PEX13 p.Val348=
c.1044T>C · rs151304822 · VCV290950
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.302%, afr)
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 1.7 | GERP 0.056, phastCons 1 |
| Overall | ||
| CADD | 5.439 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.302%
African / African-American · 227/75,044 alleles
Filtering AF
0.27%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.258%
Overall
0.02%
323/1,614,154 alleles · rare
exomes 176/1,461,870 · genomes 147/152,284 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.302% | 331 |
| Middle Eastern | 0.115% | 866 |
| Remaining individualsnot grpmax-eligible | 0.0624% | 1,603 |
| Admixed American | 0.0467% | 2,143 |
| South Asian | 0.00549% | 18,215 |
| European (non-Finnish) | 0.00144% | 69,414 |
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.Val348=
- Coding
- c.1044T>C
- MANE Select
- NM_002618
- dbSNP
- rs151304822
- Type
- single nucleotide variant
- Location
- chr2:61048602 (GRCh38)
- Gene constraint
- LOEUF 1.159 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 65.62 · 3 PDB
Similar variants
- PEX13 p.Val348Ile Uncertain significance ★ ⚠ same residue
- PEX13 p.Val348Leu 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
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-val348 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown