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NM_002769.5(PRSS1):c.365G>C (p.Arg122Pro) AND Hereditary pancreatitis

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Sep 30, 2019
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
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:
RCV001237007.8

Allele description [Variation Report for NM_002769.5(PRSS1):c.365G>C (p.Arg122Pro)]

NM_002769.5(PRSS1):c.365G>C (p.Arg122Pro)

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.365G>C (p.Arg122Pro)
HGVS:
  • NC_000007.14:g.142751938G>C
  • NG_001333.2:g.585606G>C
  • NG_008307.3:g.7455G>C
  • NM_002769.5:c.365G>CMANE SELECT
  • NP_002760.1:p.Arg122Pro
  • LRG_1013t1:c.365G>C
  • LRG_1013:g.7455G>C
  • LRG_1013p1:p.Arg122Pro
  • NC_000007.13:g.142459789G>C
  • NM_002769.4:c.365G>C
Protein change:
R122P
Links:
dbSNP: rs111033565
NCBI 1000 Genomes Browser:
rs111033565
Molecular consequence:
  • NM_002769.5:c.365G>C - 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
SCV001409752Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Uncertain significance
(Sep 30, 2019)
germlineclinical testing

PubMed (5)
[See all records that cite these PMIDs]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Hereditary pancreatitis is caused by a mutation in the cationic trypsinogen gene.

Whitcomb DC, Gorry MC, Preston RA, Furey W, Sossenheimer MJ, Ulrich CD, Martin SP, Gates LK Jr, Amann ST, Toskes PP, Liddle R, McGrath K, Uomo G, Post JC, Ehrlich GD.

Nat Genet. 1996 Oct;14(2):141-5.

PubMed [citation]
PMID:
8841182

Chronic pancreatitis: genetics and pathogenesis.

Chen JM, FĂ©rec C.

Annu Rev Genomics Hum Genet. 2009;10:63-87. doi: 10.1146/annurev-genom-082908-150009. Review.

PubMed [citation]
PMID:
19453252
See all PubMed Citations (5)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001409752.5

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (5)

Description

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. This variant disrupts the p.Arg122 amino acid residue in PRSS1. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 8841182, 19453252, 11748242, 11097832). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Tolerated"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C0"). This variant has not been reported in the literature in individuals with PRSS1-related conditions. This variant is not present in population databases (ExAC no frequency). This sequence change replaces arginine with proline at codon 122 of the PRSS1 protein (p.Arg122Pro). The arginine residue is moderately conserved and there is a moderate physicochemical difference between arginine and proline.

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

Last Updated: Sep 29, 2024