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 (
    12464, 12465, 12466, 12467, 12468, 12469, 
    12470, 12471, 12472, 12473, 12474, 
    12475, 12476, 12477, 12478, 12479, 
    12480, 12481, 12482, 12483, 12484, 
    12485, 12486, 12487, 12488, 12489, 
    12490, 12491, 12492, 12493
  ) 
  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 0.00113

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "21.01"
    },
    "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": 30,
        "rows_produced_per_join": 5,
        "filtered": "19.99",
        "index_condition": "(`test2_gaseus`.`cscart_product_prices`.`product_id` in (12464,12465,12466,12467,12468,12469,12470,12471,12472,12473,12474,12475,12476,12477,12478,12479,12480,12481,12482,12483,12484,12485,12486,12487,12488,12489,12490,12491,12492,12493))",
        "cost_info": {
          "read_cost": "20.41",
          "eval_cost": "0.60",
          "prefix_cost": "21.01",
          "data_read_per_join": "143"
        },
        "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)))"
      }
    }
  }
}