Is CDKN1B p.Ser56fs (c.166_167del) pathogenic?

CDKN1B p.Ser56fs (c.166167del) is classified Pathogenic in CDKN1B (ClinVar, Single submitter, 1 submitter; last evaluated 2023-12-28). No gnomAD frequency available for this variant; Associated with hereditary neoplastic syndrome.

What condition is associated with CDKN1B p.Ser56fs (c.166_167del)?

CDKN1B p.Ser56fs (c.166_167del) is associated with hereditary neoplastic syndrome (ClinVar).

How common is CDKN1B p.Ser56fs (c.166_167del) in the general population?

CDKN1B p.Ser56fs (c.166_167del) is no gnomAD frequency available for this variant (gnomAD).

CDKN1B p.Ser56fs

c.166_167del · rs2497404386 · VCV3223672

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

hereditary neoplastic syndrome

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 3.4	GERP 1.6, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: CDKN1B
Protein: p.Ser56fs
Coding: c.166_167del
MANE Select: NM_004064
dbSNP: rs2497404386
Type: Deletion
Location: chr12:12718004 (GRCh38)
Gene constraint: LOEUF 0.804 · pLI 0.24 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 71.08 · 19 PDB
Residue 56: the 'interaction with cdk2' region; an α-helix

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.Ser56Arg Uncertain significance ★★ ⚠ same residue
CDKN1B p.Ser56Thr Uncertain significance ★★ ⚠ same residue
CDKN1B p.Ser56= Benign/Likely benign ★★ same residue
CDKN1B p.Ser56Cys Uncertain significance ★ ⚠ same residue
CDKN1B p.Cys99fs Pathogenic ★★ same condition
CDKN1B p.Gln107fs Pathogenic ★★ same condition
CDKN1B p.Gly97fs Pathogenic ★★ same condition
CDKN1B p.Leu130fs 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-ser56fs (accessed [today's date]).

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