PLG p.Ala494=
c.1482G>A · rs745998201 · VCV2882890
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0329%, mid)
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 -7.7 | GERP -3.2 |
| Overall | ||
| CADD | 0.172 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0329%
Middle Eastern · 2/6,084 alleles
Filtering AF
0.0058%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00295%
Overall
0.00167%
27/1,613,764 alleles · ultra-rare
exomes 26/1,461,650 · genomes 1/152,114 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0329% | 3,042 |
| Admixed American | 0.01% | 10,000 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,822 |
| South Asian | 0.00329% | 30,357 |
| African / African-American | 0.00267% | 37,443 |
| East Asian | 0.00223% | 44,888 |
| European (non-Finnish) | 0.000848% | 117,984 |
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
- PLG
- Protein
- p.Ala494=
- Coding
- c.1482G>A
- MANE Select
- NM_000301
- dbSNP
- rs745998201
- Type
- single nucleotide variant
- Location
- chr6:160731788 (GRCh38)
- Gene constraint
- LOEUF 0.559 · pLI 0.17 (gnomAD)
- Structure
- AlphaFold pLDDT 83.53 · 49 PDB
- Residue 494
- the kringle 5 domain; a UniProt-annotated variant site (in)
Similar variants
- PLG p.Ala494Glu Uncertain significance ★★ ⚠ same residue
- PLG p.Ala494Val Benign/Likely benign ★★ ⚠ same residue
- PLG p.Ala494Thr Uncertain significance ★ ⚠ same residue
- PLG p.Ala494Lys Uncertain significance ★ same residue
- PLG p.Lys330Glu Pathogenic ★★ ⚠ same type
- PLG p.Lys38Glu Pathogenic/Likely pathogenic ★★ ⚠ same type
- PLG c.2271+5G>A Uncertain significance ★★ same type
- PLG c.669-3C>G 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/plg-p-ala494 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown