PEX6 p.Ser503=
c.1509T>C · rs1268177698 · VCV1153433
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000513%, nfe)
Conditions
1
peroxisome biogenesis disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.98 | GERP -3 |
| Overall | ||
| CADD | 3.324 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000513%
European (non-Finnish) · 6/1,168,582 alleles
Filtering AF
0.000185%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000121%
Overall
0.000377%
6/1,591,108 alleles · very rare
exomes 6/1,438,904 · genomes 0/152,204 · 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
- PEX6
- Protein
- p.Ser503=
- Coding
- c.1509T>C
- MANE Select
- NM_000287
- dbSNP
- rs1268177698
- Type
- single nucleotide variant
- Location
- chr6:42968469 (GRCh38)
- Gene constraint
- LOEUF 0.799 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 69.87
Similar variants
- PEX6 c.1130+1G>A Likely pathogenic ★★ same condition
- PEX6 c.1233+1G>A Likely pathogenic ★★ same condition
- PEX6 c.1688+1G>A Pathogenic ★★ same condition
- PEX6 c.1689-1G>A Likely pathogenic ★★ same condition
- PEX6 c.1885-1G>A Likely pathogenic ★★ same condition
- PEX6 c.1962-1G>A Pathogenic/Likely pathogenic ★★ same condition
- PEX6 c.2094+1G>A Likely pathogenic ★★ same condition
- PEX6 c.2095-2A>G 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/pex6-p-ser503 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown