CEP250 p.Ser1310fs
c.3928del · VCV3249632
Pathogenic
No assertion criteria
Classification
Pathogenic
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
Conditions
1
inherited retinal dystrophy
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 29 of 35 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP -0.056 | GERP -4.4 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- CEP250
- Protein
- p.Ser1310fs
- Coding
- c.3928del
- MANE Select
- NM_007186
- Type
- Deletion
- Location
- chr20:35501874 (GRCh38)
- Gene constraint
- LOEUF 0.86 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 64.68 · 1 PDB
- Residue 1310
- a UniProt-annotated variant site (in crdhl2); a UniProt-annotated variant site (in crdhl2; also found in a family with non-syndromic retinitis pigmentosa); a UniProt-annotated variant site (in crdhl2; the retinal involvement is more severe in double homozygotes also carrying a pcare truncating variant)
Similar variants
- CEP250 p.Ser1310= Likely benign ★★ same residue
- CEP250 p.Ala1988Val Uncertain significance ★★ ⚠ same condition
- CEP250 p.Arg1992His Uncertain significance ★★ ⚠ same condition
- CEP250 p.Arg519Trp Uncertain significance ★★ ⚠ same condition
- CEP250 p.Arg632Gly Uncertain significance ★★ ⚠ same condition
- CEP250 p.Leu2178Phe Uncertain significance ★★ ⚠ same condition
- CEP250 p.Arg950Ter Pathogenic ★ same condition
- CEP250 p.1176AQ[4] Conflicting classifications of pathogenicity ★ 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/cep250-p-ser1310fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown