PEX3 p.Asn285=
c.855C>T · rs998759519 · VCV2123863
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00134%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 2.7 | GERP 0.25, phastCons 1 |
| Overall | ||
| CADD | 6.466 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00134%
African / African-American · 1/74,372 alleles
Overall
0.000126%
2/1,589,696 alleles · very rare
exomes 1/1,437,720 · genomes 1/151,976 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00134% | 74,372 |
| European (non-Finnish) | 8.63e-05% | 1,158,174 |
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.Asn285=
- Coding
- c.855C>T
- MANE Select
- NM_003630
- dbSNP
- rs998759519
- Type
- single nucleotide variant
- Location
- chr6:143479112 (GRCh38)
- Gene constraint
- LOEUF 0.972 · pLI 0.12 (gnomAD)
- Structure
- AlphaFold pLDDT 88.94 · 2 PDB
- Residue 285
- 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-asn285 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown