Is CEP290 p.Val247fs (c.739_740del) pathogenic?

CEP290 p.Val247fs (c.739740del) is classified Likely pathogenic in CEP290 (ClinVar, Single submitter, 1 submitter; last evaluated 2018-08-15). Absent from gnomAD.

How common is CEP290 p.Val247fs (c.739_740del) in the general population?

CEP290 p.Val247fs (c.739_740del) is absent from gnomAD (gnomAD).

CEP290 p.Val247fs

c.739_740del · rs1592671618 · VCV817762

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

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 10 of 54
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -0.87	GERP -4.5, phastCons 0.006

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.Val247fs
Coding: c.739_740del
MANE Select: NM_025114
dbSNP: rs1592671618
Type: Deletion
Location: chr12:88129806 (GRCh38)
Gene constraint: LOEUF 1.094 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 60.90
Residue 247: the 'self-association (with itself or c-terminus)' region; a UniProt-annotated variant site (in lca10; also found in a patient with night blindness and hearing loss)

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

Similar variants

CEP290 p.Val247Ile Uncertain significance ★★ ⚠ same residue
CEP290 p.Val247Leu Uncertain significance ★★ ⚠ same residue
CEP290 p.Val247= Likely benign ★ same residue
CEP290 c.4438-3del Pathogenic ★★★ same type
CEP290 p.Asn737_Leu738insTer Pathogenic ★★★ same type
CEP290 p.Ile556fs Pathogenic ★★★ same type
CEP290 p.Lys1343fs Pathogenic ★★★ same type
CEP290 p.Lys484fs 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/cep290-p-val247fs (accessed [today's date]).

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