PRSS3 p.Ala17=
c.51G>A · rs10117993 · VCV1271011
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 25.7%, afr) — 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 · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -4.4 | GERP -2.3 |
| Overall | ||
| CADD | 1.222 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
25.7%
African / African-American · 15,609/60,760 alleles
Filtering AF
25.4%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 25.2%
Overall
1.45%
20,336/1,402,726 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 25.7% | 4 |
| Admixed American | 2.66% | 38 |
| Amishnot grpmax-eligible | 2.05% | 49 |
| Remaining individualsnot grpmax-eligible | 1.93% | 52 |
| Middle Eastern | 1.54% | 65 |
| Finnishnot grpmax-eligible | 0.66% | 152 |
| Ashkenazi Jewishnot grpmax-eligible | 0.258% | 387 |
| European (non-Finnish) | 0.178% | 561 |
| South Asian | 0.158% | 633 |
| East Asian | 0.0774% | 1,292 |
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.Ala17=
- Coding
- c.51G>A
- MANE Select
- NM_002771 · reported on NM_001197097
- dbSNP
- rs10117993
- Type
- single nucleotide variant
- Location
- chr9:33794842 (GRCh38)
- Gene constraint
- LOEUF 1.218 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 82.39 · 16 PDB
Similar variants
- PRSS3 c.200+112A>G Benign ★★ same type
- PRSS3 c.201-66G>A Benign ★★ same type
- PRSS3 c.592-188T>C Benign ★★ same type
- PRSS3 c.-285+120G>C Benign ★★ same type
- PRSS3 p.Val25Ala Uncertain significance ★ ⚠ same type
- PRSS3 c.200+256A>T Benign ★ same type
- PRSS3 c.201-66G>T Benign ★ same type
- PRSS3 c.591+35C>T Likely benign ★ same type
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-ala17 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown