CEP290 p.Ser1497Ter
c.4490C>A · rs1345994179 · VCV866451
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | nonsense (stop-gain) | predicted loss-of-function |
|---|---|---|
| NMD | predicted | premature termination codon in exon 35 of 54 |
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 12 | GERP 2.7, phastCons 1 |
| Overall | ||
| CADD | 41.0 | PHRED · no single calibrated threshold — expert panels disagree |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Population frequency
No allele count reported in gnomAD v4.1 (AN 1,610,746). 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.Ser1497Ter
- Coding
- c.4490C>A
- MANE Select
- NM_025114
- dbSNP
- rs1345994179
- Type
- single nucleotide variant
- Location
- chr12:88084800 (GRCh38)
- Gene constraint
- LOEUF 1.094 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 60.90
- Residue 1497
- 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)
Similar variants
- CEP290 c.1066-1G>A Pathogenic ★★ same condition
- CEP290 c.1190-2A>G Pathogenic/Likely pathogenic ★★ same condition
- CEP290 c.1711+1G>A Pathogenic/Likely pathogenic ★★ same condition
- CEP290 c.181-2A>G Pathogenic/Likely pathogenic ★★ same condition
- CEP290 c.2052+1G>A Pathogenic/Likely pathogenic ★★ same condition
- CEP290 c.2992-1G>T Likely pathogenic ★★ same condition
- CEP290 c.3461+1G>A Pathogenic/Likely pathogenic ★★ same condition
- CEP290 c.4705-1G>T Pathogenic/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-ser1497ter (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown