Is CPE p.Lys460= (c.1380G>A) pathogenic?

CPE p.Lys460= (c.1380G>A) is classified Likely benign in CPE (ClinVar, No assertion criteria, 1 submitter; last evaluated 2024-03-15). Absent from gnomAD v4.1; Associated with CPE-related disorder.

What condition is associated with CPE p.Lys460= (c.1380G>A)?

CPE p.Lys460= (c.1380G>A) is associated with CPE-related disorder (ClinVar).

How common is CPE p.Lys460= (c.1380G>A) in the general population?

CPE p.Lys460= (c.1380G>A) is absent from gnomAD v4.1 (gnomAD).

CPE p.Lys460=

c.1380G>A · VCV3349955

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,582,662)

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 1.7	GERP -1.9, phastCons 1
Overall
CADD	5.44	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,582,662). 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: CPE
Protein: p.Lys460=
Coding: c.1380G>A
MANE Select: NM_001873
Type: single nucleotide variant
Location: chr4:165497559 (GRCh38)
Gene constraint: LOEUF 0.565 · pLI 0.83 (gnomAD)
Structure: AlphaFold pLDDT 90.83
Residue 460: 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-lys460 (accessed [today's date]).

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