PRSS12 p.Val709=
c.2127T>A · rs1742925245 · VCV3026235
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00178%, nfe)
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 -0.28 | GERP -3.4, phastCons 0.002 |
| Overall | ||
| CADD | 0.941 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00178%
European (non-Finnish) · 21/1,180,024 alleles
Filtering AF
0.00114%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000971%
Overall
0.0015%
22/1,461,892 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00178% | 56,192 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,508 |
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
- PRSS12
- Protein
- p.Val709=
- Coding
- c.2127T>A
- MANE Select
- NM_003619
- dbSNP
- rs1742925245
- Type
- single nucleotide variant
- Location
- chr4:118283024 (GRCh38)
- Gene constraint
- LOEUF 0.965 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 77.42
- Residue 709
- the peptidase s1 domain
Similar variants
- PRSS12 c.2320+6G>C Uncertain significance ★★ same type
- PRSS12 c.821-1G>A Uncertain significance ★★ same type
- PRSS12 c.*1615C>T Uncertain significance ★★ same type
- PRSS12 c.*221A>T Uncertain significance ★★ same type
- PRSS12 p.Ala547Asp Uncertain significance ★★ ⚠ same type
- PRSS12 p.Ala79Pro Uncertain significance ★★ ⚠ same type
- PRSS12 p.Arg292Trp Uncertain significance ★★ ⚠ same type
- PRSS12 p.Arg426Gln 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/prss12-p-val709 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown