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MP 2.04.99

Genetic Testing for Hereditary Pancreatitis

Medical Policy    

Original Policy Date

Last Review Status/Date
Created with literature search/8:2013
  Return to Medical Policy Index


Our medical policies are designed for informational purposes only and are not an authorization, or an explanation of benefits, or a contract.  Receipt of benefits is subject to satisfaction of all terms and conditions of the coverage.  Medical technology is constantly changing, and we reserve the right to review and update our policies periodically. 


Chronic pancreatitis (CP) is a condition in which recurrent attacks of acute pancreatitis evolve into a chronic inflammatory state with exocrine insufficiency, diabetes mellitus, and increased risk for pancreatic cancer. Hereditary pancreatitis (HP) is a subset of chronic pancreatitis and is defined an autosomal dominant disorder that results in a familial pattern of CP. Mutations of several genes are associated with HP. Demonstration of a pathogenic genetic mutation in one or several of these genes can potentially be used to confirm the diagnosis of HP, provide information on prognosis and management, and/or determine the risk of CP in asymptomatic relatives of patients with HP.


Acute and chronic pancreatitis is caused by trypsin activation within the pancreas, resulting in autodigestion, inflammation, elevation of pancreatic enzymes in serum, and abdominal pain. Chronic pancreatitis is defined as an ongoing inflammatory state associated with chronic/recurrent symptoms and progression to exocrine and endocrine pancreatic insufficiency.

Alcohol is the major etiologic factor in 80% of chronic pancreatitis, which has a peak incidence in the 4th and 5th decades of life. Gall stones, hypercalcemia, inflammatory bowel disease, autoimmune pancreatitis, and peptic ulcer disease can also cause chronic pancreatitis. About 20% of chronic pancreatitis is idiopathic. A small percentage of chronic pancreatitis is categorized as hereditary pancreatitis (HP), which usually begins with recurrent episodes of acute pancreatitis in childhood and evolves into chronic pancreatitis by age 20 years. Multiple family members may be affected over several generations, and pedigree analysis often reveals an autosomal dominant pattern of inheritance. Clinical presentation and family history alone are sometimes insufficient to distinguish between idiopathic chronic pancreatitis and hereditary pancreatitis, especially early in the course of the disease. HP is rare disorder, in 1997 there were about 1,000 individuals with HP in the United States. (1)

Genetic determinants of hereditary pancreatitis

In 1996, Whitcomb and colleagues discovered that mutations of protease, serine, 1 (trypsin 1) (PRSS1) on chromosome 7q35 cause hereditary pancreatitis. PRSS1 encodes cationic trypsinogen. Gain of function mutations of the PRSS1 gene cause HP by prematurely and excessively converting trypsinogen to trypsin, which then results in pancreatic autodigestion. Up to 4% of individuals with chronic pancreatitis have a deleterious mutation of PRSS1. Between 60% and 80% of individuals who have a PRSS1 mutation will experience pancreatitis in their lifetimes; 30% to 40% will develop chronic pancreatitis. Most, but not all, individuals with a mutation of PRSS1 will have inherited it from one of their parents. The proportion of HP caused by a spontaneous mutation of PRSS1 is unknown. In families with two or more affected individuals in two or more generations, genetic testing shows that the majority have a demonstrable PRSS1 mutation. In 60-100%, the mutation is detected by sequencing technology (Sanger or next generation), and duplications of exons or the whole PRSS1 gene are seen in about 6%. Two PRSS1 point mutations (p.Arg122His and p.Asn29Ile) are most common, accounting for 90% of mutations in affected individuals. Over 40 other PRSS1 sequence variants have been found, but their clinical significance is uncertain. Pathogenic PRSS1 mutations are present in 10% or less of individuals with chronic pancreatitis. (2)

Targeted analysis of exons 2 and 3, where the common mutations are found, or PRSS1 sequencing, are first-line tests, followed by duplication analysis. The general indications and emphasis on pre- and post-test genetic counseling have remained central features of subsequent reviews and guidelines. (1, 3) However, several other genes have emerged as significant contributors to both HP and chronic pancreatitis. These include cystic fibrosis transmembrane conductance regulator (CFTR), serine peptidase inhibitor, Kazal type 1 (SPINK1), and chymotrypsin C (CTRC).

Autosomal recessive mutations of CFTR cause cystic fibrosis (CF), a chronic disease with onset in childhood that causes severe sinopulmonary disease and numerous gastrointestinal abnormalities. The signs and symptoms of CF can vary widely. On rare occasions, an affected individual may have mild pulmonary disease, pancreatic exocrine sufficiency, and may present with acute, recurrent acute, or chronic pancreatitis. (1) Individuals with heterozygous mutations of the CFTR gene (CF carriers) have a 3- to 4-fold increased risk for chronic pancreatitis. (3) Individuals with 2 CFTR mutations (homozygotes or compound heterozygotes) will benefit from CF-specific evaluations, therapies, and genetic counseling,

The SPINK gene encodes a protein that binds to trypsin and thereby inhibits its activity. Mutations in SPINK are not associated with acute pancreatitis but are found, primarily as modifiers, in recurrent acute pancreatitis and seem to promote the development of chronic pancreatitis, including for individuals with compound heterozygous mutations of the CFTR gene. Fink et al. in 2007 did not recommend testing asymptomatic individuals for CFTR and SPINK because of the poor predictive value. Loss of function mutations in SPINK are also associated with tropical and alcoholic pancreatitis. (4) Autosomal recessive familial pancreatitis may be caused by homozygous or compound heterozygous SPINK mutations. (5)

CTRC is important for the degradation of trypsin and trypsinogen, and 2 mutations (p.R254W and p.K247_R254del) are associated with increased risk for idiopathic chronic pancreatitis (OR 4.6), alcoholic pancreatitis (OR 4.2), and tropical pancreatitis (OR 13.6). (4)

Regulatory Status

Genetic testing for chronic pancreatitis is available as a laboratory-developed service, subject only to the general laboratory operational regulation under the Clinical Laboratory Improvement Amendments (CLIA) of 1988. Laboratories performing clinical tests must be certified for high complexity testing under CLIA. The U.S. Food and Drug Administration (FDA) has not regulated these tests to date.


Genetic testing for hereditary pancreatitis is considered investigational

Policy Guidelines 


CPT code 81401 includes the following testing for hereditary pancreatitis:

PRSS1 (protease, serine, 1 [trypsin 1]) (eg, hereditary pancreatitis), common variants (eg, N29I, A16V,R122H)

CPT code 81404 includes the following testing for hereditary pancreatitis:

PRSS1 (protease, serine, 1 [trypsin 1]) (eg, hereditary pancreatitis), full gene sequence

SPINK1 (serine peptidase inhibitor, Kazal type 1) (eg, hereditary pancreatitis), full gene sequence 

Benefit Application

BlueCard/National Account Issues

The U.S. Food and Drug Administration (FDA) has not regulated these tests because to date they have been offered as laboratory-developed services, subject only to the general laboratory operational regulation under the Clinical Laboratory Improvement Amendments (CLIA) of 1988. Laboratories performing clinical tests must be certified for high-complexity testing under CLIA.


This policy was created in August 2013 with a MEDLINE review of the literature through June 30th 2013.

Literature Review

Analytic Validity

Testing for mutations in the protease, serine, 1 (trypsin 1) (PRSS1), serine peptidase inhibitor (SPINK), and cystic fibrosis transmembrane conductance regulator (CTFR) genes is usually done by direct sequence analysis, which is the gold standard for detecting a mutation that is present and/or excluding a mutation that is absent. Testing can also be done by next-generation sequencing, which has an accuracy that approaches that of direct sequencing. In patients who test negative by either of these methods, duplication/deletion analysis may be performed to detect copy number variations. These genetic testing methods are considered to have high analytic validity.

Clinical Validity

The clinical validity of genetic testing is defined as the mutation detection rate in patients who have known hereditary pancreatitis (HP).

There is a lack of published evidence on the percent of patients who are first identified as having clinically defined HP and then tested for genetic mutations. The majority of studies that examine the mutation detection rate use a population of patients with idiopathic chronic pancreatitis (CP), and do not necessarily require that patients have a family history of CP. In other studies, cohorts of patients with HP were defined by the presence of genetic mutations or family history, which therefore may include patients with genetic mutations who do not have a family history of CP.

A summary of available studies is included in the following table:




Genes Tested

Clinical Sensitivity

Clinical Specificity

Ceppa 2013

(U.S.) (6)

87 patients (pts) with hereditary pancreatitis, defined by known genetic mutation or family history







Sultan 2012

(U.S.) (7)

29 children with recurrent acute or chronic pancreatitis







Gasiorowska 2011

(Poland) (8)

14 pts with idiopathic chronic pancreatitis.

46 control pts without pancreatitis







Joergensen 2010

(Denmark) (9)

122 pts with idiopathic pancreatitis







Rebours 2009

(France) (10)

200 pts with chronic pancreatitis





Keiles 2006

(U.S.) (11)

389 pts with recurrent or chronic pancreatitis referred for genetic testing







Truninger 2001

(Germany) (12)

104 pts with chronic pancreatitis





Applebaum-Shapiro 2001

(U.S.) (13)

115 pts with hereditary pancreatitis defined clinically

349 unaffected family members






These data on clinical validity demonstrate that genetic mutations are common in patients with chronic pancreatitis. A very limited amount of evidence reports that genetic mutations are found in a small percentage of patients without pancreatitis. However, the true clinical sensitivity and specificity are uncertain for a number of reasons. First, the populations in these studies are defined differently, with most not consisting of patients with clinically defined hereditary pancreatitis. The populations are from different geographic regions, in which the prevalence of genetic mutations may vary. Finally, mutations tested for in these studies differ, with many studies not including all of the known genes that are associated with HP.

Clinical Utility

Potential types of clinical utility for PRSS1 genetic testing include confirmation of the diagnosis of HP, predictive testing in asymptomatic relatives, and prognostic testing to determine the course of the disease. In each case, demonstration of clinical utility depends on whether identification of a genetic defect leads to changes in medical and/or surgical management options, and whether these changes lead to improved health outcomes. Preconception (carrier) testing and prenatal (in utero) testing can also be performed, but are not addressed in this literature review.

Diagnostic testing. There is no direct outcome data regarding the clinical utility of testing for confirmation of HP, i.e. there are no studies that report outcome data in patients who have been tested for HP compared to patients who have not been tested.

Confirmatory testing can be performed in patients who experience acute pancreatitis that is otherwise unexplained, for recurrent acute pancreatitis of unclear cause, and/or for idiopathic chronic pancreatitis. In all of these scenarios, a substantial percentage of patients will be found to have a genetic defect, thereby confirming the diagnosis of HP. Most treatments for the pain, maldigestion, and diabetes caused by HP are fundamentally the same as for other types of CP. Therefore, if a deleterious mutation associated with HP is found, treatment for CP is unlikely to change. Interventions for CP include a low-fat diet with multiple small meals, maintenance of good hydration, use of antioxidants, and avoidance of smoking and alcohol use. While all of these interventions may alter the natural history of the disease, there is no evidence that the impact differs for HP compared to other etiologies of CP.

Calcium channel blockers are currently being investigated as a potential treatment for HP. One small uncontrolled trial of amlodipine in 9 patients was identified in the literature. (14) This trial included patients 6 years or older who had CP and a known PRSS1 mutation. Treatment was continued for up to 11 weeks, and 4 patients successfully completed the full course of treatment. All 4 patients reported decreased symptoms, and 3 of the 4 patients had improved scores on the SF (Short Form)-36 outcome instrument. There were no differences before and after treatment in blood pressure, laboratory tests, or physical exam.

Predictive testing. Predictive testing can be performed in asymptomatic relatives of patients with known HP in order to determine the likelihood of CP. For this population, no direct evidence was identified that compared outcomes in patients tested for genetic mutations compared to patients not tested for genetic mutations. It is possible that at-risk relatives who are identified with genetic mutations may alter lifestyle factors such as diet, smoking and alcohol use, and this may delay the onset or prevent CP. However, evidence on this question is lacking, so that conclusions cannot be made on whether testing of asymptomatic family members of patients with HP improves outcomes.

Prognostic testing. Several studies were identified that examined whether the severity and/or natural history of CP differs in patients with and without genetic mutations. A number of studies have reported that patients with HP have an earlier age of onset compared to patients with other etiologies of CP. (15) Other studies have examined whether the severity and natural history differs for patients with HP, but these studies have not reported consistent findings. Some studies have reported that the progression of disease is slower in patients with HP (15-17) and that surgical intervention is required less often for patients with HP. (16) However, one study also reported that the cumulative risk for exocrine failure was more than twice as high for patients with genetic mutations compared to patients without mutations. (17) In another small study that compared the clinical course of patients with HP to those with alcoholic CP, most clinical manifestations were similar, but patients with HP had a higher rate of pseudocysts. (18)

Individuals with HP, like others with CP, are at increased risk for pancreatic cancer. In a survey of 246 patients with HP from 10 countries, the cumulative risk of pancreatic cancer by age 70 was estimated to be 40%. (19) In a series of 200 patients with HP from France, the cumulative incidence of pancreatic cancer at 50 years was 11% for men and 85 for women. At 75 years of age, the cumulative risk was 49% for men and 55% for women. There was no evidence identified that the risk of pancreatic cancer differs for patients with HP compared to patients with other forms of CP.

Screening for pancreatic cancer with computed tomography (CT) scanning, endoscopic ultrasound and/or endoscopic retrograde cholangiopancreatography (ERCP) has been recommended for patients with CP irrespective of etiology (20, 21), but close surveillance has not yet been demonstrated to improve long-term survival for any of these methods in patients with CP.

Section summary. There have been some differences reported regarding the natural course of CP in patients with and without genetic mutations. The age of onset is consistently younger, and the progression of disease may be slower, but it is not possible to conclude whether the overall severity of disease or need for surgical intervention differs. The risk of pancreatic cancer is high for patients with HP, but no evidence was identified that establishes whether the risk of cancer is greater for patients with HP compared to other etiologies of CP.

Clinical Input Received through Physician Specialty Societies and Academic Medical Centers



Hereditary pancreatitis (HP) is a form of chronic pancreatitis (CP) that is associated with mutations in several genes. Numerous studies demonstrate that genetic mutations are found in a large percentage of patients with idiopathic CP. However, these studies are limited by wide variations in the patient populations and genes tested; as a result, it is not possible to determine the true prevalence of HP among patients with idiopathic CP, nor the sensitivity and specificity of genetic testing (clinical validity) in patients with a familial pattern of disease. Clinical utility of testing has not been demonstrated empirically. While testing can confirm the diagnosis of HP, there is no evidence that treatment is altered by testing or that health outcomes are improved. Similarly, predictive testing of at-risk relatives and prognostic testing have not been shown to improve outcomes. Predictive testing can better define the risk of developing CP, but there is no evidence that early interventions based on genetic testing alter the prevalence or course of disease. The prognosis of HP may differ from other etiologies of CP, but this evidence is mixed and there are no changes in management that result from refining the prognosis of CP. As a result, genetic testing for hereditary pancreatitis is considered investigational.

Practice Guidelines and Position Statements

A 2001 European Consensus Conference developed guidelines for genetic testing of the PRSS1 gene, genetic counseling, and consent for genetic testing for HP. (22) The recommended indications for symptomatic patients included:

  • Recurrent (2 or more separate, documented episodes with hyper-amylasemia) attacks of acute pancreatitis for which there is no explanation
  • Unexplained chronic pancreatitis
  • A family history of pancreatitis in a first- or second-degree relative
  • Unexplained pancreatitis in a child – if recurrent or requiring hospitalization

Predictive genetic testing, defined as genetic testing in an asymptomatic “at-risk” relative of an individual proven to have HP, was considered more complex. Candidates for predictive testing should be a first-degree relative of an individual with a well-defined HP gene mutation, capable of informed consent, and able to demonstrate an understanding of autosomal dominant inheritance, incomplete penetrance, variable expressivity, and the natural history of HP. Written informed consent must be documented before the genetic test is performed.

Medicare National Coverage



  1. Solomon S, Whitcomb, D.C., LaRusch, J, et al. PRSS1-Related Hereditary Pancreatitis. GeneReviews 2012. Last accessed June 14, 2013.
  2. Whitcomb DC. Value of genetic testing in the management of pancreatitis. Gut 2004; 53(11):1710-7.
  3. Fink EN, Kant JA, Whitcomb DC. Genetic counseling for nonsyndromic pancreatitis. Gastroenterol Clin North Am 2007; 36(2):325-33, ix.
  4. Rosendahl J, Witt H, Szmola R et al. Chymotrypsin C (CTRC) variants that diminish activity or secretion are associated with chronic pancreatitis. Nat Genet 2008; 40(1):78-82.
  5. Whitcomb DC. Framework for interpretation of genetic variations in pancreatitis patients. Front Physiol 2012; 3:440.
  6. Ceppa EP, Pitt HA, Hunter JL et al. Hereditary pancreatitis: endoscopic and surgical management. J Gastrointest Surg 2013; 17(5):847-56; discussion 56-7.
  7. Sultan M, Werlin S, Venkatasubramani N. Genetic prevalence and characteristics in children with recurrent pancreatitis. J Pediatr Gastroenterol Nutr 2012; 54(5):645-50.
  8. Gasiorowska A, Talar-Wojnarowska R, Czupryniak L et al. The prevalence of cationic trypsinogen (PRSS1) and serine protease inhibitor, Kazal type 1 (SPINK1) gene mutations in Polish patients with alcoholic and idiopathic chronic pancreatitis. Dig Dis Sci 2011; 56(3):894-901.
  9. Joergensen MT, Brusgaard K, Cruger DG et al. Genetic, epidemiological, and clinical aspects of hereditary pancreatitis: a population-based cohort study in Denmark. Am J Gastroenterol 2010; 105(8):1876-83.
  10. Rebours V, Boutron-Ruault MC, Schnee M et al. The natural history of hereditary pancreatitis: a national series. Gut 2009; 58(1):97-103.
  11. Keiles S, Kammesheidt A. Identification of CFTR, PRSS1, and SPINK1 mutations in 381 patients with pancreatitis. Pancreas 2006; 33(3):221-7.
  12. Truninger K, Kock J, Wirth HP et al. Trypsinogen gene mutations in patients with chronic or recurrent acute pancreatitis. Pancreas 2001; 22(1):18-23.
  13. Applebaum-Shapiro SE, Finch R, Pfutzer RH et al. Hereditary pancreatitis in North America: the Pittsburgh-Midwest Multi-Center Pancreatic Study Group Study. Pancreatology 2001; 1(5):439-43.
  14. Morinville VD, Lowe ME, Elinoff BD et al. Hereditary pancreatitis amlodipine trial: a pilot study of a calcium-channel blocker in hereditary pancreatitis. Pancreas 2007; 35(4):308-12.
  15. Teich N, Mossner J. Hereditary chronic pancreatitis. Best Pract Res Clin Gastroenterol 2008; 22(1):115-30.
  16. Mullhaupt B, Truninger K, Ammann R. Impact of etiology on the painful early stage of chronic pancreatitis: a long-term prospective study. Z Gastroenterol 2005; 43(12):1293-301.
  17. Howes N, Lerch MM, Greenhalf W et al. Clinical and genetic characteristics of hereditary pancreatitis in Europe. Clin Gastroenterol Hepatol 2004; 2(3):252-61.
  18. Paolini O, Hastier P, Buckley M et al. The natural history of hereditary chronic pancreatitis: a study of 12 cases compared to chronic alcoholic pancreatitis. Pancreas 1998; 17(3):266-71.
  19. Lowenfels AB, Maisonneuve P, DiMagno EP et al. Hereditary pancreatitis and the risk of pancreatic cancer. International Hereditary Pancreatitis Study Group. J Natl Cancer Inst 1997; 89(6):442-6.
  20. Gemmel C, Eickhoff A, Helmstadter L et al. Pancreatic cancer screening: state of the art. Expert Rev Gastroenterol Hepatol 2009; 3(1):89-96.
  21. Canto MI. Screening and surveillance approaches in familial pancreatic cancer. Gastrointest Endosc Clin N Am 2008; 18(3):535-53, x.
  22. Ellis I, Lerch MM, Whitcomb DC et al. Genetic testing for hereditary pancreatitis: guidelines for indications, counselling, consent and privacy issues. Pancreatology 2001; 1(5):405-15.





CPT   See Policy Guidelines
ICD-9-CM Diagnosis    Investigational for all relevant diagnoses
  577.1 Chronic pancreatitis
 ICD-10-CM (effective 10/1/14)   Investigational for all relevant diagnoses
  K86.1 Other chronic pancreatitis
ICD-10-PCS (effective 10/1/14)   Not applicable. ICD-10-PCS codes are only used for inpatient services. There are no ICD procedure codes for laboratory tests.



Genetic testing, PRSS1
Genetic testing, SPINK1
Genetic testing, chronic pancreatitis

Policy History

Date Action Reason
08/08/13 Add policy to Medicine section, Pathology, Laboratory subsection Policy created with literature review through June 30th, 2013. Genetic testing for hereditary pancreatitis is considered investigational.