PIBF1 p.Val12=
c.36G>A · VCV4771838
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.022%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.25 | acceptor loss, 14 bp away · masked 0 · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.83 | GERP -2.6, phastCons 1 |
| Overall | ||
| CADD | 8.436 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.022%
Admixed American · 13/59,124 alleles
Filtering AF
0.0129%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0103%
Overall
0.000809%
13/1,607,540 alleles · ultra-rare
exomes 13/1,455,288 · genomes 0/152,252 · 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
- PIBF1
- Protein
- p.Val12=
- Coding
- c.36G>A
- MANE Select
- NM_006346
- Type
- single nucleotide variant
- Location
- chr13:72783505 (GRCh38)
- Gene constraint
- LOEUF 1.235 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 77.70
- Residue 12
- the 'mediates modulation of th2 dominant cytokine production' region; the 'sufficient for nk inhibitory function' region
Similar variants
- PIBF1 p.Asp637Ala Pathogenic/Likely pathogenic ★★ same type
- PIBF1 p.Tyr503Cys Likely pathogenic ★★ ⚠ same type
- PIBF1 p.Ala686Thr Uncertain significance ★★ ⚠ same type
- PIBF1 p.Arg242Cys Uncertain significance ★★ ⚠ same type
- PIBF1 p.Arg423Gly Uncertain significance ★★ ⚠ same type
- PIBF1 p.Arg441Ser Uncertain significance ★★ ⚠ same type
- PIBF1 p.Arg634Ser Uncertain significance ★★ ⚠ same type
- PIBF1 p.Gln394Glu 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/pibf1-p-val12 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown