PEX12 p.Gln199=
c.597G>A · rs756193716 · VCV598587
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0134%, afr)
Conditions
1
peroxisome biogenesis disorder 3A (Zellweger)
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 -0.53 | phastCons 0.002 |
| Overall | ||
| CADD | 5.423 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0134%
African / African-American · 10/74,894 alleles
Filtering AF
0.00723%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0055%
Overall
0.000743%
12/1,614,038 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0134% | 7,489 |
| East Asian | 0.00223% | 44,886 |
| European (non-Finnish) | 8.47e-05% | 1,180,043 |
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
- PEX12
- Protein
- p.Gln199=
- Coding
- c.597G>A
- MANE Select
- NM_000286
- dbSNP
- rs756193716
- Type
- single nucleotide variant
- Location
- chr17:35577121 (GRCh38)
- Gene constraint
- LOEUF 1.218 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 81.58
Similar variants
- PEX12 c.126+1G>T Pathogenic/Likely pathogenic ★★ same condition
- PEX12 c.680+1G>A Pathogenic/Likely pathogenic ★★ same condition
- PEX12 p.Arg154Ter Pathogenic/Likely pathogenic ★★ same condition
- PEX12 p.Arg180Ter Pathogenic ★★ same condition
- PEX12 p.Arg202Ter Pathogenic/Likely pathogenic ★★ same condition
- PEX12 p.Gln111Ter Pathogenic/Likely pathogenic ★★ same condition
- PEX12 p.Gln112Ter Pathogenic/Likely pathogenic ★★ same condition
- PEX12 p.Gln209Ter Pathogenic ★★ 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/pex12-p-gln199 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown