Is CEP63 p.Glu411= (c.1233A>G) pathogenic?

CEP63 p.Glu411= (c.1233A>G) is classified Likely benign in CEP63 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-12-11). Absent from gnomAD v4.1.

How common is CEP63 p.Glu411= (c.1233A>G) in the general population?

CEP63 p.Glu411= (c.1233A>G) is absent from gnomAD v4.1 (gnomAD).

CEP63 p.Glu411=

c.1233A>G · rs2547029984 · VCV2030294

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.056	moderately benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 1.9	GERP -0.5, phastCons 1
Overall
CADD	8.159	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: CEP63
Protein: p.Glu411=
Coding: c.1233A>G
MANE Select: NM_001353108
dbSNP: rs2547029984
Type: single nucleotide variant
Location: chr3:134550113 (GRCh38)
Gene constraint: LOEUF 1.127 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 77.95 · 4 PDB

Full CEP63 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CEP63 c.1067+2T>C Likely pathogenic ★★ same type
CEP63 c.790-2A>G Likely pathogenic ★★ same type
CEP63 p.Arg150His Uncertain significance ★★ ⚠ same type
CEP63 p.Arg215Trp Uncertain significance ★★ ⚠ same type
CEP63 p.Arg229Cys Uncertain significance ★★ ⚠ same type
CEP63 p.Arg312Gln Uncertain significance ★★ ⚠ same type
CEP63 p.Arg46His Uncertain significance ★★ ⚠ same type
CEP63 p.Arg474His Uncertain significance ★★ ⚠ 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/cep63-p-glu411 (accessed [today's date]).

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