Is CPE p.Glu459= (c.1377G>A) pathogenic?

CPE p.Glu459= (c.1377G>A) is classified Likely benign in CPE (ClinVar, No assertion criteria, 1 submitter; last evaluated 2020-04-13). Ultra-rare (popmax 0.0274%, amr); Associated with CPE-related disorder.

What condition is associated with CPE p.Glu459= (c.1377G>A)?

CPE p.Glu459= (c.1377G>A) is associated with CPE-related disorder (ClinVar).

How common is CPE p.Glu459= (c.1377G>A) in the general population?

CPE p.Glu459= (c.1377G>A) is ultra-rare (popmax 0.0274%, amr) (gnomAD).

CPE p.Glu459=

c.1377G>A · VCV3350521

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0274%, amr)

Conditions

CPE-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 2.1	GERP -3.5, phastCons 1
Overall
CADD	5.523	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0274% Admixed American · 15/54,654 alleles

Filtering AF 0.0169% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0136%

Overall 0.00112% 16/1,432,374 alleles · ultra-rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.0274%	3,644
Remaining individualsnot grpmax-eligible	0.00163%	61,264

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: CPE
Protein: p.Glu459=
Coding: c.1377G>A
MANE Select: NM_001873
Type: single nucleotide variant
Location: chr4:165497556 (GRCh38)
Gene constraint: LOEUF 0.565 · pLI 0.83 (gnomAD)
Structure: AlphaFold pLDDT 90.83
Residue 459: a UniProt-annotated variant site (in bdvs)

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

Disease context

CPE-related disorder

Similar variants

CPE p.Arg121Ter Pathogenic ★★ same condition
CPE c.974-3C>T Uncertain significance ★ same condition
CPE p.Ile415Met Uncertain significance ★ ⚠ same condition
CPE p.Pro30Ala Uncertain significance ★ ⚠ same condition
CPE c.673-2A>G Uncertain significance same condition
CPE p.Ala231Gly Uncertain significance ⚠ same condition
CPE p.Ala266Ser Uncertain significance ⚠ same condition
CPE p.Ala389Val Uncertain significance ⚠ 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-glu459 (accessed [today's date]).

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