You Can’t Raise What You Didn’t Know: The Variance Doctrine – Houston Tax Attorneys


Our income tax system uses a self-reporting process. Taxpayers, in most cases, voluntarily file income tax returns. The IRS can then evaluate the filings to determine whether they appear to be correct or warrant further investigation.

The IRS has developed a whole regime of forms to be used for this very purpose. Taxpayers who fill those out are, in theory, providing all of the information the IRS needs to evaluate whether the information reporte is correct.

The exception to this is for refund claims. Refund claims have a small box, consisting of a few lines, where taxpayers can write out an explanation for the basis of their refund claim. Despite only having a small box to write, the IRS takes the position that any theory not put forth in the small box means that the theory cannot be raised–at least that is the case when it comes to tax litigation.

So imagine that you filed a refund claim as you overpaid your taxes for a particular year and you want your money back. You do your best to fill out the small box that is provided for the “explanation.” Then after that, you discover additional facts that would have changed the text you put in the small box for the explanation. After bringing suit in tax court, the IRS moves to dismiss because the information that you did not know at the time you filled in this small box on the amended return was not listed in the small box.

This is the situation in the Salta v

This is the situation in the Salta v. United States, No. 24-254 (2d Cir. Oct. 6, 2025) case. The appeals court was tasked with deciding whether the information in the small box that was not known at the time had to be there for the litigation to proceed.

Facts & Procedural History

This case involves a common scenario–a foreclosure. In January 2015, the taxpayer-husband’s property in was in foreclosure. Rather than proceed through a lengthy foreclosure process, the taxpayer signed a deed-in-lieu-of-foreclosure arrangement. He transferred the deed to the mortgagee. In exchange, the mortgagee and loan servicer agreed to waive their rights to pursue a deficiency judgment against him.

On their 2015 joint tax return, the couple reported $113,087 in cancellation-of-indebtedness income from the discharge of the husband’s mortgage debt. They paid the tax on this income. Years later, they filed a refund claim to request a refund from the IRS because they believed the cancellation-of-indebtedness income should have been taxable in 2017 rather than 2015.

The IRS denied their refund request. Romeo and Phyllis then filed a refund suit in federal district court. The government moved for summary judgment. The taxpayers cross-moved for summary judgment. At this point in the tax litigation, they raised a new argument. The January 2015 Relocation Agreement was never enforceable because the mortgagee never signed the documents. Furthermore, the loan servicer lacked power of attorney to act on the mortgagee’s behalf.

The district court granted summary judgment for the government. The court found that the variance doctrine barred the taxpayers from raising their unenforceability argument because they had not presented this theory in their administrative refund claims. That resulted in the current court opinion.

When Debt Forgiveness Creates Taxable Income

The tax code treats income from discharge of indebtedness as taxable income under Section 61(a)(11). This provision makes sense as a matter of tax policy. When a lender forgives debt, the borrower experiences an increase in wealth. The borrower no longer has an obligation to repay money that was previously owed.

The timing of when this income must be recognized matters for income tax purposes given that our income tax system follows a strict year by year measurement process. Recognizing income in the wrong year can affect the applicable tax rates, impact the availability of deductions and credits, etc. It can also affect the statute of limitations for assessment. Getting the year wrong means paying tax when you shouldn’t have to. Then you face the burden of fighting to get that money back.

The court have explained that debt discharge creates taxable income in the year the discharge occurs. But determining exactly when a debt is “discharged” for tax purposes isn’t always straightforward.

The general rule is that debt is viewed as having been discharged the moment it becomes clear that tbe debt will never have to be paid. Any identifiable event which fixes the certainty of the discharge may be taken into consideration. This standard focuses on certainty and identifiable events. A vague possibility that debt might not be collected often isn’t enough. The taxpayer has to show a specific moment when it became definite that the debt would not have to be repaid.

The appeals court in this case found that the January 201…

The appeals court in this case found that the January 2015 deed-in-lieu arrangement constituted an identifiable event discharging his mortgage debt. The Relocation Agreement and related documents showed that the mortgagee accepted the property “as full satisfaction for the amount owed on the mortgage loan.” The documents explicitly stated that the taxpayer’s consideration for the deed transfer included “the full cancellation of all debts . . . [and] obligations . . . secured by” the mortgage.

This seemed like a straightforward application of the rules. An identifiable event occurred in January 2015 that made it clear the taxpayer’s mortgage debt would never have to be paid. Therefore, it seemed like 2015 was the proper tax year for recognizing the cancellation-of-indebtedness income.

The Variance Doctrine: You Must Raise Every Argument Administratively

This brings us to the variance doctrine. This applies to refund claims that are litigated as tax refund claims.

Before bringing a refund suit in court, taxpayers have to first file an administrative claim for refund with the IRS. This requirement is in Section 7422(a) of the tax code. This is intended to give the IRS an opportunity to correct errors administratively, create a record of the claim, and, ultimately, define the scope of any later litigation.

The variance doctrine builds on this administrative exhaustion requirement. Under this doctrine, taxpayers may not raise different grounds in their refund suit than those they brought to the IRS in their administrative claim. The courts have explained this as thge taxpayer having to advance in the administrative proceeding any contention it wishes to pursue in court.

The courts have articulated several rationales for the variance doctrine. The Sixth Circuit explained in McDonnell v. United States, 180 F.3d 721 (6th Cir. 1999), that the purpose is “to prevent surprise, and to give the IRS adequate notice of the claim and its underlying facts so that it can make an administrative investigation and determination regarding the claim.”

This makes sense in most cases

This makes sense in most cases. The IRS shouldn’t have to defend against entirely new theories that appear for the first time in litigation that would change the outcome of the litigation. The IRS should have an opportunity to investigate and resolve claims administratively. But what about when the facts are not known to the taxpayer or the IRS? That is what this court case and this article is about.

The “Should Have Known” Trap

The taxpayer argued they couldn’t have raised the unenforceability theory in their administrative refund claims because they only discovered years later that the mortgagee never signed the documentation. They argued that this created an exception to the variance doctrine.

The appeals court rejected this argument on two grounds. First, the court noted that the taxpayers cited no legal authority establishing an exception to the variance doctrine where a taxpayer learns after filing a refund request that a private contract may have been unenforceable. The court stated it was “aware of none.”

Second, the court held that the taxpayers “knew or reasonably should have known the facts underlying their unenforceability theory back in January 2015.” The court based this conclusion on the face of the documents themselves. The Relocation Agreement had no place for the mortgagee to sign. When the husband signed the Agreement in Lieu of Foreclosure and the Terms of Release of Premises, it was allegedly “clear from the face of the documents that the mortgagee had not signed them.”

Moreover, the court opinion notes that the taxpayer-husband asserted that he didn’t learn until discovery in the refund action about the loan servicer’s “lack of a power of attorney” to act on the mortgagee’s behalf. This is not information that would be apparent from the face of the documents.

The court created an impossibly high standard

The court created an impossibly high standard, partciularly for unsophisticated taxpayers. The majority of homeowners dealing with mortgage servicers during a foreclosure would naturally assume the servicer has authority to act on behalf of the mortgagee. Homeowners don’t typically scrutinize signature blocks to determine whether their lender signed or only the servicer signed.

More fundamentally

More fundamentally, the absence of a signature line for the mortgagee doesn’t necessarily signal anything unusual. Many contracts are structured to be signed only by certain parties. The loan servicer’s signature might well have been sufficient if the servicer actually possessed proper authority.

Filing Kitchen-Sink Refund Claims

Consider a taxpayer who files a refund claim based on one good-faith theory supported by known facts. Later, during discovery or further investigation, new facts emerge that support a completely different and stronger argument. That taxpayer is stuck with the original theory. The better argument is barred by the variance doctrine because the taxpayer “should have known” the facts supporting it.

Given this case, to preserve all possible arguments, taxpayers have to consider filing administrative claims that raise every conceivable theory. This includes theories that seem speculative or unsupported by facts known at the time.

This forces taxpayers to recommend the filing of protective claims that read like litigation complaints. A refund claim might need to argue simultaneously that a contract was valid and enforceable (supporting one theory) while also arguing that the same contract was void and unenforceable (supporting another theory). These contradictory positions must both be asserted simply because the facts might develop either way.

Importantly, this approach negates the practical reasons for the variance doctrine. This approach wastes IRS resources and would not give the IRS easy to access information to decide whether to investigate the claim. The IRS has to evaluate and maybe investigate and respond to kitchen-sink claims rather than focusing on the taxpayer’s actual good-faith basis for the refund. This makes the identification of claims worthy of investigation even more difficult for the IRS, not less difficult.

The Takeaway

This case points out a trap for those filing refund claims when the facts are unknown. It shows that procedural doctrines can defeat substantive tax claims even when the taxpayer may be right on the merits. The court’s strict application of the variance doctrine combined with its “should have known” standard creates a nearly impossible burden for taxpayers who discover new facts after filing administrative refund claims.

The decision fundamentally changes how taxpayers have to approach refund claims and amended tax returns when dealing with IRS audits and adjustments. Filing a focused refund claim based on a single well-supported theory is no necessarily the route to go. Instead, one may need to consider filing comprehensive claims raising every conceivable argument regardless of how speculative those arguments may be. This prevents being barred from raising theories later if new facts emerge, even though this approach benefits neither taxpayers nor the IRS.

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Imagine that you earned significant income and failed to file tax returns. You later file the tax returns once the IRS caught on to you, but you omitted a large part of your income.

The government indicts you on criminal tax evasion charges, and starts an IRS audit. Before the criminal trial, the IRS audit concludes and results in a large deficiency that you do not agree with.

You file a petition with the tax court to challenge the liability, but you do not want to participate in the tax court proceedings as you fear that this may have a negative impact on the pending criminal case. So you ask the tax court to hold off on the civil court case pending the criminal case–and the tax court says no. The result, by exercising your right to not self incriminate, you lose your ability to challenge the civil tax liability.

Is this legally correct? The court addresses this in Gottesman v. Commissioner, T.C. Memo. 2025-94. This is a case where the taxpayer asserted that fear of criminal prosecution should justify delaying civil tax assessment efforts.

Facts & Procedural History

The taxpayer in this case operated a medical practice in Arizona from 2009 through 2012. He worked as an independent contractor for various medical clinics. He also ran his own medical services business as a sole proprietorship and held membership interests in two medical partnerships.

Despite earning substantial income as a doctor, he failed to file federal income tax returns for tax years 2009 through 2012. He did not request extensions for time to file or make payments for this period.

The IRS began examining the taxpayer in 2014 for his 2008 through 2013 tax years. The court notes that the doctor refused to cooperate with the tax audit process, he failed to maintain adequate books and records for his businesses, and he used nominee arrangements to conceal assets and income from IRS investigators.

The IRS revenue agent did a bank deposit analysis using bank records obtained through administrative summonses and third-party information returns. This showed that the doctor had signficant income and income tax liabilities.

In 2015, the doctor submitted delinquent tax returns for the years in question. He did so as part of a collection due process hearing. The tax returns may have included fraudulent understatements of his actual tax liability, according to the court. This included underreported business income on Schedule C, omitted partnership distributions and guaranteed payments, and unreported investment income. The discrepancies were substantial. For 2009, the doctor’s corrected tax liability per the IRS was $206,125, but his tax return showed only $89,285. The total deficiencies for all of the years exceeded $328,000.

In 2019, a federal grand jury indicted the doctor for tax evasion under Section 7201. The indictment alleged that from 2009 through 2019, he willfully attempted to evade payment of income tax for tax year 2008. The doctor had relocated to Mexico by this time and remained outside U.S. jurisdiction despite an active arrest warrant.

The IRS issued a IRS Notice of Deficiency in May of 2021. The doctor timely petitioned the U.S. Tax Court for redetermination. In his amended petition, he acknowledged being under criminal investigation and expressed “imminent fear of prosecution.” The doctor’s participation in the tax court case was minimal. He filed seven motions for extensions of time throughout the proceedings. When the IRS filed its answer containing factual allegations, the doctor failed to respond. The court deemed all undenied allegations admitted under Tax Court Rule 37(c).

The IRS moved for summary judgment based on the deemed admissions and supporting evidence. Rather than responding to this motion, the doctor filed a motion to stay all proceedings. He argued that his pending criminal indictment and fear of arrest justified postponing the civil case indefinitely. He also asserted a blanket Fifth Amendment privilege against self-incrimination.

Tax Evasion Under Section 7201

Section 7201 makes it a felony to willfully attempt to evade or defeat any federal tax. This is the primary criminal tax evasion provision. It calls for up to five years imprisonment and substantial fines.

To establish tax evasion, prosecutors have to prove three elements under Section 7201. First, they have to show that additional tax was due and owing. Second, they have to show that the defendant willfully attempted to evade or defeat payment of that tax. Third, they have to show that the defendant committed an affirmative act constituting evasion.

The willfulness requirement distinguishes criminal tax evasion from civil tax violations. Mere failure to pay taxes, even if substantial, does not constitute criminal evasion without proof of willful intent to avoid known legal duties. This requires an “affirmative act.” These “affirmative acts” of evasion typically include filing false returns, maintaining inadequate records, concealing assets, using nominee accounts, or dealing primarily in cash to avoid detection–as noted by the tax court in this case. Compare that to passive failure to file returns or pay taxes. Passive failures generally do not satisfy this element without additional evasive conduct.

How Do Civil Deficiency Proceedings Work?

Evasion claims are criminal proceedings, on the civil side of it, there are deficiency proceedings.

A civil tax deficiency case begins when the IRS determines that a taxpayer owes additional taxes beyond what was reported on their returns. This usually means an IRS audit. The IRS must issue a statutory notice of deficiency before assessing additional taxes, except in limited circumstances.

Taxpayers then have 90 days (150 days if addressed outside the United States) to petition the tax court for redetermination of the deficiency. Filing a timely petition stops IRS collection efforts and the tax court is then tasked with determining the correct tax liability.

Tax Court Rule 142(a) generally places the burden of proof on taxpayers to show that IRS determinations are incorrect. This burden reflects the presumption that IRS deficiency determinations are correct. Taxpayers meet this burden by introducing evidence proving the deficiency is erroneous or excessive. This is the general rule. Section 7491 is an exception. It may shift the burden of proof to the IRS if taxpayers meet certain requirements.

There are also exceptions for unreported income, which the IRS has to first make an evidentiary showing connecting the taxpayer with alleged income-producing activities before the burden shifts back to taxpayers to prove by a preponderance of evidence that IRS determinations are arbitrary or erroneous.

This case involved unreported income. So the IRS had the burden. If the doctor in this case did not participate in the case, the IRS would have met its burden by default basically. That would mean that the doctor could not challenge the IRS’s determinations or meet his burden of proof. This is why the request for stay is so important in this case. It effectively decides the case and does so for the IRS if granted.

What Are the Standards for Granting Stays?

Federal courts have broad discretion to stay civil proceedings when justice requires such relief. The courts do not do them all that often–and not for long periods of time. The courts have generally said that stays pending criminal proceedings are “extraordinary remedies” requiring careful consideration.

Most courts apply a multi-factor test when evaluating stay requests in cases with parallel criminal proceedings. The specific factors vary by jurisdiction, but courts typically examine the relationship between civil and criminal actions, burdens on the court system, hardships to the parties, and the duration of any requested stay.

The relationship between cases considers whether they involve the same parties, time periods, legal theories, and evidence. Greater overlap between civil and criminal cases generally supports granting stays. But courts may proceed with civil cases that address different issues or time periods than pending criminal cases.

Judicial burden examines whether stays would promote efficiency and avoid duplicative proceedings. If criminal resolution might eliminate civil disputes or streamline discovery, courts are more inclined to grant stays. However, if civil cases can be resolved independently through documentary evidence, courts often prefer to proceed.

Hardships to parties weigh the prejudice each side would suffer from granting or denying stays. Criminal defendants worry about self-incrimination if forced to participate in civil proceedings. But plaintiffs may suffer from fading memories, lost evidence, or increasing difficulty collecting judgments over time.

Duration is often the most significant factor. Courts strongly disfavor indefinite stays, particularly when criminal defendants appear to be using delay tactics. Stays that might last years while defendants avoid prosecution are rarely granted.

In this case, the tax court found most of the factors in favor of not granting the stay. It concluded that the stay should not be granted. This begs the question of whether a taxpayer should effectively lose their ability to challenge an underlying tax liability when they are exposed to criminal liability for the same tax.

Losing the Ability to Challenge the Liability

The practical effect of denying the doctor’s stay motion was to force him into a difficult impossible choice. He could participate in the civil proceedings and risk providing evidence that prosecutors could use against him in the criminal case. Alternatively, he could remain silent and allow the IRS to win on the liability by default through deemed admissions and summary judgment.

This dilemma highlights a fundamental tension in the parallel track system. The Fifth Amendment protects against compelled self-incrimination, but it does not guarantee that taxpayers can avoid all consequences of asserting the privilege. When criminal and civil cases proceed simultaneously, taxpayers often find themselves caught between competing legal pressures.

The tax court’s analysis reveals how procedural defaults can effectively eliminate a taxpayer’s ability to contest the underlying merits of their case. The doctor’s failure to respond to pleadings resulted in deemed admissions that established both the deficiencies and the elements needed for civil fraud penalties. Once these facts were deemed admitted, summary judgment became virtually automatic regardless of whether the taxpayer had valid defenses.

This creates a circular problem. The civil judgment establishing tax liability and fraudulent intent could potentially be used as evidence in the criminal case to prove elements of tax evasion. While criminal cases require higher burdens of proof and independent evidence of willfulness, a civil judgment based on deemed admissions creates additional hurdles for criminal defense. The taxpayer’s exercise of Fifth Amendment rights in the civil case may inadvertently strengthen the government’s criminal case by allowing unchallenged factual findings to stand. And this all hinges on the court’s decision as to whether to grant or deny a stay in the civil case.

The Takeaway

This case shows that fear of criminal prosecution alone cannot justify indefinitely delaying civil tax proceedings. The court will scrutinize stay requests using multi-factor tests that weigh judicial efficiency, party hardships, and the duration of potential delays. Blanket Fifth Amendment assertions to avoid civil proceedings entirely may not work. And they may result in adverse judgments regardless of underlying merits or criminal exposure. This is a harsh reality for taxpayers facing parallel civil and criminal proceedings. The government’s dual-track enforcement strategy effectively forces taxpayers into difficult strategic choices about when and how to assert constitutional rights.

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In 40 minutes, we’ll teach you how to survive an IRS audit.

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