SELECT 
  pfv.feature_id, 
  pfv.product_id, 
  pfv.variant_id, 
  gp.group_id 
FROM 
  cscart_product_features_values AS pfv 
  INNER JOIN cscart_product_variation_group_products AS gp ON pfv.product_id = gp.product_id 
  INNER JOIN cscart_product_variation_group_features AS gpf ON gpf.group_id = gp.group_id 
  AND gpf.feature_id = pfv.feature_id 
WHERE 
  pfv.lang_code = 'en' 
  AND gp.group_id IN (39, 35, 40)

Query time 0.00048

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost": 0.029576525,
    "nested_loop": [
      {
        "table": {
          "table_name": "gp",
          "access_type": "range",
          "possible_keys": ["PRIMARY", "idx_group_id"],
          "key": "idx_group_id",
          "key_length": "3",
          "used_key_parts": ["group_id"],
          "loops": 1,
          "rows": 11,
          "cost": 0.005704015,
          "filtered": 100,
          "attached_condition": "gp.group_id in (39,35,40)",
          "using_index": true
        }
      },
      {
        "table": {
          "table_name": "gpf",
          "access_type": "ref",
          "possible_keys": ["PRIMARY", "idx_group_id"],
          "key": "idx_group_id",
          "key_length": "3",
          "used_key_parts": ["group_id"],
          "ref": ["u428615623_ecartifygonje.gp.group_id"],
          "loops": 11,
          "rows": 1,
          "cost": 0.011526655,
          "filtered": 100,
          "using_index": true
        }
      },
      {
        "table": {
          "table_name": "pfv",
          "access_type": "ref",
          "possible_keys": [
            "PRIMARY",
            "fl",
            "lang_code",
            "product_id",
            "fpl",
            "idx_product_feature_variant_id"
          ],
          "key": "lang_code",
          "key_length": "12",
          "used_key_parts": ["lang_code", "feature_id", "product_id"],
          "ref": [
            "const",
            "u428615623_ecartifygonje.gpf.feature_id",
            "u428615623_ecartifygonje.gp.product_id"
          ],
          "loops": 11,
          "rows": 1,
          "cost": 0.012345855,
          "filtered": 100,
          "attached_condition": "pfv.lang_code = 'en'",
          "using_index": true
        }
      }
    ]
  }
}