PIGO p.Phe100=
c.300C>T · rs760405794 · VCV383994
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00668%, eas)
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 2.5 | GERP -3, phastCons 1 |
| Overall | ||
| CADD | 7.843 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00668%
East Asian · 3/44,894 alleles
Filtering AF
0.00177%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000891%
Overall
0.000248%
4/1,614,036 alleles · very rare
exomes 1/1,461,868 · genomes 3/152,168 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00668% | 14,965 |
| European (non-Finnish) | 8.47e-05% | 1,180,025 |
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
- PIGO
- Protein
- p.Phe100=
- Coding
- c.300C>T
- MANE Select
- NM_032634
- dbSNP
- rs760405794
- Type
- single nucleotide variant
- Location
- chr9:35095266 (GRCh38)
- Gene constraint
- LOEUF 0.89 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 82.57
Similar variants
- PIGO p.Phe100Leu Uncertain significance ★ ⚠ same residue
- PIGO p.Phe100Ser Uncertain significance ★ ⚠ same residue
- PIGO p.Phe100Val Uncertain significance ★ ⚠ same residue
- PIGO c.2648-1G>A Likely pathogenic ★★ same type
- PIGO c.3069+2T>C Likely pathogenic ★★ same type
- PIGO c.3069+5G>A Pathogenic/Likely pathogenic ★★ same type
- PIGO p.Arg119Trp Likely pathogenic ★★ ⚠ same type
- PIGO p.Arg122Ter Pathogenic/Likely pathogenic ★★ 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/pigo-p-phe100 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown