PLG p.Glu653=
c.1959A>G · rs761856716 · VCV716757
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 6 submitters
gnomAD v4.1
Rare
rare (popmax 0.874%, 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 -2 | GERP -2.6 |
| Overall | ||
| CADD | 0.147 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.874%
Middle Eastern · 53/6,062 alleles
Filtering AF
0.687%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.619%
Overall
0.0162%
262/1,614,172 alleles · rare
exomes 241/1,461,882 · genomes 21/152,290 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.874% | 114 |
| Admixed American | 0.03% | 3,335 |
| Remaining individualsnot grpmax-eligible | 0.0288% | 3,473 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0203% | 4,934 |
| South Asian | 0.0143% | 7,006 |
| European (non-Finnish) | 0.0127% | 7,867 |
| African / African-American | 0.00533% | 18,758 |
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.Glu653=
- Coding
- c.1959A>G
- MANE Select
- NM_000301
- dbSNP
- rs761856716
- Type
- single nucleotide variant
- Location
- chr6:160739149 (GRCh38)
- Gene constraint
- LOEUF 0.559 · pLI 0.17 (gnomAD)
- Structure
- AlphaFold pLDDT 83.53 · 49 PDB
- Residue 653
- the peptidase s1 domain; a β-strand
Similar variants
- 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
- PLG p.Ala216Thr Uncertain significance ★★ ⚠ same type
- PLG p.Ala459Val Uncertain significance ★★ ⚠ same type
- PLG p.Ala494Glu Uncertain significance ★★ ⚠ same type
- PLG p.Ala507Val 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-glu653 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown