CDKN1B p.Phe64=
c.192T>C · rs2136355753 · VCV2846942
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
multiple endocrine neoplasia type 4
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.13 | GERP -3.1, phastCons 0.69 |
| Overall | ||
| CADD | 8.099 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- CDKN1B
- Protein
- p.Phe64=
- Coding
- c.192T>C
- MANE Select
- NM_004064
- dbSNP
- rs2136355753
- Type
- single nucleotide variant
- Location
- chr12:12718031 (GRCh38)
- Gene constraint
- LOEUF 0.804 · pLI 0.24 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 71.08 · 19 PDB
- Residue 64
- the 'interaction with cdk2' region; a turn
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.Phe64Leu Uncertain significance ★★ ⚠ same residue
- CDKN1B p.Arg154Ter Pathogenic ★★ same condition
- CDKN1B p.Arg5Ter Pathogenic/Likely pathogenic ★★ same condition
- CDKN1B p.Gln104Ter Pathogenic ★★ same condition
- CDKN1B p.Gln107Ter Pathogenic ★★ same condition
- CDKN1B p.Gln141Ter Pathogenic ★★ same condition
- CDKN1B p.Gln163Ter Pathogenic ★★ same condition
- CDKN1B p.Gln20Ter 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-phe64 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown