree/MergeTreeDataSelectExecutor.cpp
@@ -383,7 +383,8 @@ MergeTreeDataSelectSamplingData MergeTreeDataSelectExecutor::getSampling(
             if (has_lower_limit)
             {
                 if (!key_condition.addCondition(
-                        sampling_key.column_names[0], Range::createLeftBounded(lower, true, sampling_key.data_types[0]->isNullable())))
+                        sampling_key.column_names[0],
+                        Range::createLeftBounded(lower, true, isNullableOrLowCardinalityNullable(sampling_key.data_types[0]))))
                     throw Exception(ErrorCodes::ILLEGAL_COLUMN, "Sampling column not in primary key");
 
                 ASTPtr args = std::make_shared<ASTExpressionList>();
@@ -401,7 +402,8 @@ MergeTreeDataSelectSamplingData MergeTreeDataSelectExecutor::getSampling(
             if (has_upper_limit)
             {
                 if (!key_condition.addCondition(
-                        sampling_key.column_names[0], Range::createRightBounded(upper, false, sampling_key.data_types[0]->isNullable())))
+                        sampling_key.column_names[0],
+                        Range::createRightBounded(upper, false, isNullableOrLowCardinalityNullable(sampling_key.data_types[0]))))
                     throw Exception(ErrorCodes::ILLEGAL_COLUMN, "Sampling column not in primary key");
 
                 ASTPtr args = std::make_shared<ASTExpressionList>();
diff --git a/tests/queries/0_stateless/03129_low_cardinality_nullable_non_first_primary_key.reference b/tests/queries/0_stateless/03129_low_cardinality_nullable_non_first_primary_key.reference
new file mode 100644
index 00000000000..712cd79a3f2
--- /dev/null
+++ b/tests/queries/0_stateless/03129_low_cardinality_nullable_non_first_primary_key.reference
@@ -0,0 +1 @@
+1650
diff --git a/tests/queries/0_stateless/03129_low_cardinality_nullable_non_first_primary_key.sql b/tests/queries/0_stateless/03129_low_cardinality_nullable_non_first_primary_key.sql
new file mode 100644
index 00000000000..457c288da69
--- /dev/null
+++ b/tests/queries/0_stateless/03129_low_cardinality_nullable_non_first_primary_key.sql
@@ -0,0 +1,10 @@
+DROP TABLE IF EXISTS small;
+
+CREATE TABLE small (`dt` DateTime, `user_email` LowCardinality(Nullable(String)))
+ENGINE = MergeTree order by (dt, user_email) settings allow_nullable_key = 1, min_bytes_for_wide_part=0, min_rows_for_wide_part=0;
+
+INSERT INTO small (dt, user_email) SELECT number, if(number % 3 = 2, NULL, number) FROM numbers(1e2);
+
+SELECT SUM(dt::int) FROM small WHERE user_email IS NULL;
+
+DROP TABLE small;