PEX3 p.Val336=
c.1008T>C · rs141932856 · VCV286358
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.412%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.27 | donor gain, 30 bp away · masked 0 · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.61 | GERP -3.1, phastCons 0.073 |
| Overall | ||
| CADD | 4.55 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.412%
African / African-American · 308/74,810 alleles
Filtering AF
0.374%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.359%
Overall
0.0213%
342/1,603,870 alleles · rare
exomes 157/1,451,660 · genomes 185/152,210 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.412% | 243 |
| Remaining individualsnot grpmax-eligible | 0.0209% | 4,780 |
| Admixed American | 0.0167% | 5,995 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00339% | 29,488 |
| Finnishnot grpmax-eligible | 0.00156% | 63,984 |
| European (non-Finnish) | 0.000769% | 130,100 |
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
- PEX3
- Protein
- p.Val336=
- Coding
- c.1008T>C
- MANE Select
- NM_003630
- dbSNP
- rs141932856
- Type
- single nucleotide variant
- Location
- chr6:143485218 (GRCh38)
- Gene constraint
- LOEUF 0.972 · pLI 0.12 (gnomAD)
- Structure
- AlphaFold pLDDT 88.94 · 2 PDB
- Residue 336
- an α-helix
Similar variants
- PEX3 c.288-1G>A Pathogenic/Likely pathogenic ★★ same type
- PEX3 c.942-1G>T Likely pathogenic ★★ same type
- PEX3 p.Arg256Ter Pathogenic/Likely pathogenic ★★ same type
- PEX3 p.Arg286Ter Pathogenic ★★ same type
- PEX3 p.Trp6Ter Pathogenic ★★ same type
- PEX3 c.818+3A>G Uncertain significance ★★ same type
- PEX3 c.-96G>T Uncertain significance ★★ same type
- PEX3 p.Ala358Val Uncertain significance ★★ ⚠ same type
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/pex3-p-val336 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown