PLAA p.Pro479=
c.1437G>A · rs201133026 · VCV1915201
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0117%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.089 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -5.5 | GERP -3.8 |
| Overall | ||
| CADD | 2.155 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0117%
Admixed American · 7/59,968 alleles
Filtering AF
0.00544%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00381%
Overall
0.00143%
23/1,613,640 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0117% | 8,567 |
| South Asian | 0.00329% | 30,354 |
| East Asian | 0.00223% | 44,866 |
| European (non-Finnish) | 0.00102% | 98,320 |
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
- PLAA
- Protein
- p.Pro479=
- Coding
- c.1437G>A
- MANE Select
- NM_001031689
- dbSNP
- rs201133026
- Type
- single nucleotide variant
- Location
- chr9:26917146 (GRCh38)
- Gene constraint
- LOEUF 0.678 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 84.87 · 5 PDB
Similar variants
- PLAA p.Pro479Leu Uncertain significance ★★ same residue
- PLAA p.Arg524Ter Likely pathogenic ★★ same type
- PLAA p.Ala156Val Uncertain significance ★★ ⚠ same type
- PLAA p.Ala264Thr Uncertain significance ★★ ⚠ same type
- PLAA p.Ala271Val Uncertain significance ★★ ⚠ same type
- PLAA p.Arg268Gln Uncertain significance ★★ ⚠ same type
- PLAA p.Arg373Thr Uncertain significance ★★ ⚠ same type
- PLAA p.Arg499Cys 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/plaa-p-pro479 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown