PLAA p.Tyr534=
c.1602T>C · rs543116052 · VCV1666236
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0648%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.312 | indeterminate |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 6.2 | GERP -1.1, phastCons 1 |
| Overall | ||
| CADD | 7.81 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0648%
East Asian · 29/44,772 alleles
Filtering AF
0.0462%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.04%
Overall
0.00198%
32/1,613,486 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0648% | 1,544 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,239 |
| South Asian | 0.0011% | 91,072 |
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.Tyr534=
- Coding
- c.1602T>C
- MANE Select
- NM_001031689
- dbSNP
- rs543116052
- Type
- single nucleotide variant
- Location
- chr9:26910393 (GRCh38)
- Gene constraint
- LOEUF 0.678 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 84.87 · 5 PDB
- Residue 534
- the pul domain
Similar variants
- 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
- PLAA p.Arg7Ser 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-tyr534 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown