NM_002769.5(PRSS1):c.361G>A (p.Ala121Thr) AND Hereditary pancreatitis

Germline classification:
Uncertain significance (3 submissions)
Last evaluated:
Jan 6, 2024
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:
RCV000012660.14

Allele description [Variation Report for NM_002769.5(PRSS1):c.361G>A (p.Ala121Thr)]

NM_002769.5(PRSS1):c.361G>A (p.Ala121Thr)

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.361G>A (p.Ala121Thr)
HGVS:
  • NC_000007.14:g.142751934G>A
  • NG_001333.2:g.585602G>A
  • NG_008307.3:g.7451G>A
  • NM_002769.5:c.361G>AMANE SELECT
  • NP_002760.1:p.Ala121Thr
  • LRG_1013t1:c.361G>A
  • LRG_1013:g.7451G>A
  • LRG_1013p1:p.Ala121Thr
  • NC_000007.13:g.142459785G>A
  • NM_002769.4:c.361G>A
Protein change:
A121T; ALA121THR
Links:
OMIM: 276000.0011; dbSNP: rs199422123
NCBI 1000 Genomes Browser:
rs199422123
Molecular consequence:
  • NM_002769.5:c.361G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

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

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000032895OMIM
no assertion criteria provided
Uncertain significance
(May 1, 2010)
germlineliterature only

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

SCV000961857Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Uncertain significance
(Jan 6, 2024)
germlineclinical testing

PubMed (6)
[See all records that cite these PMIDs]

SCV002616316Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)
Uncertain significance
(Nov 22, 2023)
germlineclinical testing

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

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
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

Prevalence of pancreatic diabetes in patients carrying mutations or polymorphisms of the PRSS1 gene in the Han population.

Liu QC, Zhuang ZH, Zeng K, Cheng ZJ, Gao F, Wang ZQ.

Diabetes Technol Ther. 2009 Dec;11(12):799-804. doi: 10.1089/dia.2009.0051.

PubMed [citation]
PMID:
20001681
See all PubMed Citations (6)

Details of each submission

From OMIM, SCV000032895.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (2)

Description

This variant, formerly titled HEREDITARY PANCREATITIS, has been reclassified based on the findings of Szmola and Sahin-Toth (2010).

In affected members of a family with hereditary pancreatitis (167800), Felderbauer et al. (2008) identified a heterozygous G-to-A transition in exon 3 of the PRSS1 gene, resulting in an ala121-to-thr (A121T) substitution. The proband had relatively late disease onset in his thirties, and family history indicated reduced penetrance. In vitro functional expression studies showed that the mutant protein resulted in increased digestion by trypsin (more than 80% compared to wildtype PRSS1) that was calcium-dependent. The findings were consistent with a increased autodegradation and a loss of function mechanism, which was opposite to that observed with the common R122H mutation (276000.0001).

Szmola and Sahin-Toth (2010) presented evidence that the A121T variant is functionally innocuous and not a cause of pancreatitis. The authors noted that only the index patient in the report of Felderbauer et al. (2008) carried the A121T variant and suffered from chronic pancreatitis. The patient's brother and first cousin, who both carried the variant, had cholelithiasis, and his niece and her mother were asymptomatic carriers. Functional expression studies by Szmola and Sahin-Toth (2010) indicated that autoactivation of trypsinogens by the A121T variant was similar to wildtype with equal enzyme kinetics. Szmola and Sahin-Toth (2010) suggested that the variant may have been assigned clinical relevance based on a perceived analogy with the neighboring disease-causing R122H mutations (276000.0001 and 276000.0008).

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

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000961857.6

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (6)

Description

This sequence change replaces alanine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 121 of the PRSS1 protein (p.Ala121Thr). 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 chronic pancreatitis (PMID: 16791840, 18272034, 18511571, 20001681). ClinVar contains an entry for this variant (Variation ID: 11885). 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 with a negative predictive value of 80%. Experimental studies are conflicting or provide insufficient evidence to determine the effect of this variant on PRSS1 function (PMID: 18511571, 20452997). 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.

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

From Ambry Genetics, SCV002616316.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)

Description

The p.A121T variant (also known as c.361G>A), located in coding exon 3 of the PRSS1 gene, results from a G to A substitution at nucleotide position 361. The alanine at codon 121 is replaced by threonine, an amino acid with similar properties. This alteration was first described in an individual with pancreatitis; however, four family members who carried this variant did not have pancreatitis. The same study found this variant resulted in an increased rate of trypsin cleavage (Felderbauer P et al. J. Med. Genet. 2008; 45:507-12). One study found a significant correlation between individuals who carried this alteration and pancreatitis (Liu QC et al. Chin. Med. J. 2008; 121:108-11). However, an additional study found this variant had no effect on auto-activation, degradation, secretion, or kinetic parameters of trypsin (Szmola R and Sahin-Tóth M J. Med. Genet. 2010; 47:348-50). This amino acid position is poorly conserved in available vertebrate species. In addition, the in silico prediction for this alteration is inconclusive. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.

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

Last Updated: Sep 29, 2024