SELECT 
  prices.product_id, 
  prices.lower_limit, 
  usergroup_id, 
  prices.percentage_discount, 
  IF(
    prices.percentage_discount = 0, 
    prices.price, 
    prices.price - (
      prices.price * prices.percentage_discount
    )/ 100
  ) as price 
FROM 
  cscart_product_prices prices 
WHERE 
  prices.product_id = 1059 
  AND lower_limit > 1 
  AND prices.usergroup_id IN (0, 0, 1) 
ORDER BY 
  lower_limit

Query time 0.00049

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "1.20"
    },
    "ordering_operation": {
      "using_filesort": true,
      "table": {
        "table_name": "prices",
        "access_type": "ref",
        "possible_keys": [
          "usergroup",
          "product_id",
          "lower_limit",
          "usergroup_id"
        ],
        "key": "product_id",
        "used_key_parts": [
          "product_id"
        ],
        "key_length": "3",
        "ref": [
          "const"
        ],
        "rows_examined_per_scan": 1,
        "rows_produced_per_join": 0,
        "filtered": "5.00",
        "index_condition": "(`eshopuga_upgr_4122`.`prices`.`product_id` <=> 1059)",
        "cost_info": {
          "read_cost": "1.00",
          "eval_cost": "0.01",
          "prefix_cost": "1.20",
          "data_read_per_join": "1"
        },
        "used_columns": [
          "product_id",
          "price",
          "percentage_discount",
          "lower_limit",
          "usergroup_id"
        ],
        "attached_condition": "((`eshopuga_upgr_4122`.`prices`.`lower_limit` > 1) and (`eshopuga_upgr_4122`.`prices`.`usergroup_id` in (0,0,1)))"
      }
    }
  }
}