CDKN1C p.Pro133fs
c.398del · rs1554938069 · VCV502216
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-escape possible for C-terminal truncations |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 0.032 | GERP -0.74 |
| Region caveats | ||
| Repeat context | tandem | G-rich low complexity, simple repeat · ambiguous alignment · confidence, not pathogenicity |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Population frequency
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- CDKN1C
- Protein
- p.Pro133fs
- Coding
- c.398del
- MANE Select
- NM_001122630
- dbSNP
- rs1554938069
- Type
- Deletion
- Location
- chr11:2885059 (GRCh38)
- Gene constraint
- LOEUF 1.943 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 63.93
- Residue 133
- the 'disordered' region
Similar variants
- CDKN1C p.Pro133Leu Uncertain significance ★ ⚠ same residue
- CDKN1C p.Pro133= Likely benign ★ same residue
- CDKN1C p.Pro137fs Pathogenic ★★ same type
- CDKN1C p.Ser73fs Pathogenic/Likely pathogenic ★★ same type
- CDKN1C p.Val130fs Pathogenic/Likely pathogenic ★★ same type
- CDKN1C p.Ala246_Ala252del Uncertain significance ★★ same type
- CDKN1C p.Gly242_Ala245del Uncertain significance ★★ same type
- CDKN1C c.787+16_787+25del Likely benign ★★ 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/cdkn1c-p-pro133fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown