Is CEP290 p.Ser804= (c.2412T>C) pathogenic?

CEP290 p.Ser804= (c.2412T>C) is classified Likely benign in CEP290 (ClinVar, Single submitter, 2 submitters; last evaluated 2025-06-10). Very rare (popmax 0.00141%, sas); Associated with Joubert syndrome.

What condition is associated with CEP290 p.Ser804= (c.2412T>C)?

CEP290 p.Ser804= (c.2412T>C) is associated with Joubert syndrome, Meckel syndrome, Leber congenital amaurosis (ClinVar).

How common is CEP290 p.Ser804= (c.2412T>C) in the general population?

CEP290 p.Ser804= (c.2412T>C) is very rare (popmax 0.00141%, sas) (gnomAD).

CEP290 p.Ser804=

c.2412T>C · VCV4064242

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00141%, sas)

Conditions

Joubert syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.053	moderately benign-leaning
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 2.3	GERP -3.1, phastCons 1
Overall
CADD	7.889	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00141% South Asian · 1/70,714 alleles

Overall 6.86e-05% 1/1,457,790 alleles · very rare exomes 1/1,305,512 · genomes 0/152,278 · joint denominator

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: CEP290
Protein: p.Ser804=
Coding: c.2412T>C
MANE Select: NM_025114
Type: single nucleotide variant
Location: chr12:88109137 (GRCh38)
Gene constraint: LOEUF 1.094 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 60.90
Residue 804: 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

Joubert syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: Meckel syndrome Leber congenital amaurosis nephronophthisis

Similar variants

CEP290 p.Ser804Tyr Uncertain significance ★ ⚠ same residue
CEP290 c.1189+1G>A Pathogenic ★★★ same condition
CEP290 c.1189+2T>C Pathogenic ★★★ same condition
CEP290 c.297+1G>T Pathogenic ★★★ same condition
CEP290 c.2991+1655A>G Pathogenic ★★★ same condition
CEP290 c.6271-8T>G Pathogenic ★★★ same condition
CEP290 p.Arg1272Ter Pathogenic ★★★ same condition
CEP290 p.Arg1465Ter 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-ser804 (accessed [today's date]).

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