Is Encephalopathy Making Your Head Hurt? Documentation Tips for the Physician Advisor 

By Ben Kartchner, MD

Encephalopathy remains a notoriously difficult diagnosis for clinical documentation specialists, clinicians and physician advisors to correctly identify and document. Despite its importance, it is almost universally a manifestation of some other underlying condition which can result in it being overlooked. However, it is critical that the physician advisor have an understanding to educate and establish accurate and complete documentation. 

The NIH defines encephalopathy as “any diffuse disease of the brain that alters brain function or structure” and the National Institute of Neurological Disorders and Stroke (NINDS) describes the hallmark of encephalopathy as “altered mental status”. (1) It is generally classified as acute or chronic with each group can being further defined depending on the specific etiology. Acute encephalopathy is “characterized by an acute global alteration in mental status due to systemic factors” and is generally reversible if treated. (2) Chronic encephalopathy is generally a permanent alteration in brain function with variable mental status manifestations. It also has multiple causes including genetic factors, infections, long term exposure to toxic substances and other pathology which can cause permanent structural changes in the brain. Chronic encephalopathy can be due to focal disease whereas acute is typically diffuse. 

Differentiation of acute and chronic encephalopathies is important for the physician advisor and clinician to understand due to the underlying payment, quality and risk adjustment implications. Many acute encephalopathy codes are either MCCs or CCs while almost all chronic encephalopathy codes are not. However, the definitions are malleable and as discussed below, it is quite possible to have an acute encephalopathy due to or related to underlying structural changes superimposed on chronic disease. This is an important distinction as auditors often attempt to deny acute encephalopathy codes in the setting of structural changes despite the record clearly noting a change from baseline. Examples of this include acute encephalopathy superimposed on chronic dementia, acute encephalopathy in the setting of brain tumors or stroke. It is important that the documentation notes the change from baseline and the underlying acute etiology. 

Acute encephalopathy, as a general term, encompasses multiple diagnoses which are further specified by the underlying etiology. Metabolic encephalopathy and toxic encephalopathy are both designated major complication or comorbidity (MCC) by CMS. The distinction between the different types of acute encephalopathy is clinical but the documentation by the provider has significant implications. Other types of specified acute encephalopathy include hypertensive encephalopathy and other encephalopathy. It is notable that anoxic/hypoxic encephalopathy codes as G93.1, anoxic brain damage and is a CC. Encephalopathy due to hypoxia in the acute phase with expected or documented improvement should be documented as acute metabolic encephalopathy for the appropriate risk adjustment implication. 

Acute metabolic encephalopathy (G93.41/MCC) can be caused by fever, dehydration, electrolyte imbalance, acidosis, hypoxia, infection and organ failure. However, this list is not comprehensive, and it is up to the clinician to make the correct diagnosis based on their patient’s clinical presentation. As a physician advisor, you may see or hear of “septic encephalopathy” being documented. Unless it is due to direct attack on brain tissue by organisms (i.e., encephalitis), coding guidelines advise assignment of G93.41, Metabolic encephalopathy. 

Toxic encephalopathy (G92.9, Unspecified toxic encephalopathy/MCC) is generally due to external drugs or toxins which should be clearly linked in the documentation. Acute toxic encephalopathy secondary to lithium overdose is an example. The physician advisor should reinforce that providers document toxic encephalopathy when the source of the toxin is external such as overdose, poisoning, or adverse events from a medication taken normally but results in encephalopathy. Sometimes the clinical literature uses the term, “toxic-metabolic encephalopathy,” such as in the case of uremia. ICD-10-CM codes this expression as G92.8, Other toxic encephalopathy (MCC). Per Coding Clinic, Q1 2022, Vol. 9, Number 1, this can be used for toxins which do not come from outside the body. 

Recently our CDI group raised several questions regarding the validity of encephalopathy in the setting of stroke and COVID-19. They wondered if encephalopathy would be considered integral to the underlying condition. AHA Coding Clinic acknowledges that encephalopathy in the setting of stroke is not considered inherent to. (3) It also notes that, “When encephalopathy is linked to a specific condition, such as stroke or urinary tract infection, it is appropriate to use the code describing “other encephalopathy”. Assign G93.49, Other encephalopathy, when encephalopathy is linked to a condition, but a specific encephalopathy (e.g., metabolic, toxic, hypertensive etc.) is not documented.” (4)

It is important to remember that Coding Clinic is not responsible for defining clinical criteria for a diagnosis but offers only guidance on the coding of documentation. The advice is coming from coders, not clinicians. Physician advisors need to be aware of this guidance so they can assist in the education of providers, CDIS and assist with clinical validation denials, but there are times when the advice is contrary to clinical practice. Best practice is for providers to be accurate and specific in their descriptions of the patient condition, etiology of the encephalopathy, and treatment. There may be financial and quality implications if the chart lacks specificity because other and unspecified encephalopathy are only CCs. If there are clinical indicators generally associated with metabolic encephalopathy, a query should be issued for potential addition of specificity. Since hypoxia may be seen in the setting of COVID-19, a query for metabolic encephalopathy may be warranted which would more accurately reflect the appropriate ROM/SOI and MCC. Studies show that encephalopathy is a common presentation with COVID-19(5); however, with the limited information available, we cannot confuse correlation with causation and trust auditors when they claim it is inherent. The majority of patients with COVID-19 are neither hypoxic nor encephalopathic. 

Encephalopathy is a broad and often difficult topic for coders, CDIS, physician advisors and providers. I encourage you to visit the CDI Resource Page under the Education tab on the ACPA website for materials on encephalopathy.