PEX3 p.Thr367=
c.1101C>A · rs376501875 · VCV2007758
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 -0.09 | GERP -3.4, phastCons 0.68 |
| Overall | ||
| CADD | 5.079 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00134%
African / African-American · 1/74,538 alleles
Filtering AF
0.000185%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000122%
Overall
0.000438%
7/1,598,848 alleles · very rare
exomes 6/1,446,876 · genomes 1/151,972 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00134% | 74,538 |
| European (non-Finnish) | 0.000514% | 194,423 |
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.Thr367=
- Coding
- c.1101C>A
- MANE Select
- NM_003630
- dbSNP
- rs376501875
- Type
- single nucleotide variant
- Location
- chr6:143489205 (GRCh38)
- Gene constraint
- LOEUF 0.972 · pLI 0.12 (gnomAD)
- Structure
- AlphaFold pLDDT 88.94 · 2 PDB
Similar variants
- PEX3 p.Thr367Ile Uncertain significance ★★ ⚠ same residue
- 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
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-thr367 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown