PEX10 p.Ala28=
c.84G>A · rs1425799977 · VCV1514774
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00146%, sas)
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 -0.46 | GERP -3.9, phastCons 0.097 |
| Overall | ||
| CADD | 13.01 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00146%
South Asian · 1/68,398 alleles
Filtering AF
3.1e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.1e-05%
Overall
0.000212%
3/1,414,268 alleles · very rare
exomes 2/1,262,124 · genomes 1/152,144 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00146% | 68,398 |
| European (non-Finnish) | 0.000184% | 544,310 |
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.Ala28=
- Coding
- c.84G>A
- MANE Select
- NM_002617
- dbSNP
- rs1425799977
- Type
- single nucleotide variant
- Location
- chr1:2412419 (GRCh38)
- Gene constraint
- LOEUF 1.234 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 82.81
Similar variants
- 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
- PEX10 p.Ala163Val Uncertain significance ★★ ⚠ same condition
- PEX10 p.Ala260Asp 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-ala28 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown