rs193922659
Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1_StrongPP5_Very_Strong
The NM_001379610.1(SPINK1):c.27del(p.Ser10ValfsTer6) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000242 in 1,613,610 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Pathogenic (★★).
Frequency
Genomes: 𝑓 0.000020 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000025 ( 0 hom. )
Consequence
SPINK1
NM_001379610.1 frameshift
NM_001379610.1 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.786
Genes affected
SPINK1 (HGNC:11244): (serine peptidase inhibitor Kazal type 1) The protein encoded by this gene is a trypsin inhibitor, which is secreted from pancreatic acinar cells into pancreatic juice. It is thought to function in the prevention of trypsin-catalyzed premature activation of zymogens within the pancreas and the pancreatic duct. Mutations in this gene are associated with hereditary pancreatitis and tropical calcific pancreatitis. [provided by RefSeq, Oct 2008]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 12 ACMG points.
PVS1
?
Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant located near the start codon (<100nt), not predicted to undergo nonsense mediated mRNA decay. There are 13 pathogenic variants in the truncated region.
PP5
?
Variant 5-147831550-TG-T is Pathogenic according to our data. Variant chr5-147831550-TG-T is described in ClinVar as [Pathogenic]. Clinvar id is 36780.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SPINK1 | NM_001379610.1 | c.27del | p.Ser10ValfsTer6 | frameshift_variant | 1/4 | ENST00000296695.10 | |
LOC124901101 | XR_007058987.1 | n.509del | non_coding_transcript_exon_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SPINK1 | ENST00000296695.10 | c.27del | p.Ser10ValfsTer6 | frameshift_variant | 1/4 | 1 | NM_001379610.1 | P1 | |
SPINK1 | ENST00000510027.2 | c.27del | p.Ser10ValfsTer6 | frameshift_variant | 1/3 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152218Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000120 AC: 3AN: 250684Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135506
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GnomAD4 exome AF: 0.0000246 AC: 36AN: 1461392Hom.: 0 Cov.: 30 AF XY: 0.0000193 AC XY: 14AN XY: 727018
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ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:4Other:1
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Hereditary pancreatitis Pathogenic:3Other:1
Pathogenic, criteria provided, single submitter | clinical testing | Invitae | Jan 10, 2024 | This sequence change creates a premature translational stop signal (p.Ser10Valfs*6) in the SPINK1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in SPINK1 are known to be pathogenic (PMID: 17681820, 22572128). This variant is present in population databases (rs193922659, gnomAD 0.003%). This premature translational stop signal has been observed in individual(s) with chronic pancreatitis (PMID: 14722925, 22572128). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 36780). For these reasons, this variant has been classified as Pathogenic. - |
Pathogenic, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Aug 12, 2021 | Variant summary: SPINK1 c.27delC (p.Ser10ValfsX6) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay, which are commonly known mechanisms for disease. The variant allele was found at a frequency of 1.2e-05 in 251284 control chromosomes (gnomAD and Marechal_2004). c.27delC has been reported in the literature in multiple individuals affected with Chronic Pancreatitis. In one family, the variant segregated with the disease in two generations and had penetrance as high as 75%, while in another family the variant seemed to act as a low-penetrance susceptibility factor (Marechal_2004). In a third family with chronic pancreatitis, the reported penetrance was for the variant was 44% (LaRusch_2012). These data indicate that the variant is very likely to be associated with chronic pancreatitis, albeit with variable penetrance. Two other clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. Both laboratories classified the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. - |
not provided, no classification provided | literature only | GeneReviews | - | - - |
Pathogenic, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 24, 2023 | The c.27delC pathogenic mutation, located in coding exon 1 of the SPINK1 gene, results from a deletion of one nucleotide at nucleotide position 27, causing a translational frameshift with a predicted alternate stop codon (p.S10Vfs*6). This mutation has been detected in two families with chronic pancreatitis with reduced penetrance (Le Maréchal C et al. Hum. Mutat., 2004 Feb;23:205; LaRusch J et al. JOP, 2012 May;13:258-62). In HEK293 cells, this mutation showed reduced mRNA levels compared to wild type (Wu H et al. Gut, 2017 12;66:2195-2196). In addition to the clinical data presented in the literature, this alteration is expected to result in loss of function by premature protein truncation or nonsense-mediated mRNA decay. As such, this alteration is interpreted as a disease-causing mutation. - |
not provided Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Sep 28, 2023 | The SPINK1 c.27delC; p.Ser10ValfsTer6 variant (rs193922659) is reported in multiple patients with hereditary pancreatitis (LaRusch 2012, Le Marechal 2004, Masson 2015, Rosendahl 2013). This variant is found in the heterozygous state in affected individuals, but is also present in relatives that do not develop pancreatitis, suggesting that the variant could be associated with an increased risk with pancreatitis even in a heterozygous state (LaRusch 2012, Le Marechal 2004). This variant is reported in ClinVar (Variation ID: 36780), and is only found on three alleles in the Genome Aggregation Database, indicating it is not a common polymorphism. This variant causes a frameshift by deleting a single nucleotide, so it is predicted to result in a truncated protein or mRNA subject to nonsense-mediated decay. Based on available information, this variant is considered pathogenic. References: LaRusch J et al. Whole exome sequencing identifies multiple, complex etiologies in an idiopathic hereditary pancreatitis kindred. JOP. 2012; 13(3):258-62. PMID: 22572128. Le Marechal C et al. Two novel severe mutations in the pancreatic secretory trypsin inhibitor gene (SPINK1) cause familial and/or hereditary pancreatitis. Hum Mutat. 2004; 23(2):205. PMID: 14722925. Masson E et al. Report of 2 CTRC Intronic Mutations Associated With Acute or Chronic Pancreatitis and Delineation of Their Pathogenic Molecular Mechanisms. Pancreas. 2015; 44(6):999-1001. PMID: 26166474. Rosendahl J et al. CFTR, SPINK1, CTRC and PRSS1 variants in chronic pancreatitis: is the role of mutated CFTR overestimated? Gut. 2013; 62(4):582-92. PMID: 22427236. - |
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at