PPIB p.Val11=
c.33G>C · rs568054483 · VCV786272
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.02%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · C>T here scores Δ0.61 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.41 | GERP -3.5, phastCons 0.032 |
| Overall | ||
| CADD | 8.67 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.02%
African / African-American · 15/75,034 alleles
Filtering AF
0.0123%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00988%
Overall
0.000992%
16/1,613,566 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.02% | 5,002 |
| European (non-Finnish) | 8.48e-05% | 1,179,866 |
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.Val11=
- Coding
- c.33G>C
- MANE Select
- NM_000942
- dbSNP
- rs568054483
- Type
- single nucleotide variant
- Location
- chr15:64162954 (GRCh38)
- Gene constraint
- LOEUF 1.104 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 91.98 · 8 PDB
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-val11 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown