PEX10 p.Val229=
c.687G>A · rs752135780 · VCV2812896
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 1,611,006)
Conditions
1
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 -6.2 | GERP -4 |
| Overall | ||
| CADD | 0.517 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
No allele count reported in gnomAD v4.1 (AN 1,611,006). 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
- PEX10
- Protein
- p.Val229=
- Coding
- c.687G>A
- MANE Select
- NM_002617
- dbSNP
- rs752135780
- Type
- single nucleotide variant
- Location
- chr1:2406809 (GRCh38)
- Gene constraint
- LOEUF 1.234 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 82.81
Similar variants
- PEX10 p.Val229Leu Benign/Likely benign ★★ same residue
- PEX10 p.Val229Ala Uncertain significance ⚠ same residue
- PEX10 c.113-1G>A Likely pathogenic ★★ same condition
- PEX10 c.776+1G>A Likely pathogenic ★★ same condition
- PEX10 p.Arg125Ter Pathogenic/Likely pathogenic ★★ same condition
- PEX10 p.Met1Ile Pathogenic/Likely pathogenic ★★ same condition
- PEX10 c.776+5G>A Uncertain significance ★★ same condition
- PEX10 p.Ala150Val 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/pex10-p-val229 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown