SELECT 
  pfv.variant_id, 
  COUNT(p.product_id) AS product_count 
FROM 
  cscart_product_features_values AS pfv 
  INNER JOIN cscart_products AS p ON p.product_id = pfv.product_id 
  AND p.status = "A" 
  INNER JOIN cscart_product_prices AS pp ON pp.product_id = p.product_id 
  AND pp.lower_limit = 1 
WHERE 
  1 
GROUP BY 
  pfv.variant_id

Query time 1.31032

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "360719.58"
    },
    "grouping_operation": {
      "using_filesort": false,
      "nested_loop": [
        {
          "table": {
            "table_name": "pfv",
            "access_type": "index",
            "possible_keys": [
              "PRIMARY",
              "fl",
              "variant_id",
              "product_id",
              "idx_product_feature_variant_id"
            ],
            "key": "variant_id",
            "used_key_parts": [
              "variant_id"
            ],
            "key_length": "3",
            "rows_examined_per_scan": 367512,
            "rows_produced_per_join": 367512,
            "filtered": "100.00",
            "cost_info": {
              "read_cost": "449.12",
              "eval_cost": "36751.20",
              "prefix_cost": "37200.32",
              "data_read_per_join": "277M"
            },
            "used_columns": [
              "product_id",
              "variant_id"
            ]
          }
        },
        {
          "table": {
            "table_name": "p",
            "access_type": "eq_ref",
            "possible_keys": [
              "PRIMARY",
              "status"
            ],
            "key": "PRIMARY",
            "used_key_parts": [
              "product_id"
            ],
            "key_length": "3",
            "ref": [
              "s2cart.pfv.product_id"
            ],
            "rows_examined_per_scan": 1,
            "rows_produced_per_join": 355900,
            "filtered": "96.84",
            "cost_info": {
              "read_cost": "162202.74",
              "eval_cost": "35590.09",
              "prefix_cost": "236154.26",
              "data_read_per_join": "2G"
            },
            "used_columns": [
              "product_id",
              "status"
            ],
            "attached_condition": "(`s2cart`.`p`.`status` = 'A')"
          }
        },
        {
          "table": {
            "table_name": "pp",
            "access_type": "ref",
            "possible_keys": [
              "usergroup",
              "product_id",
              "lower_limit"
            ],
            "key": "product_id",
            "used_key_parts": [
              "product_id"
            ],
            "key_length": "3",
            "ref": [
              "s2cart.pfv.product_id"
            ],
            "rows_examined_per_scan": 1,
            "rows_produced_per_join": 355898,
            "filtered": "100.00",
            "cost_info": {
              "read_cost": "88975.23",
              "eval_cost": "35589.83",
              "prefix_cost": "360719.58",
              "data_read_per_join": "8M"
            },
            "used_columns": [
              "product_id",
              "lower_limit"
            ],
            "attached_condition": "(`s2cart`.`pp`.`lower_limit` = 1)"
          }
        }
      ]
    }
  }
}