PEX13 p.Lys386=
c.1158G>A · rs371789976 · VCV336671
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 0.0117%, amr)
Conditions
1
peroxisome biogenesis disorder 11A (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 5.7 | GERP 0.91, phastCons 1 |
| Overall | ||
| CADD | 6.767 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0117%
Admixed American · 7/59,988 alleles
Filtering AF
0.00543%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00381%
Overall
0.00105%
17/1,613,862 alleles · ultra-rare
exomes 12/1,461,702 · genomes 5/152,160 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0117% | 8,570 |
| Remaining individualsnot grpmax-eligible | 0.0064% | 15,622 |
| African / African-American | 0.00267% | 37,453 |
| European (non-Finnish) | 0.000339% | 294,970 |
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
- PEX13
- Protein
- p.Lys386=
- Coding
- c.1158G>A
- MANE Select
- NM_002618
- dbSNP
- rs371789976
- Type
- single nucleotide variant
- Location
- chr2:61048716 (GRCh38)
- Gene constraint
- LOEUF 1.159 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 65.62 · 3 PDB
Similar variants
- PEX13 p.Lys386Asn Uncertain significance ★★ ⚠ same residue
- PEX13 p.Arg16Ter Pathogenic/Likely pathogenic ★★ same condition
- PEX13 p.Arg170Ter Pathogenic/Likely pathogenic ★★ same condition
- PEX13 p.Arg226Ter Pathogenic ★★ same condition
- PEX13 p.Gln131Ter Pathogenic ★★ same condition
- PEX13 p.Glu123Ter Pathogenic ★★ same condition
- PEX13 p.Tyr155Ter Pathogenic/Likely pathogenic ★★ same condition
- PEX13 c.913+3A>G 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/pex13-p-lys386 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown