Is PRSS1 p.Ala134= (c.402C>T) pathogenic?

PRSS1 p.Ala134= (c.402C>T) is classified Likely benign in PRSS1 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-08-31). Very rare (popmax 0.00168%, amr); Associated with hereditary chronic pancreatitis.

What condition is associated with PRSS1 p.Ala134= (c.402C>T)?

PRSS1 p.Ala134= (c.402C>T) is associated with hereditary chronic pancreatitis (ClinVar).

How common is PRSS1 p.Ala134= (c.402C>T) in the general population?

PRSS1 p.Ala134= (c.402C>T) is very rare (popmax 0.00168%, amr) (gnomAD).

PRSS1 p.Ala134=

Q: How is Autosomal dominant hereditary chronic pancreatitis inherited?

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

c.402C>T · rs762609976 · VCV1737175

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00168%, amr)

Conditions

hereditary chronic pancreatitis

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -14	GERP -3.7
Overall
CADD	0.836	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00168% Admixed American · 1/59,474 alleles

Overall 0.000249% 4/1,609,228 alleles · very rare exomes 3/1,461,850 · genomes 1/147,378 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00168%	59,474
Remaining individualsnot grpmax-eligible	0.0016%	62,432
African / African-American	0.00137%	72,980
European (non-Finnish)	8.49e-05%	1,178,486

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.Ala134=
Coding: c.402C>T
MANE Select: NM_002769
dbSNP: rs762609976
Type: single nucleotide variant
Location: chr7:142751975 (GRCh38)
Gene constraint: LOEUF 1.301 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 92.24 · 12 PDB
Residue 134: 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.Ala134Thr Uncertain significance ★★ ⚠ same residue
PRSS1 p.Ala16Val Pathogenic/Likely pathogenic ★★ ⚠ same condition
PRSS1 p.Arg116Cys 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
PRSS1 c.200+1G>C Uncertain significance ★★ same condition
PRSS1 c.201-7C>A Uncertain significance ★★ 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-ala134 (accessed [today's date]).

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