U.S. flag

An official website of the United States government

NM_002769.5(PRSS1):c.346C>T (p.Arg116Cys) AND Hereditary pancreatitis

Germline classification:
Pathogenic/Likely pathogenic (6 submissions)
Last evaluated:
May 11, 2023
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV000022814.43

Allele description [Variation Report for NM_002769.5(PRSS1):c.346C>T (p.Arg116Cys)]

NM_002769.5(PRSS1):c.346C>T (p.Arg116Cys)

Genes:
TRB:T cell receptor beta locus [Gene - HGNC]
PRSS1:serine protease 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
7q34
Genomic location:
Preferred name:
NM_002769.5(PRSS1):c.346C>T (p.Arg116Cys)
HGVS:
  • NC_000007.14:g.142751919C>T
  • NG_001333.2:g.585587C>T
  • NG_008307.3:g.7436C>T
  • NM_002769.5:c.346C>TMANE SELECT
  • NP_002760.1:p.Arg116Cys
  • LRG_1013t1:c.346C>T
  • LRG_1013:g.7436C>T
  • LRG_1013p1:p.Arg116Cys
  • NC_000007.13:g.142459770C>T
  • NM_002769.4:c.346C>T
  • P07477:p.Arg116Cys
Protein change:
R116C; ARG116CYS
Links:
UniProtKB: P07477#VAR_011655; OMIM: 276000.0012; dbSNP: rs387906698
NCBI 1000 Genomes Browser:
rs387906698
Molecular consequence:
  • NM_002769.5:c.346C>T - missense variant - [Sequence Ontology: SO:0001583]
Observations:
1

Condition(s)

Name:
Hereditary pancreatitis (PCTT)
Synonyms:
Hereditary chronic pancreatitis
Identifiers:
MONDO: MONDO:0008185; MedGen: C0238339; Orphanet: 676; OMIM: 167800

Recent activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...

Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000044103OMIM
no assertion criteria provided
Pathogenic
(Apr 1, 2009)
germlineliterature only

PubMed (3)
[See all records that cite these PMIDs]

SCV001158034ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
criteria provided, single submitter

(ARUP Molecular Germline Variant Investigation Process 2024)
Pathogenic
(Mar 27, 2023)
germlineclinical testing

Citation Link,

SCV001218550Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Likely pathogenic
(May 5, 2023)
germlineclinical testing

PubMed (10)
[See all records that cite these PMIDs]

SCV001571365Centre for Inherited Metabolic Diseases, Karolinska University Hospital
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Apr 13, 2021)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV002613930Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)
Pathogenic
(May 11, 2023)
germlineclinical testing

PubMed (2)
[See all records that cite these PMIDs]

Citation Link,

SCV003815666Revvity Omics, Revvity
criteria provided, single submitter

(ACMG Guidelines, 2015)
Likely pathogenic
(May 13, 2022)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes1not providednot provided1not providedclinical testing
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Mutations of human cationic trypsinogen (PRSS1) and chronic pancreatitis.

Teich N, Rosendahl J, Tóth M, Mössner J, Sahin-Tóth M.

Hum Mutat. 2006 Aug;27(8):721-30. Review.

PubMed [citation]
PMID:
16791840
PMCID:
PMC2793115

Mutational screening of patients with nonalcoholic chronic pancreatitis: identification of further trypsinogen variants.

Teich N, Bauer N, Mössner J, Keim V.

Am J Gastroenterol. 2002 Feb;97(2):341-6.

PubMed [citation]
PMID:
11866271
See all PubMed Citations (13)

Details of each submission

From OMIM, SCV000044103.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (3)

Description

Teich et al. (2006) reported that the 346C-T transition in exon 3 of the PRSS1 gene, resulting in an arg116-to-cys (R116C) substitution, had been identified by 4 independent groups in Turkish, German, and Thai families with hereditary pancreatitis (167800) and in 2 unrelated French patients with pancreatitis.

In an 11-year-old German girl with hereditary pancreatitis, originally reported by Teich et al. (2002), Kereszturi et al. (2009) showed that trypsinogen misfolding is the likely disease mechanism. The R116C substitution occurs in a surface loop that is highly sensitive to autolytic cleavage. In vitro functional expression studies showed that the R116C mutation resulted in misfolding of the protein, but residual amounts of properly folded protein showed normal activation, catalytic properties, and degradation. Expression of the mutant protein in HEK 293T cells showed decreased secretion compared to wildtype, suggesting that the unpaired cysteine residue at codon 116 interferes with proper protein folding, resulting in the mutant protein being retained inside the cell. Biochemical evidence indicated activation of the unfolded protein response, although there was no evidence of increased caspase-3 (CASP3; 600636) activity. The R116C mutation was also found in the girl's 57-year-old affected maternal grandfather and her 38-year-old unaffected mother, indicating incomplete penetrance.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot providednot providednot providednot providednot provided

From ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories, SCV001158034.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The PRSS1 c.346C>T; p.Arg116Cys variant (rs387906698), is reported in the literature in multiple individuals and families affected with pancreatitis (Kereszturi 2009, Kurian 2014, see link to Chronic Pancreatitis database and references therein). This variant is also reported in ClinVar (Variation ID: 29923). It is observed in the East Asian population with an allele frequency of 0.07% (14/19950 alleles) in the Genome Aggregation Database. Computational analyses are uncertain whether this variant is neutral or deleterious (REVEL: 0.597). However, functional analyses of the variant protein show misfolding and intracellular retention, leading to endoplasmic reticular stress (Kereszturi 2009). Based on available information, the p.Arg116Cys variant is considered to be pathogenic. References: Link to Genetic Risk Factors in Chronic Pancreatitis database: http://pancreasgenetics.org/e107_plugins/aacgc_itemlist/Item_List.php?det.1 Kereszturi E et al. Hereditary pancreatitis caused by mutation-induced misfolding of human cationic trypsinogen: a novel disease mechanism. Hum Mutat. 2009 Apr;30(4):575-82. PMID: 19191323. Kurian AW et al. Clinical evaluation of a multiple-gene sequencing panel for hereditary cancer risk assessment. J Clin Oncol. 2014 Jul 1;32(19):2001-9. PMID: 24733792.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Invitae, SCV001218550.5

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (10)

Description

Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt PRSS1 protein function. ClinVar contains an entry for this variant (Variation ID: 29923). This missense change has been observed in individual(s) with pancreatitis (PMID: 11708864, 11842279, 15786540, 19191323, 19433603, 20502448, 24909264, 30420730). It has also been observed to segregate with disease in related individuals. 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 sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 116 of the PRSS1 protein (p.Arg116Cys). Experimental studies have shown that this missense change affects PRSS1 function (PMID: 19191323, 31521106). In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Centre for Inherited Metabolic Diseases, Karolinska University Hospital, SCV001571365.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednoclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyes1not provideddiscovery1not providednot providednot provided

From Ambry Genetics, SCV002613930.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)

Description

The p.R116C pathogenic mutation (also known as c.346C>T), located in coding exon 3 of the PRSS1 gene, results from a C to T substitution at nucleotide position 346. The arginine at codon 116 is replaced by cysteine, an amino acid with highly dissimilar properties. This mutation has been reported in several unrelated families with hereditary pancreatitis. Furthermore, this mutation was shown to promote misfolding of the enzyme, leading to abnormal retention within cells (Kereszturi E et al. Hum Mutat. 2009; 30(4):575-582). Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Revvity Omics, Revvity, SCV003815666.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: May 1, 2024