Is CPE p.Ser404fs (c.1208dup) pathogenic?

CPE p.Ser404fs (c.1208dup) is classified Likely pathogenic in CPE (ClinVar, Single submitter, 1 submitter; last evaluated 2024-09-03). Associated with BDV syndrome.

What condition is associated with CPE p.Ser404fs (c.1208dup)?

CPE p.Ser404fs (c.1208dup) is associated with BDV syndrome (ClinVar).

CPE p.Ser404fs

c.1208dup · VCV3340503

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

Conditions

BDV syndrome

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 7 of 9
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 9.2	GERP 2, phastCons 1

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

Variant & gene context

Gene: CPE
Protein: p.Ser404fs
Coding: c.1208dup
MANE Select: NM_001873
Type: Duplication
Location: chr4:165493264 (GRCh38)
Gene constraint: LOEUF 0.565 · pLI 0.83 (gnomAD)
Structure: AlphaFold pLDDT 90.83
Residue 404: a UniProt-annotated variant site (in bdvs)

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

Disease context

BDV syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For CPE-related Prader-Willi-like syndrome (Orphanet):

Onset: Childhood, Infancy

Similar variants

CPE c.505-3dup Benign/Likely benign ★★ same condition
CPE p.Arg121Ter Pathogenic ★★ same condition
CPE p.Leu474= Benign/Likely benign ★★ same condition
CPE p.Ser333fs Pathogenic ★ same condition
CPE p.Glu26fs Pathogenic same condition
CPE p.Tyr135Ter 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/cpe-p-ser404fs (accessed [today's date]).

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