ClinVar Genomic variation as it relates to human health

Variant summary: SPINK1 c.194+2T>C is located in a canonical splice-site and is predicted to affect mRNA splicing resulting in a significantly altered protein due to either exon skipping, shortening, or inclusion of intronic material. 5/5 computational tools predict a significant impact on normal splicing. These predictions are supported by multiple functional studies, Kume_2006 and Kereszturi_2009, found the variant to significantly affect splicing. Multiple publications have cited the variant in affected individuals diagnosed with chronic pancreatitis, predominantly of Asian origin. Multiple clinical diagnostic laboratories have ClinVar submissions (after 2014) classifying the variant as "pathogenic." GeneReviews, a well-established database, classifies the variant as "pathogenic." Based on the evidence outlined above, the variant was classified as pathogenic.

The SPINK1 c.194+2T>C variant (rs148954387) has been reported in the literature in numerous individuals diagnosed with chronic pancreatitis (Cho 2016, Kume 2006, Witt 2000, Zou 2018) and is one of the most common pathogenic variants in East Asian individuals affected with pancreatitis (Cho 2016, Zou 2018). This variant is reported as pathogenic by multiple laboratories in ClinVar (Variation ID: 132142), and it is found in the general population with an overall allele frequency of 0.03% (85/280290 alleles) in the Genome Aggregation Database. This variant abolishes the canonical splice donor site of intron 4, which is likely to disrupt gene function. Indeed, functional studies indicate a significant reduction of mRNA levels, skipping of exon 3, and undetectable levels of the SPINK1 protein (Kereszturi 2009, Kume 2006, Zou 2016). Based on available information, the c.194+2T>C variant is considered to be pathogenic. References: Cho SM et al. PRSS1, SPINK1, CFTR, and CTRC Pathogenic Variants in Korean Patients With Idiopathic Pancreatitis. Ann Lab Med. 2016 Nov;36(6):555-60. Kereszturi E et al. Minigene analysis of intronic variants in common SPINK1 haplotypes associated with chronic pancreatitis. Gut. 2009; 58(4):545-9. Kume K et al. [-215G>A; IVS3+2T>C] mutation in the SPINK1 gene causes exon 3 skipping and loss of the trypsin binding site. Gut. 2006; 55(8):1214. Witt H et al. Mutations in the gene encoding the serine protease inhibitor, Kazal type 1 are associated with chronic pancreatitis. Nat Genet. 2000; 25(2):213-6. Zou WB et al. Clarifying the clinical relevance of SPINK1 intronic variants in chronic pancreatitis. Gut. 2016 May;65(5):884-6. Zou WB et al. SPINK1, PRSS1, CTRC, and CFTR Genotypes Influence Disease Onset and Clinical Outcomes in Chronic Pancreatitis. Clin Transl Gastroenterol. 2018 Nov 12;9(11):204.

This sequence change affects a donor splice site in intron 4 of the SPINK1 gene. RNA analysis indicates that disruption of this splice site induces altered splicing and may result in an absent or disrupted protein product. This variant is present in population databases (rs148954387, gnomAD 0.3%), and has an allele count higher than expected for a pathogenic variant. Disruption of this splice site has been observed in individual(s) with chronic pancreatitis (PMID: 15980664, 23017645, 26632706). ClinVar contains an entry for this variant (Variation ID: 132142). Studies have shown that disruption of this splice site alters mRNA splicing and is expected to lead to the loss of protein expression (PMID: 18978175, 26719302). For these reasons, this variant has been classified as Pathogenic.

The c.194+2T>C intronic pathogenic mutation results from a T to C substitution two nucleotides after coding exon 3 in the SPINK1 gene. This alteration occurs at the 3' terminus of the SPINK1 gene, is not expected to trigger nonsense-mediated mRNA decay, and only impacts the last 16 amino acids of the protein. The exact functional effect of this alteration is unknown; however, the impacted region is critical for protein function (Ambry internal data). This alteration was first reported in an individual with chronic pancreatitis (Witt H et al. Nat. Genet., 2000 Jun;25:213-6). A functional study found this mutation causes a splicing defect that significantly diminishes SPINK1 expression at the mRNA level and results in diminished trypsin inhibitor secretion (Kereszturi E et al. Gut, 2009 Apr;58:545-9). This mutation has been seen in individuals affected with idiopathic, familial, alcoholic, autoimmune and tropical chronic pancreatitis (Kereszturi E et al. Gut, 2009 Apr;58:545-9; Chang MC et al. J Gastroenterol Hepatol, 2014 Dec;29:2038-42; Cho SM et al. Ann Lab Med, 2016 Nov;36:555-60; Tang XY et al. Dig Liver Dis, 2020 02;52:143-148). This alteration has also been identified in individuals diagnosed with breast and/or pancreatic cancer (Yang X et al. PLoS One, 2015 Apr;10:e0125571; Boortalary T et al. Pancreas, 2018 Apr;47:e24-e25). Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation.

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. However, the evidence from the literature, in combination with allele frequency data from public databases where available, was not sufficient to rule this variant in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance.

SPINK1: PVS1:Strong, PS4:Moderate, PM2:Supporting, PS3:Supporting

PVS1 PS1 PP2

The SPINK1 c.194+2T>C variant is predicted to disrupt the GT donor site and interfere with normal splicing. This variant has been reported as causative for SPINK1-related disorders, including chronic pancreatitis, and functional studies support its pathogenicity (Witt et al. 2000. PubMed ID: 10835640; Kereszturi et al. 2008. PubMed ID: 18978175; Sun et al. 2015. PubMed ID: 26632706). This variant is reported in 0.33% of alleles in individuals of East Asian descent in gnomAD. Variants that disrupt a consensus splice donor site in SPINK1 are expected to be pathogenic. This variant is interpreted as pathogenic.