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 (
    12928, 3135, 12850, 12869, 12752, 12802, 
    3403, 3404, 3405, 3406, 3408, 3409
  ) 
  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 0.00089

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "16.81"
    },
    "grouping_operation": {
      "using_filesort": false,
      "table": {
        "table_name": "cscart_product_prices",
        "access_type": "range",
        "possible_keys": [
          "usergroup",
          "product_id",
          "lower_limit",
          "usergroup_id"
        ],
        "key": "usergroup",
        "used_key_parts": [
          "product_id",
          "usergroup_id",
          "lower_limit"
        ],
        "key_length": "9",
        "rows_examined_per_scan": 24,
        "rows_produced_per_join": 24,
        "filtered": "100.00",
        "index_condition": "((`test2_gaseus`.`cscart_product_prices`.`lower_limit` = 1) and (`test2_gaseus`.`cscart_product_prices`.`product_id` in (12928,3135,12850,12869,12752,12802,3403,3404,3405,3406,3408,3409)) and (`test2_gaseus`.`cscart_product_prices`.`usergroup_id` in (0,1)))",
        "cost_info": {
          "read_cost": "14.41",
          "eval_cost": "2.40",
          "prefix_cost": "16.81",
          "data_read_per_join": "576"
        },
        "used_columns": [
          "product_id",
          "price",
          "percentage_discount",
          "lower_limit",
          "usergroup_id"
        ]
      }
    }
  }
}