Is CEP290 p.Glu802fs (c.2404_2433delinsAC) pathogenic?

CEP290 p.Glu802fs (c.24042433delinsAC) is classified Likely pathogenic in CEP290 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-02-15). Absent from gnomAD; Associated with Bardet-Biedl syndrome 14.

What condition is associated with CEP290 p.Glu802fs (c.2404_2433delinsAC)?

CEP290 p.Glu802fs (c.2404_2433delinsAC) is associated with Bardet-Biedl syndrome 14 (ClinVar).

How common is CEP290 p.Glu802fs (c.2404_2433delinsAC) in the general population?

CEP290 p.Glu802fs (c.2404_2433delinsAC) is absent from gnomAD (gnomAD).

How is Bardet-Biedl syndrome inherited?

Typically Autosomal recessive, Oligogenic (Orphanet). A genetic counselor can assess individual risk for a family.

CEP290 p.Glu802fs

c.2404_2433delinsAC · rs2500681450 · VCV2680661

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

Bardet-Biedl syndrome 14

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 23 of 54
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 1.5	GERP 1.2, 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: CEP290
Protein: p.Glu802fs
Coding: c.2404_2433delinsAC
MANE Select: NM_025114
dbSNP: rs2500681450
Type: Indel
Location: chr12:88109116 (GRCh38)
Gene constraint: LOEUF 1.094 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 60.90
Residue 802: a UniProt-annotated variant site (in lca10; also found in a patient with night blindness and hearing loss); the 'interaction with iqcb1' region

Full CEP290 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Bardet-Biedl syndrome 14 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Bardet-Biedl syndrome (Orphanet):

Inheritance: Autosomal recessive, Oligogenic
Onset: Antenatal, Childhood, Infancy, Neonatal
Prevalence: 1-9 / 100 000 (Specific population)

Similar variants

CEP290 p.Glu802Gln Uncertain significance ★★ ⚠ same residue
CEP290 c.7031_7034+7delinsAT Pathogenic/Likely pathogenic ★★ same condition
CEP290 p.Arg1622fs Pathogenic ★★ same condition
CEP290 p.Pro1450fs Likely pathogenic ★★ same condition
CEP290 p.Ala1277Leu Uncertain significance ★★ same condition
CEP290 p.Ala76fs Likely pathogenic ★ same condition
CEP290 p.Glu2443_Lys2444delinsTyrTer Likely pathogenic ★ same condition
CEP290 p.Glu480fs Likely 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/cep290-p-glu802fs (accessed [today's date]).

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