PEPD p.Ser142fs
c.425_426del · VCV3628768
Pathogenic
Single submitter
Classification
Pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
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 5 of 15 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 4 | GERP -0.82, phastCons 1 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- PEPD
- Protein
- p.Ser142fs
- Coding
- c.425_426del
- MANE Select
- NM_000285
- Type
- Microsatellite
- Location
- chr19:33493305 (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 142
- a β-strand
Similar variants
- PEPD p.Ser142Phe Uncertain significance ★ ⚠ same residue
- PEPD p.Phe434fs Pathogenic/Likely pathogenic ★★ same type
- PEPD p.Phe363fs Pathogenic ★ same type
- PEPD p.Glu453del Uncertain significance ★ same type
- PEPD p.Phe71del Uncertain significance ★ same type
- PEPD c.1153-13_1153-12del Likely benign ★ same type
- PEPD c.1345-23GT[2] Likely benign ★ same type
- PEPD c.330-16TG[3] Likely benign ★ 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-ser142fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown