PEX16 p.Ser54=
c.162T>C · rs552583175 · VCV1660854
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0944%, sas)
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 -0.4 | GERP -3.9, phastCons 0.001 |
| Overall | ||
| CADD | 5.071 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0944%
South Asian · 86/91,084 alleles
Filtering AF
0.0782%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0723%
Overall
0.00551%
89/1,613,938 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0944% | 1,059 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,836 |
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.Ser54=
- Coding
- c.162T>C
- MANE Select
- NM_004813
- dbSNP
- rs552583175
- Type
- single nucleotide variant
- Location
- chr11:45916290 (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-ser54 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown