PPIB p.Phe24del
c.67TTC[1] · rs775722308 · VCV1392035
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.011%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 2.2 | GERP -0.45, phastCons 1 |
| Overall | ||
| CADD | 19.36 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.011%
South Asian · 10/90,954 alleles
Filtering AF
0.00594%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00454%
Overall
0.00136%
22/1,613,526 alleles · ultra-rare
exomes 16/1,461,144 · genomes 6/152,382 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.011% | 9,095 |
| Admixed American | 0.01% | 9,998 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,440 |
| African / African-American | 0.00133% | 75,058 |
| European (non-Finnish) | 0.000339% | 294,964 |
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.Phe24del
- Coding
- c.67TTC[1]
- MANE Select
- NM_000942
- dbSNP
- rs775722308
- Type
- Microsatellite
- Location
- chr15:64162915 (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 p.Thr147fs Pathogenic ★ same type
- PPIB c.344-16_344-15del Likely benign ★ 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-phe24del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown