CPLANE1 p.Ser2746fs
c.8237del · VCV4279011
Pathogenic
Single submitter
Classification
Pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
Conditions
1
Joubert syndrome 17
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 42 of 53 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP -0.064 | GERP -3, phastCons 0.2 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- CPLANE1
- Protein
- p.Ser2746fs
- Coding
- c.8237del
- MANE Select
- NM_001384732
- Type
- Deletion
- Location
- chr5:37153876 (GRCh38)
- Gene constraint
- LOEUF 0.728 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Residue 2746
- a UniProt-annotated variant site (in ofd6; likely pathogenic)
Similar variants
- CPLANE1 p.Asn1182fs Pathogenic ★★ same condition
- CPLANE1 p.Gly2717fs Pathogenic ★★ same condition
- CPLANE1 p.Ile165fs Pathogenic ★★ same condition
- CPLANE1 p.Ile1889_Asp1890insTer Likely pathogenic ★★ same condition
- CPLANE1 p.Leu465fs Pathogenic/Likely pathogenic ★★ same condition
- CPLANE1 p.Lys1071fs Likely pathogenic ★★ same condition
- CPLANE1 p.Lys1186fs Pathogenic/Likely pathogenic ★★ same condition
- CPLANE1 p.Lys2345fs 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/cplane1-p-ser2746fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown