PEX10 p.Cys288=
c.864C>T · rs762621687 · VCV749376
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.136%, sas)
Conditions
2
Peroxisome biogenesis disorder, complementation group 7
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 -3.7 | GERP -4.1 |
| Overall | ||
| CADD | 6.315 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.136%
South Asian · 124/91,082 alleles
Filtering AF
0.117%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.109%
Overall
0.00862%
139/1,613,074 alleles · rare
exomes 135/1,460,876 · genomes 4/152,198 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.136% | 735 |
| Middle Eastern | 0.0496% | 2,017 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,238 |
| Admixed American | 0.00167% | 60,004 |
| European (non-Finnish) | 0.000763% | 131,109 |
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
- PEX10
- Protein
- p.Cys288=
- Coding
- c.864C>T
- MANE Select
- NM_002617
- dbSNP
- rs762621687
- Type
- single nucleotide variant
- Location
- chr1:2406532 (GRCh38)
- Gene constraint
- LOEUF 1.234 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 82.81
- Residue 288
- a binding site; a UniProt-annotated variant site (in pbd6b and pbd6a)
Similar variants
- PEX10 c.113-1G>A Likely pathogenic ★★ same condition
- PEX10 c.600+1G>A Pathogenic/Likely pathogenic ★★ same condition
- PEX10 c.776+1G>A Likely pathogenic ★★ same condition
- PEX10 c.776+1G>C Pathogenic/Likely pathogenic ★★ same condition
- PEX10 c.776+2T>C Likely pathogenic ★★ same condition
- PEX10 c.777-1G>A Likely pathogenic ★★ same condition
- PEX10 c.912+1G>C Pathogenic/Likely pathogenic ★★ same condition
- PEX10 c.913-1G>A 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/pex10-p-cys288 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown