Is PRSS1 p.Arg116= (c.348T>G) pathogenic?

PRSS1 p.Arg116= (c.348T>G) is classified Likely benign in PRSS1 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-06-14). Absent from gnomAD v4.1; Associated with hereditary chronic pancreatitis.

What condition is associated with PRSS1 p.Arg116= (c.348T>G)?

PRSS1 p.Arg116= (c.348T>G) is associated with hereditary chronic pancreatitis (ClinVar).

How common is PRSS1 p.Arg116= (c.348T>G) in the general population?

PRSS1 p.Arg116= (c.348T>G) is absent from gnomAD v4.1 (gnomAD).

PRSS1 p.Arg116=

Q: How is Autosomal dominant hereditary chronic pancreatitis inherited?

Typically Autosomal dominant (Orphanet). A genetic counselor can assess individual risk for a family.

c.348T>G · rs773085470 · VCV2563200

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

hereditary chronic pancreatitis

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal.
Splicing
SpliceAI	Δ0.42	acceptor loss, 5 bp away · masked 0 · deltas
Constraint at this position
Conservation	phyloP -7.9	GERP -3.7
Overall
CADD	1.436	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: PRSS1
Protein: p.Arg116=
Coding: c.348T>G
MANE Select: NM_002769
dbSNP: rs773085470
Type: single nucleotide variant
Location: chr7:142751921 (GRCh38)
Gene constraint: LOEUF 1.301 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 92.24 · 12 PDB
Residue 116: a disulfide bond; a UniProt-annotated variant site (in pctt); an α-helix; the peptidase s1 domain

Full PRSS1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

hereditary chronic pancreatitis — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Autosomal dominant hereditary chronic pancreatitis (Orphanet):

Inheritance: Autosomal dominant
Onset: Adolescent, Childhood
Prevalence: 1-9 / 1 000 000 (France)

Similar variants

PRSS1 p.Arg116Cys Pathogenic/Likely pathogenic ★★ same residue
PRSS1 p.Arg116His Uncertain significance ★★ ⚠ same residue
PRSS1 p.Arg116Ser Uncertain significance ★ ⚠ same residue
PRSS1 p.Arg116Pro Likely pathogenic ⚠ same residue
PRSS1 p.Ala16Val Pathogenic/Likely pathogenic ★★ ⚠ same condition
PRSS1 p.Arg122Cys Pathogenic ★★ same condition
PRSS1 p.Arg122His Pathogenic/Likely pathogenic ★★ ⚠ same condition
PRSS1 p.Asn29Ile Pathogenic ★★ ⚠ same condition

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/prss1-p-arg116 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown