PEX3 p.Lys373=
c.1119A>G · rs2128748372 · VCV1668944
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
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 -0.043 | GERP -3.9, phastCons 0.013 |
| Overall | ||
| CADD | 3.609 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- PEX3
- Protein
- p.Lys373=
- Coding
- c.1119A>G
- MANE Select
- NM_003630
- dbSNP
- rs2128748372
- Type
- single nucleotide variant
- Location
- chr6:143489223 (GRCh38)
- Gene constraint
- LOEUF 0.972 · pLI 0.12 (gnomAD)
- Structure
- AlphaFold pLDDT 88.94 · 2 PDB
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-lys373 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown