CCN6 p.Ser228fs
c.680dup · VCV3725411
Pathogenic
Single submitter
Classification
Pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
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 4 of 5 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 7 | GERP 0.31, phastCons 1 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- CCN6
- Protein
- p.Ser228fs
- Coding
- c.680dup
- MANE Select
- NM_198239
- Type
- Duplication
- Location
- chr6:112068294 (GRCh38)
- Gene constraint
- LOEUF 1.055 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 74.30
- Residue 228
- a UniProt-annotated variant site (in pprd); the tsp type-1 domain; a UniProt-annotated variant site (in pprd; uncertain significance)
Similar variants
- CCN6 p.Cys209fs Pathogenic ★★ same type
- CCN6 p.Gln289fs Pathogenic/Likely pathogenic ★★ same type
- CCN6 c.48+2dup Pathogenic ★ same type
- CCN6 p.Glu243fs Pathogenic ★ same type
- CCN6 p.Leu160fs Pathogenic ★ same type
- CCN6 p.Ser290fs Pathogenic ★ same type
- CCN6 p.Thr267fs Pathogenic ★ same type
- CCN6 p.Thr294fs 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/ccn6-p-ser228fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown