PPIB p.Pro124=
c.372C>T · rs11558597 · VCV1582290
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00668%, afr)
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 -11 | GERP -4.5 |
| Overall | ||
| CADD | 2.621 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00668%
African / African-American · 5/74,892 alleles
Filtering AF
0.00255%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00162%
Overall
0.0013%
21/1,614,014 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00668% | 14,978 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,830 |
| South Asian | 0.00329% | 30,360 |
| European (non-Finnish) | 0.000847% | 118,004 |
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.Pro124=
- Coding
- c.372C>T
- MANE Select
- NM_000942
- dbSNP
- rs11558597
- Type
- single nucleotide variant
- Location
- chr15:64156881 (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 124
- 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-pro124 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown