PPIG p.Lys231=
c.693A>G · rs141485021 · VCV2651529
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.331%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 8 | GERP 0.61, phastCons 1 |
| Overall | ||
| CADD | 11.48 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.331%
Middle Eastern · 20/6,042 alleles
Filtering AF
0.219%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.183%
Overall
0.157%
2,521/1,603,666 alleles · rare
exomes 2,333/1,451,418 · genomes 188/152,248 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.331% | 302 |
| Ashkenazi Jewishnot grpmax-eligible | 0.204% | 489 |
| European (non-Finnish) | 0.187% | 534 |
| Remaining individualsnot grpmax-eligible | 0.153% | 654 |
| Admixed American | 0.0771% | 1,297 |
| Finnishnot grpmax-eligible | 0.061% | 1,640 |
| South Asian | 0.0377% | 2,653 |
| African / African-American | 0.031% | 3,225 |
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
- PPIG
- Protein
- p.Lys231=
- Coding
- c.693A>G
- MANE Select
- NM_004792
- dbSNP
- rs141485021
- Type
- single nucleotide variant
- Location
- chr2:169630919 (GRCh38)
- Gene constraint
- LOEUF 0.472 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 56.64 · 4 PDB
- Residue 231
- the 'disordered' region
Similar variants
- PPIG c.929+11A>G Benign ★★ same type
- PPIG p.Asn672= Benign ★★ same type
- PPIG p.Glu495= Benign ★★ same type
- PPIG p.Thr54= Benign ★★ same type
- PPIG p.Ala542Thr Uncertain significance ★ ⚠ same type
- PPIG p.Arg235Gln Uncertain significance ★ ⚠ same type
- PPIG p.Arg239Gln Uncertain significance ★ ⚠ same type
- PPIG p.Arg350Lys 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/ppig-p-lys231 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown