PEPD p.Phe23fs
c.68_69del · rs754287293 · VCV2900634
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | frameshift | predicted loss-of-function |
|---|---|---|
| NMD | predicted | premature termination codon in exon 2 of 15 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 2.8 | GERP 1.9, phastCons 0.99 |
| 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 |
|---|---|---|
| East Asiangrpmax | 0.00223% | 44,876 |
| European (non-Finnish) | 8.48e-05% | 1,179,926 |
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
- PEPD
- Protein
- p.Phe23fs
- Coding
- c.68_69del
- MANE Select
- NM_000285
- dbSNP
- rs754287293
- Type
- Deletion
- Location
- chr19:33512725 (GRCh38)
- Gene constraint
- LOEUF 1.132 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 97.62 · 21 PDB
- Residue 23
- an α-helix
Similar variants
- PEPD p.Phe275fs Pathogenic/Likely pathogenic ★★ same type
- PEPD p.Tyr231del Pathogenic/Likely pathogenic ★★ same type
- PEPD c.968-2_980del Likely pathogenic ★ same type
- PEPD p.Arg233fs Likely pathogenic ★ same type
- PEPD p.Arg99fs Pathogenic ★ same type
- PEPD p.Gln55fs Pathogenic ★ same type
- PEPD p.Glu280fs Pathogenic ★ same type
- PEPD p.Ile180fs Pathogenic ★ 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/pepd-p-phe23fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown