PPIB p.Gly112=
c.336C>T · rs868257669 · VCV3046326
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.066%, mid)
Conditions
1
PPIB-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.24 | donor gain · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 8.4 | GERP 1.2, phastCons 1 |
| Overall | ||
| CADD | 16.41 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.066%
Middle Eastern · 4/6,058 alleles
Filtering AF
0.0225%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0135%
Overall
0.000248%
4/1,612,398 alleles · ultra-rare
exomes 4/1,460,066 · genomes 0/152,332 · joint denominator
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
- PPIB
- Protein
- p.Gly112=
- Coding
- c.336C>T
- MANE Select
- NM_000942
- dbSNP
- rs868257669
- Type
- single nucleotide variant
- Location
- chr15:64160111 (GRCh38)
- Gene constraint
- LOEUF 1.104 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 91.98 · 8 PDB
- Residue 112
- the ppiase cyclophilin-type domain; a β-strand
Disease context
PPIB-related disorder
Similar variants
- PPIB p.Ala15Thr Uncertain significance ★★ ⚠ same condition
- PPIB p.Asn142Lys Uncertain significance ⚠ same condition
- PPIB c.249+9C>T Likely benign same condition
- PPIB p.Asp99= Likely benign same condition
- PPIB c.-5dup Likely benign same condition
- PPIB c.344-1G>T Pathogenic/Likely pathogenic ★★ same type
- PPIB c.-91A>C Uncertain significance ★★ same type
- PPIB 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/ppib-p-gly112 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown