PEX12 p.Phe330fs
c.987_988del · rs764657253 · VCV557980
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | frameshift | predicted loss-of-function |
|---|---|---|
| NMD | escapes | premature termination codon in the last exon (3 of 3) — the truncated protein is likely expressed. PVS1 input, not an applied code |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 7.4 | phastCons 1 |
| Overall | ||
| CADD | 32.0 | PHRED · no single calibrated threshold — expert panels disagree |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Population frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00934% | 10,704 |
| South Asian | 0.0022% | 45,546 |
| Admixed American | 0.00167% | 60,010 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,490 |
| European (non-Finnish) | 0.00119% | 84,288 |
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
- PEX12
- Protein
- p.Phe330fs
- Coding
- c.987_988del
- MANE Select
- NM_000286
- dbSNP
- rs764657253
- Type
- Microsatellite
- Location
- chr17:35575874 (GRCh38)
- Gene constraint
- LOEUF 1.218 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 81.58
- Residue 330
- a UniProt-annotated variant site (in pbd3a)
Similar variants
- PEX12 p.Asn291_Ser292insTer Pathogenic ★★ same condition
- PEX12 p.Cys304fs Pathogenic/Likely pathogenic ★★ same condition
- PEX12 p.Cys307fs Pathogenic/Likely pathogenic ★★ same condition
- PEX12 p.Gln178del Pathogenic/Likely pathogenic ★★ same condition
- PEX12 p.Gln349del Pathogenic/Likely pathogenic ★★ same condition
- PEX12 p.Leu297fs Pathogenic ★★ same condition
- PEX12 p.Phe324fs Pathogenic/Likely pathogenic ★★ same condition
- PEX12 p.Arg102fs Pathogenic ★ same condition
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/pex12-p-phe330fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown