PEX19 p.Ser286=
c.858G>C · VCV4804560
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000169%, nfe)
Conditions
1
peroxisome biogenesis disorder 12A (Zellweger)
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 Δ0.47 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -9.1 | GERP -5.4 |
| Overall | ||
| CADD | 5.088 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000169%
European (non-Finnish) · 2/1,180,012 alleles
Filtering AF
2.8e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.1e-05%
Overall
0.000124%
2/1,614,132 alleles · very rare
exomes 2/1,461,872 · genomes 0/152,260 · 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
- PEX19
- Protein
- p.Ser286=
- Coding
- c.858G>C
- MANE Select
- NM_002857
- Type
- single nucleotide variant
- Location
- chr1:160279593 (GRCh38)
- Gene constraint
- LOEUF 1.066 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 71.95 · 5 PDB
Similar variants
- PEX19 p.Ser286Ala Uncertain significance ★★ ⚠ same residue
- PEX19 p.Ser286Leu Uncertain significance ★★ ⚠ same residue
- PEX19 p.Ser286Trp Uncertain significance ★★ ⚠ same residue
- PEX19 c.346+2T>C Likely pathogenic ★★ same condition
- PEX19 p.Leu94Ter Likely pathogenic ★★ same condition
- PEX19 p.Lys193Ter Pathogenic/Likely pathogenic ★★ same condition
- PEX19 p.Ser54Leu Pathogenic ★★ ⚠ same condition
- PEX19 c.*1335G>T Uncertain significance ★★ same condition
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/pex19-p-ser286 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown