PEX16 p.Ile113=
c.339C>A · rs947543439 · VCV1403789
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
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.34 | donor gain · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -2.4 | GERP -4.3 |
| Overall | ||
| CADD | 9.394 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000169%
European (non-Finnish) · 2/1,179,998 alleles
Filtering AF
2.8e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.1e-05%
Overall
0.000124%
2/1,614,058 alleles · very rare
exomes 2/1,461,852 · genomes 0/152,206 · 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
- PEX16
- Protein
- p.Ile113=
- Coding
- c.339C>A
- MANE Select
- NM_004813
- dbSNP
- rs947543439
- Type
- single nucleotide variant
- Location
- chr11:45915723 (GRCh38)
- Gene constraint
- LOEUF 0.957 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 83.07
Similar variants
- PEX16 c.888-1G>C Likely pathogenic ★★ same condition
- PEX16 p.Arg176Ter Pathogenic ★★ same condition
- PEX16 p.Arg227Trp Likely pathogenic ★★ same condition
- PEX16 p.Arg287Cys Pathogenic/Likely pathogenic ★★ same condition
- PEX16 p.Arg287His Pathogenic/Likely pathogenic ★★ ⚠ same condition
- PEX16 c.225+3G>A Uncertain significance ★★ same condition
- PEX16 p.Ala114Thr Uncertain significance ★★ ⚠ same condition
- PEX16 p.Arg124Trp 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/pex16-p-ile113 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown