CDKN1B p.Phe87fs
c.258dup · VCV4720420
Pathogenic
Single submitter
Classification
Pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
Conditions
1
multiple endocrine neoplasia type 4
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 1 of 3 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 11 | GERP 1.6, phastCons 1 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- CDKN1B
- Protein
- p.Phe87fs
- Coding
- c.258dup
- MANE Select
- NM_004064
- Type
- Duplication
- Location
- chr12:12718096 (GRCh38)
- Gene constraint
- LOEUF 0.804 · pLI 0.24 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 71.08 · 19 PDB
- Residue 87
- the 'interaction with cdk2' region; the 'disordered' region; an α-helix
Disease context
multiple endocrine neoplasia type 4 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Multiple endocrine neoplasia type 4 (Orphanet):
- Inheritance
- Autosomal dominant, Not applicable
- Onset
- Adult
Similar variants
- CDKN1B p.Phe87= Likely benign ★★ same residue
- CDKN1B p.Phe87Leu Uncertain significance ★ ⚠ same residue
- CDKN1B p.Asn8Ter Pathogenic/Likely pathogenic ★★ same condition
- CDKN1B p.Gln104fs Pathogenic ★★ same condition
- CDKN1B p.Glu126Ter Pathogenic ★★ same condition
- CDKN1B p.Lys96fs Pathogenic/Likely pathogenic ★★ same condition
- CDKN1B p.Gly192fs Uncertain significance ★★ same condition
- CDKN1B p.Ala123fs 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/cdkn1b-p-phe87fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown