PPIB p.Tyr119=
c.357C>T · VCV3713080
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0174%, 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 -3.4 | GERP -4.5 |
| Overall | ||
| CADD | 6.472 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0174%
African / African-American · 13/74,918 alleles
Filtering AF
0.0103%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00813%
Overall
0.00279%
45/1,614,004 alleles · ultra-rare
exomes 37/1,461,838 · genomes 8/152,166 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0174% | 5,763 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,606 |
| European (non-Finnish) | 0.00246% | 40,690 |
| Admixed American | 0.00167% | 59,990 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,484 |
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.Tyr119=
- Coding
- c.357C>T
- MANE Select
- NM_000942
- Type
- single nucleotide variant
- Location
- chr15:64156896 (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 119
- the ppiase cyclophilin-type domain; a β-strand
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-tyr119 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown