ClinVar Genomic variation as it relates to human health

One of the most common PRSS1 pathogenic variants observed in families with pancreatitis and suggested to have a reduced penetrance compared to other pathogenic PRSS1 variants given unaffected carriers in some families (Witt 1999, Howes 2004, Grocock 2010, Joergensen 2010, Chen 2012); Published functional studies demonstrate a damaging effect: increased rate of chymotrypsin C (CTRC)-mediated trypsinogen activation (Nemoda 2006); Case control studies suggest this variant is associated with pancreatitis (Rosendahl 2013); In silico analysis supports that this missense variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 17204147, 24002981, 15082592, 19453252, 19191323, 22539344, 23143602, 27535533, 19951905, 10381903, 26658045, 25546417, 22749696, 15017610, 11788572, 16791840, 16542853, 24458023, 21907651, 11260229, 22427236, 20502448, 32547704, 32268488, 27555793, 34065437, 33504001, 34036232, 16505482)

The PRSS1 c.47C>T; p.Ala16Val variant (rs202003805) is one of the most common pathogenic PRSS1 variants (Rebours 2012), has been reported to co-segregate with disease in families with hereditary pancreatitis (Grocock 2010, Joergensen 2010, Rebours 2012), and is reported in the literature in individuals affected with idiopathic chronic pancreatitis (Grocock 2010, Howes 2004, Witt 1999). This variant is reported in ClinVar (Variation ID: 38363), and is found in the general population with an overall allele frequency of 0.65% (1680/256738 alleles) in the Genome Aggregation Database, but is considered a low confidence variant in the database. This variant has been described to have variable penetrance (Grocock 2010, Joergensen 2010), and in vitro assays have shown p.Ala16Val to increase cationic trypsinogen activity (Nemoda 2006, Szabo 2012). Based on functional assays and this variant's strong association with pancreatitis, the p.Ala16Val variant is considered to be pathogenic. References: Grocock CJ et al. The variable phenotype of the p.A16V mutation of cationic trypsinogen (PRSS1) in pancreatitis families. 2010 Gut. 59(3):357-63. PMID: 19951905. Howes N et al. Clinical and genetic characteristics of hereditary pancreatitis in Europe. Clin Gastroenterol Hepatol. 2004 2(3):252-61. PMID: 15017610. Joergensen MT 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. PMID: 20502448. Nemoda Z et al. Chymotrypsin C (caldecrin) stimulates autoactivation of human cationic trypsinogen. J Biol Chem. 2006 281(17):11879-86. PMID: 16505482. Rebours V et al. An overview of hereditary pancreatitis. Dig Liver Dis. 2012 44(1):8-15. PMID: 21907651. Szabo A et al. Increased activation of hereditary pancreatitis-associated human cationic trypsinogen mutants in presence of chymotrypsin C. J Biol Chem. 2012 287(24):20701-10. PMID: 22539344. Witt H et al. A signal peptide cleavage site mutation in the cationic trypsinogen gene is strongly associated with chronic pancreatitis. Gastroenterology. 1999 117(1):7-10. PMID: 10381903.

This sequence change replaces alanine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 16 of the PRSS1 protein (p.Ala16Val). The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This missense change has been observed in individual(s) with pancreatic cancer (PMID: 10381903, 11260229, 15017610, 19453252, 19951905, 20502448, 21907651, 22749696). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 38363). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Not Available"; PolyPhen-2: "Benign"; Align-GVGD: "Not Available". The valine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. Experimental studies have shown that this missense change affects PRSS1 function (PMID: 16505482, 22539344). For these reasons, this variant has been classified as Pathogenic.

The p.A16V pathogenic mutation (also known as c.47C>T), located in coding exon 2 of the PRSS1 gene, results from a C to T substitution at nucleotide position 47. The alanine at codon 16 is replaced by valine, an amino acid with similar properties. In pediatric individuals, heterozygosity for this mutation was associated with chronic pancreatitis (Witt H et al. Gastroenterology, 1999 Jul;117:7-10). Subsequent studies also observed this mutation in affected individuals of all ages, but suggested a reduced penetrance given the presence of asymptomatic family members (Grocock CJ et al. Gut, 2010 Mar;59:357-63; Joergensen MT et al. Am. J. Gastroenterol., 2010 Aug;105:1876-83). In addition, two functional studies demonstrated increased trypsinogen activation in vitro due to a 4- and 5.8-fold increased rate of chymotrypsin C-mediated N-terminal processing relative to wild type, respectively (Nemoda Z et al. J. Biol. Chem., 2006 Apr;281:11879-86; Szabó A et al. J. Biol. Chem., 2012 Jun;287:20701-10). Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation.

Variant summary: RSS1 c.47C>T (p.Ala16Val) results in a non-conservative amino acid change in the encoded protein sequence. Ala16 is the first residue of the trypsinogen activation peptide, as the secretory signal peptide (amino acids 1-15) is cleaved off during endoplasmic reticulum entry. The activation peptide is also released during the activation process, thus A16V is not present in the active trypsin and cannot alter trypsin function, however it might affect the processing of trypsinogen by CTRC (chymotrypsin C) (Szabo_2012). Four of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 9e-05 in 244118 control chromosomes, predominantly within the Non-Finnish European subpopulation at a frequency of 0.00016 in the gnomAD database exomes dataset (of note, although the variant is located within a region of segmental duplication and therefore these values can be affected by pseudogene interference, the gnomAD database exomes dataset indicates no variant quality control issues). This frequency is not higher than the estimated expected maximum for a pathogenic variant in PRSS1 causing Chronic Pancreatitis (0.00025), allowing no conclusion about variant significance. Per published data, this variant is the third most commonly inherited mutation in the PRSS1 gene (Moran_2016) and has been reported in numerous affected individuals in dominant or compound recessive inheritance with a reported penetrance of ~50% (Grocock_2010, Rosendahl_2012). However, none of the reports confirmed that the presence of pseudogene had been ruled out. Co-occurrences with other variants have been reported (SPINK1 c.101A>G (p.Asn34Ser), in Rosendahl_2012 and Moran_2016; CFTR TG11-5T in Moran_2016; PRSS1 c.364C>T (p.Arg122Cys) in Giefer_2017) that are known as causal variants linked to pancreatitis. Trans-heterozygosity for this variant with other pathogenic variants in SPINK1 and CFTR genes and especially in the context of risk factors such as smoking could increase the risk for pancreatitis (Moran_2016). In functional studies, A16V had no effect on trypsinogen secretion and autoactivation in the absence of chymotrypsin C (Kereszturi_2009). In presence of chymotrypsin C, A16V increased the rate of autoactivation compared with wild-type cationic trypsinogen by increasing N-terminal processing, (Nemoda_2006, Nemeth_2017), albeit the magnitude of this increase was much smaller than in the case of the highly penetrant, common PRSS1 pathogenic variants (e.g. R122H, V39A; Szabo 2012). The following publications have been ascertained in the context of this evaluation (PMID: 17204147, 19191323, 22427236, 22539344, 22749696, 11260229, 24458023, 19951905, 16505482, 26658045, 25546417, 23143602, 28502372, 29173301, 29215622, 30850667, 30113427, 28536777, 15017610, 30018304, 34065437, 10381903). Eight submitters have cited clinical-significance assessments for this variant to ClinVar after 2014 and classified as pathogenic/likely pathogenic (n=7) and VUS (n=1). In summary, although co-occurrences with known pancreatitis causative variants and a possibility the variant being derived from a pseudogene (in at least some of the reported cases) provide somewhat contradicting evidence for pathogenicity, however the lower penetrance for the variant is in accordance with a milder biochemical phenotype in functional studies, therefore the variant has been classified as likely pathogenic

The missesne c.47C>T (p.Ala16Val) variant in PRSS1 gene has been reported previously in heterozygous state in individual(s) affected with Chronic pancreatitis (Chen JM et al., 2012). Experimental studies have shown that this missense change affects PRSS1 function (Szabó et al., 2012). It has also been observed to segregate with disease in related individuals. This variant is reported with the allele frequency of 0.009% in the gnomAD Exomes. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This variant has been submitted to the ClinVar database as Likely benign / Uncertain Significance / Likely Pathogenic / Pathogenic (multiple submissions). Computational evidence (Polyphen - Benign, SIFT - Tolerated, and MutationTaster - Polymorphism) predicts no effect on protein structure and function for this variant. The reference amino acid change p.Ala16Val in PRSS1 is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. The amino acid Ala at position 16 is changed to a Val changing protein sequence and it might alter its composition and physico-chemical properties. For these reasons, this variant has been classified as Pathogenic.

The variant PRSS1:c.47C>T (p.Ala16Val) was identified in dbSNP (ID: rs202003805) and Clinvar (classified as pathogenic). The PRSS1 p.Ala16Val variant is the third most common PRSS1 mutation and is significantly associated with pancreatitis. The variant was identified in 22 individuals across 10 different families, with 15 individuals across 6 families reporting symptoms of pancreatitis. Of these, two individuals confirmed as being PRSS1 p.Ala16Val carriers had pancreatic cancer (Grocock_2009_ PMID:19951905). In another study, the variant was detected in 4 out of 44 patients. Three of these patients had no family history of chronic pancreatitis, although the mutation was inherited in all cases by one parent. Only 1 of 7 first-degree relatives with p.Ala16Val was affected, indicating a low penetrance of this mutation (Witt_2001_PMID:12120220). The variant was identified in control databases in 22 of 244,118 chromosomes (0 homozygous) at a frequency of 0.009%, and was observed at the highest frequency in the European-Non Finnish (NFE) population in 1800 of 110,396 chromosomes (freq: 0.0163%) (Genome Aggregation Database March 6, 2019, v2.1.1. The p.Ala16Val residue is conserved in mammals and computational analyses (MUT Assesor, PolyPhen-2, SIFT, MutationTaster, Revel, FATHMM, MetaLR, DANN) provide inconsistent predictions regarding the impact to the protein; this information is not very predictive of pathogenicity. The variant occurs outside of the splicing consensus sequence and in silico or computational prediction software programs (Splice AI exome) do not predict a deleterious effect on splicing. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time. This variant is classified as a variant of uncertain significance.