Is CEP152 p.Glu883fs (c.2646del) pathogenic?

CEP152 p.Glu883fs (c.2646del) is classified Pathogenic in CEP152 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-11-24). Absent from gnomAD.

How common is CEP152 p.Glu883fs (c.2646del) in the general population?

CEP152 p.Glu883fs (c.2646del) is absent from gnomAD (gnomAD).

CEP152 p.Glu883fs

c.2646del · rs2504641181 · VCV2698435

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 19 of 27
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 3.5	GERP 4.8, 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: CEP152
Protein: p.Glu883fs
Coding: c.2646del
MANE Select: NM_001194998
dbSNP: rs2504641181
Type: Deletion
Location: chr15:48760183 (GRCh38)
Gene constraint: LOEUF 0.784 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 61.54 · 3 PDB

Full CEP152 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CEP152 p.Glu883Gly Uncertain significance ★ ⚠ same residue
CEP152 p.Glu883Lys Uncertain significance ★ ⚠ same residue
CEP152 p.Gln1058fs Pathogenic/Likely pathogenic ★★ same type
CEP152 p.Leu1071fs Pathogenic/Likely pathogenic ★★ same type
CEP152 p.Lys764fs Likely pathogenic ★★ same type
CEP152 p.Phe225_Leu226insTer Pathogenic/Likely pathogenic ★★ same type
CEP152 p.Thr1006fs Pathogenic/Likely pathogenic ★★ same type
CEP152 p.Thr386fs 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/cep152-p-glu883fs (accessed [today's date]).

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