PSMA1 p.Val229=
c.687G>A · rs61732660 · VCV716419
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 3.02%, afr)
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 -0.64 | GERP -3.7, phastCons 0.018 |
| Overall | ||
| CADD | 4.491 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.02%
African / African-American · 2,262/74,870 alleles
Filtering AF
2.92%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.88%
Overall
0.158%
2,544/1,613,034 alleles · low-frequency
exomes 1,220/1,460,974 · genomes 1,324/152,060 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 3.02% | 33 |
| Admixed American | 0.2% | 500 |
| Remaining individualsnot grpmax-eligible | 0.176% | 568 |
| Middle Eastern | 0.132% | 757 |
| European (non-Finnish) | 0.00356% | 28,080 |
| South Asian | 0.0022% | 45,518 |
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
- PSMA1
- Protein
- p.Val229=
- Coding
- c.687G>A
- MANE Select
- NM_002786
- dbSNP
- rs61732660
- Type
- single nucleotide variant
- Location
- chr11:14507704 (GRCh38)
- Gene constraint
- LOEUF 0.343 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 91.79 · 177 PDB
- Residue 229
- an α-helix
Similar variants
- PSMA1 p.Ala257Thr Uncertain significance ★ ⚠ same type
- PSMA1 p.Arg164His Uncertain significance ★ ⚠ same type
- PSMA1 p.Arg89Leu Uncertain significance ★ ⚠ same type
- PSMA1 p.Asp100Asn Uncertain significance ★ ⚠ same type
- PSMA1 p.Gln166His Uncertain significance ★ ⚠ same type
- PSMA1 p.Glu252Lys Uncertain significance ★ ⚠ same type
- PSMA1 p.Ile144Val Uncertain significance ★ ⚠ same type
- PSMA1 p.Ile161Val 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/psma1-p-val229 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown