I have application run inside the kuberentes pod that update the user configuration file and on every deployment it flush the data, as the file reside in a folder which cann't be mounted so I created the empty configmap to mount that file as configmap with subpath mounting and also set the defaultmode of file 777 but still my application is unable to update the content of the file.
Is there way I can mount a file with read/write permission enable for all user so my application can update the file at runtime.
No, a configmap mount is read-only since you need to go through the API to update things. If you just want scratch storage that is temporary you can use an emptyDir volume but it sounds like you want this to stick around so check out the docs on persistent volumes (https://kubernetes.io/docs/concepts/storage/persistent-volumes/). There's a lot of options and complexity, you'll need to work out what is the best match for your use case.