Is PEPD p.Arg99fs (c.297del) pathogenic?

PEPD p.Arg99fs (c.297del) is classified Pathogenic in PEPD (ClinVar, Single submitter, 1 submitter; last evaluated 2023-08-16). Absent from gnomAD.

How common is PEPD p.Arg99fs (c.297del) in the general population?

PEPD p.Arg99fs (c.297del) is absent from gnomAD (gnomAD).

PEPD p.Arg99fs

c.297del · rs2513524236 · VCV2752938

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 3 of 15
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 8.7	GERP 2, 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.Arg99fs
Coding: c.297del
MANE Select: NM_000285
dbSNP: rs2513524236
Type: Deletion
Location: chr19:33511060 (GRCh38)
Gene constraint: LOEUF 1.132 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 97.62 · 21 PDB

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

Similar variants

PEPD p.Arg99Gly Uncertain significance ★ ⚠ same residue
PEPD p.Arg99Met Uncertain significance ★ ⚠ same residue
PEPD p.Arg99Ser Uncertain significance ★ ⚠ same residue
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.Gln55fs 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-arg99fs (accessed [today's date]).

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