PRSS1 p.Leu166=
c.498G>A · rs1798828517 · VCV2099379
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
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 -0.39 | GERP -3.3 |
| Overall | ||
| CADD | 2.737 | 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.Leu166=
- Coding
- c.498G>A
- MANE Select
- NM_002769
- dbSNP
- rs1798828517
- Type
- single nucleotide variant
- Location
- chr7:142752474 (GRCh38)
- Gene constraint
- LOEUF 1.301 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 92.24 · 12 PDB
- Residue 166
- a disulfide bond; the peptidase s1 domain
Disease context
hereditary chronic pancreatitis — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Autosomal dominant hereditary chronic pancreatitis (Orphanet):
- Inheritance
- Autosomal dominant
- Onset
- Adolescent, Childhood
- Prevalence
- 1-9 / 1 000 000 (France)
Similar variants
- PRSS1 p.Leu166Pro 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-leu166 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown