rs143014431

chr5-147824703-T-G

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_Moderate BS2

The NM_001379610.1(SPINK1):c.198A>C(p.Lys66Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000422 in 1,613,856 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

• Frequency:
  • Genomes: 𝑓 0.00034 (0 hom., cov: 32)
  • Exomes 𝑓: 0.00043 (0 hom.)
• Consequence: SPINK1 NM_001379610.1 missense
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:1 U:4
• Conservation: PhyloP100: -0.0960

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]

ACMG classification

Verdict is Likely_benign. Variant got -6 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.068697184).
• BS2: High AC in GnomAd at 51 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SPINK1	NM_001379610.1	c.198A>C	p.Lys66Asn	missense_variant	4/4	ENST00000296695.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SPINK1	ENST00000296695.10	c.198A>C	p.Lys66Asn	missense_variant	4/4	1	NM_001379610.1	P1
SPINK1	ENST00000505722.1	n.113A>C		non_coding_transcript_exon_variant	2/2	2

Frequencies

GnomAD3 genomes AF: 0.000335 AC: 51 AN: 152146 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.000121

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000655

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000661

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.000200 AC: 50 AN: 250312 Hom.: 0 AF XY: 0.000185 AC XY: 25 AN XY: 135352

Gnomad AFR exome AF: 0.000247

Gnomad AMR exome AF: 0.000145

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000345

Gnomad OTH exome AF: 0.000328

GnomAD4 exome AF: 0.000431 AC: 630 AN: 1461710 Hom.: 0 Cov.: 31 AF XY: 0.000414 AC XY: 301 AN XY: 727154

Gnomad4 AFR exome AF: 0.000239

Gnomad4 AMR exome AF: 0.000179

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.000508

Gnomad4 OTH exome AF: 0.000811

GnomAD4 genome AF: 0.000335 AC: 51 AN: 152146 Hom.: 0 Cov.: 32 AF XY: 0.000269 AC XY: 20 AN XY: 74330

Gnomad4 AFR AF: 0.000121

Gnomad4 AMR AF: 0.0000655

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000661

Gnomad4 OTH AF: 0.00

Alfa AF: 0.000302 Hom.: 0

Bravo AF: 0.000272

TwinsUK AF: 0.000539 AC: 2

ALSPAC AF: 0.00 AC: 0

ESP6500AA AF: 0.00 AC: 0

ESP6500EA AF: 0.000465 AC: 4

ExAC AF: 0.000148 AC: 18

EpiCase AF: 0.000382

EpiControl AF: 0.000415

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:1 Uncertain:4

Revision: criteria provided, conflicting classifications

Submissions by phenotype

Hereditary pancreatitis Pathogenic:1 Uncertain:1

Pathogenic, criteria provided, single submitter	clinical testing	Ambry Genetics	Oct 18, 2021	The p.K66N pathogenic mutation (also known as c.198A>C), located in coding exon 4 of the SPINK1 gene, results from an A to C substitution at nucleotide position 198. The lysine at codon 66 is replaced by asparagine, an amino acid with similar properties. This mutation was identified in an individual with pancreatitis (Keiles S et al. Pancreas, 2006 Oct;33:221-7). It was also identified in a child with pancreatitis in conjunction with additional SPINK1 alterations (Giefer MJ et al. J. Pediatr., 2017 Jul;186:95-100). In one study, this mutation resulted in loss of expression of pancreatic secretory trypsin inhibitor (PSTI) in embryonic kidney 293T cells (Boulling A et al. Pancreas, 2012 Mar;41:329-30). Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. -
Uncertain significance, criteria provided, single submitter	clinical testing	Invitae	Dec 16, 2023	This sequence change replaces lysine, which is basic and polar, with asparagine, which is neutral and polar, at codon 66 of the SPINK1 protein (p.Lys66Asn). This variant is present in population databases (rs143014431, gnomAD 0.04%), and has an allele count higher than expected for a pathogenic variant. This missense change has been observed in individual(s) with pancreatitis (PMID: 17003641, 28502372, 33515547). ClinVar contains an entry for this variant (Variation ID: 410699). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. Experimental studies have shown that this missense change affects SPINK1 function (PMID: 22343981). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -

not specified Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Jan 11, 2023

Variant summary: SPINK1 c.198A>C (p.Lys66Asn) results in a non-conservative amino acid change located in the Kazal domain (IPR002350) of the encoded protein sequence. 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 0.0002 in 250312 control chromosomes, predominantly at a frequency of 0.00035 within the Non-Finnish European subpopulation in the gnomAD database. The observed variant frequency within Non-Finnish European control individuals in the gnomAD database is approximately equal to the estimated maximal expected allele frequency for a pathogenic variant in SPINK1 causing Chronic Pancreatitis phenotype (0.00025), suggesting that the variant may be a benign polymorphism found primarily in populations of Non-Finnish European origin. c.198A>C has been reported in the literature in at least two children affected with pancreatitis, one 15-year-old caucasian male referred to genetic testing in whom no other sequence variant in PRSS1, SPINK1 or CFTR genes were identified (Keiles_2006), and in a 1-year-old evaluated as part of the International Study Group of Pediatric Pancreatitis: In Search for a Cure (INSPIRRE) study in whom a co-occurring pathogenic SPINK1 variant (c.101A>G/p.Asn34Ser) was also identified (Giefer_2017). It has also been subsequently cited as a non-primary reference by others (example, Chua_2011, Chen_2012, Kume_2012, Szabo_2021). These data however do not allow any conclusion about variant significance. One study reported a complete loss of expression of the protein product encoding the SPINK1 gene (PTS1) in human embryonic kidney 293T cells transfected with a mutant construct bearing this variant (Boulling_2012). The authors speculate that the possibility of reduced or lack of binding activity of the mutant protein to the monoclonal anti-hPST1 antibody used in their experimental system cannot be ruled out (Boulling_2007). Contradicting this observation, another study reported no difference in splicing or mRNA expression associated with this variant when compared to the wild type, thereby ruling out any impact of this missense variant on pre-mRNA splicing and/or mRNA stability (Wu_2017). Therefore, the functional evidence surrounding this variant is conflicting with authorship overlap between reported studies and later reports (Wu_2017) not citing the previous report (Boulling_2012). Three submitters have provided clinical-significance assessments for this variant to ClinVar after 2014 and classified the variant as either VUS (n=2) or pathogenic (n=1), citing overlapping evidence utilized in the context of this evaluation. Based on the evidence outlined above, until additional reports of this variant segregating with inherited pancreatitis in multiplex families supported by conclusive functional evidence is identified, the variant retained its classification as a variant of uncertain significance. -

not provided Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Mayo Clinic Laboratories, Mayo Clinic

Oct 29, 2019

- -

SPINK1-related condition Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

Jan 29, 2024

The SPINK1 c.198A>C variant is predicted to result in the amino acid substitution p.Lys66Asn. This variant has been reported in the heterozygous state in an individual with chronic pancreatitis and to co-occur with another SPINK1 variant (phase unknown) in an individual with early onset acute pancreatitis (Table 3, Keiles et al. 2006. PubMed ID: 17003641; Table III, Giefer et al. 2017. PubMed ID: 28502372). A full-length gene assay to assess pre-mRNA splicing suggests that this variant does not affect pre-mRNA splicing and/or mRNA stability (Table 1, Wu H et al. 2017. PubMed ID: 28994706). However, a study of protein expression in human embryonic kidney 293T (HEK293T) cells showed this variant causes complete loss of SPINK1 protein compared to control (Figure 1, Boulling et al. 2012. PubMed ID: 22343981). This variant is reported in 0.041% of alleles in individuals of European (Non-Finnish) descent in gnomAD, which is likely too common to be a primary cause of autosomal dominant disease. Conflicting interpretations of pathogenic and uncertain are present in the ClinVar database for the c.198A>C variant (https://www.ncbi.nlm.nih.gov/clinvar/variation/410699). Although this variant may contribute to chronic pancreatitis phenotypes with reduced penetrance, at this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.36
BayesDel_addAF	Benign	-0.48	T
BayesDel_noAF	Benign	-0.54
Cadd	Benign	10
Dann	Uncertain	0.98
DEOGEN2	Benign	0.17	T
Eigen	Benign	-1.1
Eigen_PC	Benign	-1.2
FATHMM_MKL	Benign	0.032	N
LIST_S2	Benign	0.37	T
M_CAP	Benign	0.058	D
MetaRNN	Benign	0.069	T
MetaSVM	Benign	-0.92	T
MutationTaster	Benign	1.0	N
PrimateAI	Benign	0.38	T
PROVEAN	Benign	-2.3	N
REVEL	Benign	0.17
Sift	Uncertain	0.021	D
Sift4G	Benign	0.15	T
Polyphen		0.30	B
Vest4		0.095
MutPred		0.80		Loss of ubiquitination at K66 (P = 0.0326);
MVP		0.43
MPC		0.074
ClinPred		0.032	T
GERP RS		-2.8
Varity_R		0.42
gMVP		0.74

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs143014431; hg19: chr5-147204266;