PPIG p.Gly136=
c.408G>A · VCV3423540
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0874%, eas)
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 4.4 | GERP 1, phastCons 1 |
| Overall | ||
| CADD | 14.07 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0874%
East Asian · 39/44,644 alleles
Filtering AF
0.0656%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0581%
Overall
0.00256%
41/1,599,520 alleles · ultra-rare
exomes 39/1,447,652 · genomes 2/151,868 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0874% | 1,145 |
| European (non-Finnish) | 0.00017% | 588,100 |
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.Gly136=
- Coding
- c.408G>A
- MANE Select
- NM_004792
- Type
- single nucleotide variant
- Location
- chr2:169614585 (GRCh38)
- Gene constraint
- LOEUF 0.472 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 56.64 · 4 PDB
- Residue 136
- the ppiase cyclophilin-type domain; a turn
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-gly136 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown