PSMA2 p.Pro129=
c.387A>G · rs28503255 · VCV708758
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.706%, 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 -1.2 | GERP -5, phastCons 0.002 |
| Overall | ||
| CADD | 6.18 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.706%
European (non-Finnish) · 8,320/1,178,562 alleles
Filtering AF
0.693%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.688%
Overall
0.564%
9,093/1,612,378 alleles · rare
exomes 8,494/1,460,086 · genomes 599/152,292 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.706% | 142 |
| Remaining individualsnot grpmax-eligible | 0.561% | 178 |
| Admixed American | 0.338% | 296 |
| Ashkenazi Jewishnot grpmax-eligible | 0.173% | 580 |
| African / African-American | 0.129% | 773 |
| Middle Eastern | 0.0991% | 1,009 |
| Finnishnot grpmax-eligible | 0.0875% | 1,143 |
| South Asian | 0.011% | 9,103 |
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
- PSMA2
- Protein
- p.Pro129=
- Coding
- c.387A>G
- MANE Select
- NM_002787
- dbSNP
- rs28503255
- Type
- single nucleotide variant
- Location
- chr7:42923394 (GRCh38)
- Gene constraint
- LOEUF 0.243 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 94.74 · 177 PDB
- Residue 129
- an α-helix
Similar variants
- PSMA2 p.Ala2Thr Uncertain significance ★ ⚠ same type
- PSMA2 p.Asp58Glu Uncertain significance ★ ⚠ same type
- PSMA2 p.Gln96Arg Uncertain significance ★ ⚠ same type
- PSMA2 p.Glu215Gly Uncertain significance ★ ⚠ same type
- PSMA2 p.Pro144Ser Uncertain significance ★ ⚠ same type
- PSMA2 p.Ser9Trp 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/psma2-p-pro129 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown