SELECT 
  pf.feature_id 
FROM 
  cscart_product_variation_group_features AS gf 
  INNER JOIN cscart_product_filters AS pf ON gf.feature_id = pf.feature_id 
WHERE 
  pf.feature_id > 0 
  AND pf.filter_id IN (331) 
LIMIT 
  1

Query time 0.00010

JSON explain

{
  "query_block": {
    "select_id": 1,
    "table": {
      "table_name": "pf",
      "access_type": "const",
      "possible_keys": ["PRIMARY", "feature_id"],
      "key": "PRIMARY",
      "key_length": "3",
      "used_key_parts": ["filter_id"],
      "ref": ["const"],
      "rows": 1,
      "filtered": 100
    },
    "table": {
      "table_name": "gf",
      "access_type": "ref",
      "possible_keys": ["PRIMARY"],
      "key": "PRIMARY",
      "key_length": "3",
      "used_key_parts": ["feature_id"],
      "ref": ["const"],
      "rows": 1,
      "filtered": 100,
      "using_index": true
    }
  }
}