CEP290 p.Lys2139fs
c.6416_6417del · VCV4813872
Likely pathogenic
Single submitter
Classification
Likely pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
Conditions
1
focal segmental glomerulosclerosis
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 47 of 54 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 7.7 | GERP 2.4, phastCons 1 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- CEP290
- Protein
- p.Lys2139fs
- Coding
- c.6416_6417del
- MANE Select
- NM_025114
- Type
- Deletion
- Location
- chr12:88060935 (GRCh38)
- Gene constraint
- LOEUF 1.094 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 60.90
- Residue 2139
- 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
Similar variants
- CEP290 p.Lys2139_Val2140insTer Likely pathogenic ★ same residue
- CEP290 p.Glu842fs Likely pathogenic ★ same condition
- CEP290 p.Leu821fs Likely pathogenic ★ same condition
- CEP290 p.Lys2139Asn Uncertain significance ★ ⚠ 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
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-lys2139fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown