Is CEP290 p.Phe2416fs (c.7248del) pathogenic?

CEP290 p.Phe2416fs (c.7248del) is classified Likely pathogenic in CEP290 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-03-06). Absent from gnomAD; Associated with Bardet-Biedl syndrome 14.

What condition is associated with CEP290 p.Phe2416fs (c.7248del)?

CEP290 p.Phe2416fs (c.7248del) is associated with Bardet-Biedl syndrome 14 (ClinVar).

How common is CEP290 p.Phe2416fs (c.7248del) in the general population?

CEP290 p.Phe2416fs (c.7248del) 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.Phe2416fs

c.7248del · rs2499343371 · VCV2680629

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	escapes	premature termination codon in the last exon (54 of 54) — the truncated protein is likely expressed. PVS1 input, not an applied code
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 7.7	GERP 1.5, phastCons 1
Region caveats
Repeat context	seg dup	· reads may not map uniquely · confidence, not pathogenicity

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.Phe2416fs
Coding: c.7248del
MANE Select: NM_025114
dbSNP: rs2499343371
Type: Deletion
Location: chr12:88049376 (GRCh38)
Gene constraint: LOEUF 1.094 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 60.90
Residue 2416: a UniProt-annotated variant site (in lca10; also found in a patient with night blindness and hearing loss); a UniProt-annotated variant site (in lca10); a UniProt-annotated variant site (in lca10, slsn6 and mks4); a UniProt-annotated variant site (in lca10 and slsn6); a UniProt-annotated variant site (in mks4 and jbts5); the 'self-association (with itself or n-terminus)' 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 c.4438-3del Pathogenic ★★★ same condition
CEP290 p.Asn737_Leu738insTer Pathogenic ★★★ same condition
CEP290 p.Ile556fs Pathogenic ★★★ same condition
CEP290 p.Lys1343fs Pathogenic ★★★ same condition
CEP290 p.Lys484fs Pathogenic ★★★ same condition
CEP290 p.Phe1950fs Pathogenic ★★★ same condition
CEP290 p.Ser319fs Pathogenic ★★★ same condition
CEP290 p.Thr55fs 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-phe2416fs (accessed [today's date]).

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