CTNNB1 p.Pro100fs
c.299_300del · VCV3342782
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 in a haploinsufficient gene (ClinGen) |
|---|---|---|
| NMD | predicted | premature termination codon in exon 4 of 15 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 7.7 | GERP 2.1, phastCons 1 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- CTNNB1
- Protein
- p.Pro100fs
- Coding
- c.299_300del
- MANE Select
- NM_001904
- Type
- Deletion
- Location
- chr3:41225011 (GRCh38)
- Gene constraint
- LOEUF 0.139 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 81.02 · 50 PDB
Similar variants
- CTNNB1 p.Pro100= Likely benign ★ same residue
- CTNNB1 p.Pro100Ser Likely benign ★ same residue
- CTNNB1 p.Arg661fs Pathogenic ★★ same type
- CTNNB1 p.Asp695fs Pathogenic ★★ same type
- CTNNB1 p.Ile140fs Pathogenic ★★ same type
- CTNNB1 p.Met271fs Pathogenic ★★ same type
- CTNNB1 p.Met437fs Pathogenic/Likely pathogenic ★★ same type
- CTNNB1 p.Val349fs 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/ctnnb1-p-pro100fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown