PEX3 p.Thr116=
c.348T>C · rs760092536 · VCV1528456
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00331%, nfe)
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 -12 | GERP -3.3 |
| Overall | ||
| CADD | 0.147 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00331%
European (non-Finnish) · 39/1,178,976 alleles
Filtering AF
0.00248%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00217%
Overall
0.0026%
42/1,612,632 alleles · very rare
exomes 36/1,460,388 · genomes 6/152,244 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00331% | 30,230 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,209 |
| Admixed American | 0.00167% | 59,996 |
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.Thr116=
- Coding
- c.348T>C
- MANE Select
- NM_003630
- dbSNP
- rs760092536
- Type
- single nucleotide variant
- Location
- chr6:143470977 (GRCh38)
- Gene constraint
- LOEUF 0.972 · pLI 0.12 (gnomAD)
- Structure
- AlphaFold pLDDT 88.94 · 2 PDB
- Residue 116
- an α-helix
Similar variants
- PEX3 p.Thr116Ala 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-thr116 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown