Is PEPD p.Phe363fs (c.1086_1087del) pathogenic?

PEPD p.Phe363fs (c.10861087del) is classified Pathogenic in PEPD (ClinVar, Single submitter, 1 submitter; last evaluated 2022-10-13). Absent from gnomAD.

How common is PEPD p.Phe363fs (c.1086_1087del) in the general population?

PEPD p.Phe363fs (c.1086_1087del) is absent from gnomAD (gnomAD).

PEPD p.Phe363fs

c.1086_1087del · rs2513380450 · VCV2146250

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

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 13 of 15
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 11	GERP 2.1, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: PEPD
Protein: p.Phe363fs
Coding: c.1086_1087del
MANE Select: NM_000285
dbSNP: rs2513380450
Type: Microsatellite
Location: chr19:33391360 (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 363: an α-helix

Full PEPD gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

PEPD p.Phe363= Likely benign ★ same residue
PEPD p.Phe434fs Pathogenic/Likely pathogenic ★★ same type
PEPD p.Ser142fs 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-phe363fs (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown