SELECT 
  cscart_product_prices.product_id, 
  MIN(
    IF(
      cscart_product_prices.percentage_discount = 0, 
      cscart_product_prices.price, 
      cscart_product_prices.price - (
        cscart_product_prices.price * cscart_product_prices.percentage_discount
      )/ 100
    )
  ) AS price 
FROM 
  cscart_product_prices 
WHERE 
  cscart_product_prices.product_id IN (
    12684, 12714, 13260, 13267, 6962, 6966, 
    6967, 6965, 6963, 6952, 6953, 6947, 
    6959, 3425, 6958, 6960, 6968, 6961, 
    6964, 6957, 6956, 6954, 6955, 6948, 
    6950, 6949, 13127, 12464, 12624, 12654, 
    13148, 13153, 12928, 12752
  ) 
  AND cscart_product_prices.lower_limit = 1 
  AND cscart_product_prices.usergroup_id IN (0, 1) 
GROUP BY 
  cscart_product_prices.product_id

Query time 0.00086

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "49.91"
    },
    "grouping_operation": {
      "using_filesort": false,
      "table": {
        "table_name": "cscart_product_prices",
        "access_type": "range",
        "possible_keys": [
          "usergroup",
          "product_id",
          "lower_limit",
          "usergroup_id"
        ],
        "key": "product_id",
        "used_key_parts": [
          "product_id"
        ],
        "key_length": "3",
        "rows_examined_per_scan": 92,
        "rows_produced_per_join": 18,
        "filtered": "19.99",
        "index_condition": "(`test2_gaseus`.`cscart_product_prices`.`product_id` in (12684,12714,13260,13267,6962,6966,6967,6965,6963,6952,6953,6947,6959,3425,6958,6960,6968,6961,6964,6957,6956,6954,6955,6948,6950,6949,13127,12464,12624,12654,13148,13153,12928,12752))",
        "cost_info": {
          "read_cost": "48.07",
          "eval_cost": "1.84",
          "prefix_cost": "49.91",
          "data_read_per_join": "441"
        },
        "used_columns": [
          "product_id",
          "price",
          "percentage_discount",
          "lower_limit",
          "usergroup_id"
        ],
        "attached_condition": "((`test2_gaseus`.`cscart_product_prices`.`lower_limit` = 1) and (`test2_gaseus`.`cscart_product_prices`.`usergroup_id` in (0,1)))"
      }
    }
  }
}