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 = 47486 
  AND lower_limit > 1 
  AND prices.usergroup_id IN (0, 0, 1) 
ORDER BY 
  lower_limit

Query time 0.00291

JSON explain

{
  "query_block": {
    "select_id": 1,
    "nested_loop": [
      {
        "table": {
          "table_name": "prices",
          "access_type": "range",
          "possible_keys": [
            "usergroup",
            "product_id",
            "lower_limit",
            "usergroup_id"
          ],
          "key": "lower_limit",
          "key_length": "3",
          "used_key_parts": ["lower_limit"],
          "rowid_filter": {
            "range": {
              "key": "product_id",
              "used_key_parts": ["product_id"]
            },
            "rows": 2,
            "selectivity_pct": 0.007891414
          },
          "rows": 1,
          "filtered": 0.011837121,
          "index_condition": "prices.lower_limit > 1",
          "attached_condition": "prices.product_id = 47486 and prices.usergroup_id in (0,0,1)"
        }
      }
    ]
  }
}