Is PRSS1 p.Ser174Phe (c.521C>T) pathogenic?

PRSS1 p.Ser174Phe (c.521C>T) is classified Uncertain significance in PRSS1 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-03-16). AlphaMissense: ambiguous (0.4198); Ultra-rare (popmax 0.0165%, mid); Associated with hereditary chronic pancreatitis.

What condition is associated with PRSS1 p.Ser174Phe (c.521C>T)?

PRSS1 p.Ser174Phe (c.521C>T) is associated with hereditary chronic pancreatitis (ClinVar).

How common is PRSS1 p.Ser174Phe (c.521C>T) in the general population?

PRSS1 p.Ser174Phe (c.521C>T) is ultra-rare (popmax 0.0165%, mid) (gnomAD).

What do computational predictors say about PRSS1 p.Ser174Phe (c.521C>T)?

AlphaMissense predicts ambiguous (score 0.4198) — an in-silico prediction, not a clinical call.

PRSS1 p.Ser174Phe

Q: How is Autosomal dominant hereditary chronic pancreatitis inherited?

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

c.521C>T · rs746669985 · VCV1746152

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.4198 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0165%, mid)

Conditions

hereditary chronic pancreatitis

Computational evidence

Protein change
AlphaMissense	0.4198	ambiguous
REVEL	0.599	indeterminate
SaProt	LLR -9.62	tolerated
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 1.7	GERP 1.7, phastCons 0.002
Regional constraint	o/e 1.20	unconstrained · MANE · 3,532 bp · p 0.00039 · regional, not allelic
Overall
CADD	21.5	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0165% Middle Eastern · 1/6,062 alleles

Overall 6.2e-05% 1/1,614,182 alleles · ultra-rare exomes 1/1,461,862 · genomes 0/152,320 · joint denominator

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: PRSS1
Protein: p.Ser174Phe
Coding: c.521C>T
MANE Select: NM_002769
dbSNP: rs746669985
Type: single nucleotide variant
Location: chr7:142752497 (GRCh38)

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)

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-ser174phe (accessed [today's date]).

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