PRSS3 p.Glu32del
c.91GAG[1] · rs3831310 · VCV1225003
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Common
common (popmax 28.2%, sas) — too common for a highly-penetrant pathogenic allele
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -5.7 | GERP -3.7 |
| Overall | ||
| CADD | 10.31 | PHRED · no single calibrated threshold — expert panels disagree |
| Region caveats | ||
| Repeat context | seg dup | · reads may not map uniquely · confidence, not pathogenicity |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
28.2%
South Asian · 25,606/90,698 alleles
Filtering AF
27.9%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 27.8%
Overall
16.8%
270,011/1,610,864 alleles · common
exomes 248,064/1,459,164 · genomes 21,947/151,700 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 28.2% | 4 |
| Finnishnot grpmax-eligible | 20% | 5 |
| European (non-Finnish) | 16.8% | 6 |
| Remaining individualsnot grpmax-eligible | 16.7% | 6 |
| Admixed American | 16.1% | 6 |
| Ashkenazi Jewishnot grpmax-eligible | 13.4% | 7 |
| Middle Eastern | 12.7% | 8 |
| Amishnot grpmax-eligible | 10.4% | 10 |
| East Asian | 8.27% | 12 |
| African / African-American | 6.16% | 16 |
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
- PRSS3
- Protein
- p.Glu32del
- Coding
- c.91GAG[1]
- MANE Select
- NM_002771
- dbSNP
- rs3831310
- Type
- Microsatellite
- Location
- chr9:33796693 (GRCh38)
- Gene constraint
- LOEUF 1.218 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 82.39 · 16 PDB
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/prss3-p-glu32del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown