Is CDKN1B p.Pro117Ser (c.348_349delinsCT) pathogenic?

CDKN1B p.Pro117Ser (c.348349delinsCT) is classified Benign in CDKN1B (ClinVar, Single submitter, 1 submitter; last evaluated 2025-04-21). Associated with hereditary neoplastic syndrome.

What condition is associated with CDKN1B p.Pro117Ser (c.348_349delinsCT)?

CDKN1B p.Pro117Ser (c.348_349delinsCT) is associated with hereditary neoplastic syndrome (ClinVar).

CDKN1B p.Pro117Ser

c.348_349delinsCT · VCV3999745

Benign Single submitter

Classification

Benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

Conditions

hereditary neoplastic syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 3.9	GERP -0.42, phastCons 1
Regional constraint	o/e 1.29	unconstrained · MANE · 1,103 bp · p 3.6e-06 · regional, not allelic

Variant & gene context

Gene: CDKN1B
Protein: p.Pro117Ser
Coding: c.348_349delinsCT
MANE Select: NM_004064
Type: Indel
Location: chr12:12718187 (GRCh38)
Gene constraint: LOEUF 0.804 · pLI 0.24 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 71.08 · 19 PDB
Residue 117: the 'disordered' region

Full CDKN1B gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

hereditary neoplastic syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

CDKN1B p.Pro117Arg Uncertain significance ★ ⚠ same residue
CDKN1B p.Pro117Leu Conflicting classifications of pathogenicity ★ ⚠ same residue
CDKN1B p.Leu84_Pro85delinsPheSer Uncertain significance ★★ same condition
CDKN1B p.Val109Ser Uncertain significance ★★ same condition
CDKN1B c.476-6_476-5delinsAT Benign/Likely benign ★★ same condition
CDKN1B p.Arg43fs Pathogenic ★ same condition
CDKN1B p.Glu86fs Pathogenic ★ same condition
CDKN1B p.Gly143fs Uncertain significance ★ 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-pro117ser (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown