PEX16 p.Pro19=
c.57G>A · rs911795242 · VCV2697346
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Not reported
no allele count reported in gnomAD v4.1 (AN 1,556,640)
Conditions
1
peroxisome biogenesis disorder
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 -1.1 | GERP -1.7, phastCons 0.001 |
| Overall | ||
| CADD | 12.69 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
No allele count reported in gnomAD v4.1 (AN 1,556,640). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.
Variant & gene context
- Gene
- PEX16
- Protein
- p.Pro19=
- Coding
- c.57G>A
- MANE Select
- NM_004813
- dbSNP
- rs911795242
- Type
- single nucleotide variant
- Location
- chr11:45917755 (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-pro19 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown