• Test code: 01745
  • Turnaround time:
    10–21 calendar days (14 days on average)
  • Preferred specimen:
    3mL whole blood in a purple-top EDTA tube (K2EDTA or K3EDTA)
  • Alternate specimens:
    Saliva, assisted saliva, buccal swab and gDNA
  • Sample requirements
  • Request a sample kit

Invitae Chronic Pancreatitis Panel

Test description

The Invitae Chronic Pancreatitis Panel analyzes genes associated with chronic pancreatitis (CP), a condition that results in irreversible morphological changes and impairment of both exocrine and endocrine functions of the pancreas. These genes were selected based on the available evidence to date to provide Invitae’s most comprehensive test for chronic pancreatitis.

Genetic testing of these genes may confirm a diagnosis and help guide treatment and management decisions. Identification of a disease-causing variant may also guide testing and diagnosis of at-risk relatives.

CFTR: Analysis includes the intronic variants: NM_000492.3:c.3718-2477C>T (also known as 3849+10kbC>T), c.1210-34TG [13]T [5] (also known as T5TG13), c.1210-34TG [12]T [5] (also known as T5TG12), c.1210-34TG [11]T [5] (also known as T5TG11), and c.1679+1634A>G.

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Primary panel (6 genes)


  • chronic pancreatitis
  • cystic fibrosis
  • CASR-associated conditions, including familial isolated hyperparathyroidism (FIHP), hypocalcemia (ADH) and benign familial hypocalciuric hypercalcemia (BFHH)

The pancreas is responsible for synthesizing enzymes for protein, fat and carbohydrate digestion in the intestines and for producing insulin and glucagon for maintaining blood-sugar balance. Chronic pancreatitis is a progressive inflammatory disorder in which overly active digestive enzymes destroy the pancreatic secretory cells. The primary features of chronic pancreatitis include intractable pain and maldigestion, followed by diabetes mellitus and malnutrition with advancing disease. Chronic pancreatitis is a risk factor for the development of pancreatic cancer.

Alcoholism is the leading cause of chronic pancreatitis and accounts for approximately 50% of all cases worldwide. Approximately 10% of cases with alcoholic chronic pancreatitis (ACP) have been found to have a pathogenic variant in one of the genes on this panel, and pathogenic variants in these genes have been identified in approximately 90% of individuals with idiopathic (previously unexplained) chronic pancreatitis (ICP).

The inheritance pattern of chronic pancreatitis varies by gene:

  • CPA1, PRSS1, SPINK1 – autosomal dominant
  • CASR, CFTR, CTRC – increased risk
    CFTR is also known to cause autosomal recessive cystic fibrosis (CF) and congenital bilateral absence of vas deferens (CBAVD).
  • Gain-of-function variants (pathogenic missense and copy number variants) in PRSS1 have a penetrance of 80%.
  • Gain-of-function variants (pathogenic missense and copy number variants) in CPA1 have shown to increase the risk of developing chronic pancreatitis, but the penetrance of this effect is still unknown.
  • Loss-of-function variants (pathogenic splicing and truncating variants) in SPINK1 have a penetrance of 30%–75%, depending on the specific variant.
  • Loss-of-function variants (pathogenic missense, splicing, and truncating variants) in CASR, CFTR, and CTRC have low penetrance. Pathogenic variants in these genes have been shown to increase the risk of chronic pancreatitis between two- and tenfold, depending on the variant.

The prevalence of chronic pancreatitis is ~1 in 4,000 on average, with considerably higher rates (~1 in 1,000) in southern India.

Testing for chronic pancreatitis may be considered in any individual with a personal and/or family history of:

  • unexplained episodes of acute pancreatitis in childhood
  • recurrent acute attacks of pancreatitis of unknown cause
  • chronic pancreatitis of unknown cause, particularly with onset before age 25 years
  • signs and symptoms of pancreatitis-associated syndromes, such as cystic fibrosis (CF) or atypical CF

  1. Rebours, V, et al. The natural history of hereditary pancreatitis: a national series. Gut. 2009; 58(1):97-103. doi: 10.1136/gut.2008.149179. PMID: 18755888
  2. Witt, H, et al. Variants in CPA1 are strongly associated with early onset chronic pancreatitis. Nat. Genet. 2013; 45(10):1216-20. PMID: 23955596
  3. Kujko, AA, et al. A novel p.Ser282Pro CPA1 variant is associated with autosomal dominant hereditary pancreatitis. Gut. 2017; 66(9):1728-1730. PMID: 28258133
  4. Solomon, S, et al. PRSS1-Related Hereditary Pancreatitis. 2012 Mar 01. In: Pagon, RA, et al, editors. GeneReviews(®) (Internet). University of Washington, Seattle. PMID: 22379635
  5. Chen, JM, Férec, C. Chronic pancreatitis: genetics and pathogenesis. Annu Rev Genomics Hum Genet. 2009; 10:63-87. PMID: 19453252
  6. Braganza, JM, et al. Chronic pancreatitis. Lancet. 2011; 377(9772):1184-97. PMID: 21397320
  7. Etemad, B, Whitcomb, DC. Chronic pancreatitis: diagnosis, classification, and new genetic developments. Gastroenterology. 2001; 120(3):682-707. PMID: 11179244
  8. Witt, H, et al. Chronic pancreatitis: challenges and advances in pathogenesis, genetics, diagnosis, and therapy. Gastroenterology. 2007; 132(4):1557-73. PMID: 17466744
  9. Ellis, I, et al. Genetic testing for hereditary pancreatitis: guidelines for indications, counselling, consent and privacy issues. Pancreatology. 2001; 1(5):405-15. PMID: 12120217
  10. Solomon, S, Whitcomb, DC. Genetics of pancreatitis: an update for clinicians and genetic counselors. Curr Gastroenterol Rep. 2012; 14(2):112-7. PMID: 22314809
  11. Ellis, I. Genetic counseling for hereditary pancreatitis--the role of molecular genetics testing for the cationic trypsinogen gene, cystic fibrosis and serine protease inhibitor Kazal type 1. Gastroenterol. Clin. North Am. 2004; 33(4):839-54. PMID: 15528021
  12. Rickels, MR, et al. Detection, evaluation and treatment of diabetes mellitus in chronic pancreatitis: recommendations from PancreasFest 2012. Pancreatology. 2013; 13(4):336-42. PMID: 23890130
  13. Bellin, MD, et al. Total pancreatectomy and islet autotransplantation in chronic pancreatitis: recommendations from PancreasFest. Pancreatology. 2014; 14(1):27-35. PMID: 24555976
  14. Noone, PG, et al. Cystic fibrosis gene mutations and pancreatitis risk: relation to epithelial ion transport and trypsin inhibitor gene mutations. Gastroenterology. 2001; 121(6):1310-9. PMID: 11729110
  15. Keiles, S, Kammesheidt, A. Identification of CFTR, PRSS1, and SPINK1 mutations in 381 patients with pancreatitis. Pancreas. 2006; 33(3):221-7. PMID: 17003641
  16. Masson E, et al. A conservative assessment of the major genetic causes of idiopathic chronic pancreatitis: data from a comprehensive analysis of PRSS1, SPINK1, CTRC and CFTR genes in 253 young French patients. PLoS ONE. 2013;8(8):e73522. PMID: 23951356
  17. Pelletier AL, et al. CFTR gene mutation in patients with apparently idiopathic pancreatitis: lack of phenotype-genotype correlation. Pancreatology. 2010;10(2-3):158-64. PMID: 20460946
  18. Applebaum-shapiro SE, et al. Hereditary pancreatitis in North America: the Pittsburgh-Midwest Multi-Center Pancreatic Study Group Study. Pancreatology. 2001;1(5):439-43. PMID: 12120221
  19. LaRusch, J, Whitcomb, DC. Genetics of pancreatitis. Curr. Opin. Gastroenterol. 2011; 27(5):467-74. doi: 10.1097/MOG.0b013e328349e2f8. PMID: 21844754
  20. LaRusch, J, et al. Pancreatitis Overview. 2014 Mar 13. In: Pagon, RA, et al, editors. GeneReviews (Internet). University of Washington, Seattle; Available from: http://www.ncbi.nlm.nih.gov/books/NBK190101/ PMID: 24624459

Assay and technical information

Invitae is a College of American Pathologists (CAP)-accredited and Clinical Laboratory Improvement Amendments (CLIA)-certified clinical diagnostic laboratory performing full-gene sequencing and deletion/duplication analysis using next-generation sequencing technology (NGS).

Our sequence analysis covers clinically important regions of each gene, including coding exons and 10 to 20 base pairs of adjacent intronic sequence on either side of the coding exons in the transcript listed below, depending on the specific gene or test. In addition, the analysis covers select non-coding variants. Any variants that fall outside these regions are not analyzed. Any limitations in the analysis of these genes will be listed on the report. Contact client services with any questions.

Based on validation study results, this assay achieves >99% analytical sensitivity and specificity for single nucleotide variants, insertions and deletions <15bp in length, and exon-level deletions and duplications. Invitae's methods also detect insertions and deletions larger than 15bp but smaller than a full exon but sensitivity for these may be marginally reduced. Invitae’s deletion/duplication analysis determines copy number at a single exon resolution at virtually all targeted exons. However, in rare situations, single-exon copy number events may not be analyzed due to inherent sequence properties or isolated reduction in data quality. Certain types of variants, such as structural rearrangements (e.g. inversions, gene conversion events, translocations, etc.) or variants embedded in sequence with complex architecture (e.g. short tandem repeats or segmental duplications), may not be detected. Additionally, it may not be possible to fully resolve certain details about variants, such as mosaicism, phasing, or mapping ambiguity. Unless explicitly guaranteed, sequence changes in the promoter, non-coding exons, and other non-coding regions are not covered by this assay. Please consult the test definition on our website for details regarding regions or types of variants that are covered or excluded for this test. This report reflects the analysis of an extracted genomic DNA sample. In very rare cases, (circulating hematolymphoid neoplasm, bone marrow transplant, recent blood transfusion) the analyzed DNA may not represent the patient's constitutional genome.

Gene Transcript reference Sequencing analysis Deletion/Duplication analysis
CASR NM_000388.3
CFTR* NM_000492.3
CPA1 NM_001868.3
CTRC NM_007272.2
PRSS1* NM_002769.4
SPINK1 NM_003122.4

CFTR: Analysis includes the intronic variants: NM_000492.3:c.3718-2477C>T (also known as 3849+10kbC>T), c.1210-34TG[13]T[5] (also known as T5TG13), c.1210-34TG[12]T[5] (also known as T5TG12), c.1210-34TG[11]T[5] (also known as T5TG11), and c.1679+1634A>G. Sequencing analysis for exons 7 includes only cds +/- 10 bp.
PRSS1: Sequencing analysis for exon 4 is limited to cds +/-10 bp.