PRSS56 p.Pro603=
c.1809C>G · VCV4960561
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.272%, sas)
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 -3.5 | GERP -1.9 |
| Overall | ||
| CADD | 0.563 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.272%
South Asian · 210/77,130 alleles
Filtering AF
0.242%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.23%
Overall
0.0202%
298/1,476,266 alleles · rare
exomes 284/1,324,158 · genomes 14/152,108 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.272% | 367 |
| Remaining individualsnot grpmax-eligible | 0.014% | 7,157 |
| European (non-Finnish) | 0.00683% | 14,634 |
| African / African-American | 0.00421% | 23,765 |
| Finnishnot grpmax-eligible | 0.00235% | 42,488 |
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
- PRSS56
- Protein
- p.Pro603=
- Coding
- c.1809C>G
- MANE Select
- NM_001195129
- Type
- single nucleotide variant
- Location
- chr2:232525503 (GRCh38)
- Gene constraint
- LOEUF 1.11 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 74.35
- Residue 603
- the 'disordered' region
Similar variants
- PRSS56 p.Ala502Thr Uncertain significance ★★ ⚠ same type
- PRSS56 p.Ala57Val Uncertain significance ★★ ⚠ same type
- PRSS56 p.Ala600Thr Uncertain significance ★★ ⚠ same type
- PRSS56 p.Arg247Cys Uncertain significance ★★ ⚠ same type
- PRSS56 p.Asp254Asn Uncertain significance ★★ ⚠ same type
- PRSS56 p.Asp285Asn Uncertain significance ★★ ⚠ same type
- PRSS56 p.Gly538Ser Uncertain significance ★★ ⚠ same type
- PRSS56 p.Leu483Phe Uncertain significance ★★ ⚠ 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/prss56-p-pro603 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown