PPIB p.Gly85=
c.255A>G · rs1317320371 · VCV2870885
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00034%, nfe)
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 -0.038 | GERP -3.7, phastCons 0.9 |
| Overall | ||
| CADD | 11.94 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00034%
European (non-Finnish) · 4/1,177,934 alleles
Filtering AF
8e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 5.4e-05%
Overall
0.000248%
4/1,611,852 alleles · very rare
exomes 4/1,459,616 · genomes 0/152,236 · 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.Gly85=
- Coding
- c.255A>G
- MANE Select
- NM_000942
- dbSNP
- rs1317320371
- Type
- single nucleotide variant
- Location
- chr15:64160192 (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 85
- the ppiase cyclophilin-type domain
Similar variants
- PPIB c.344-1G>T Pathogenic/Likely pathogenic ★★ same type
- PPIB c.-91A>C Uncertain significance ★★ same type
- PPIB p.Ala15Thr Uncertain significance ★★ ⚠ same type
- PPIB p.Arg7Ser Uncertain significance ★★ ⚠ same type
- PPIB p.Asn75Ser Uncertain significance ★★ ⚠ same type
- PPIB p.Glu183Ala Uncertain significance ★★ ⚠ same type
- PPIB p.Gly39Trp Uncertain significance ★★ ⚠ same type
- PPIB p.Lys116Arg 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-gly85 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown