Is CDKN1B p.Arg43Ter (c.127delinsTAA) pathogenic?

CDKN1B p.Arg43Ter (c.127delinsTAA) is classified Likely pathogenic in CDKN1B (ClinVar, No assertion criteria, 1 submitter; last evaluated 2014-09-05). Absent from gnomAD; Associated with neuroendocrine neoplasm.

What condition is associated with CDKN1B p.Arg43Ter (c.127delinsTAA)?

CDKN1B p.Arg43Ter (c.127delinsTAA) is associated with neuroendocrine neoplasm (ClinVar).

How common is CDKN1B p.Arg43Ter (c.127delinsTAA) in the general population?

CDKN1B p.Arg43Ter (c.127delinsTAA) is absent from gnomAD (gnomAD).

CDKN1B p.Arg43Ter

c.127delinsTAA · rs797044481 · VCV157518

Likely pathogenic No assertion criteria

Classification

Likely pathogenic

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

Consequence

nonsense (stop-gain)

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

neuroendocrine neoplasm

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	nonsense (stop-gain)	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 4.7	GERP 1.4, 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.Arg43Ter
Coding: c.127delinsTAA
MANE Select: NM_004064
dbSNP: rs797044481
Type: Indel
Location: chr12:12717966 (GRCh38)
Gene constraint: LOEUF 0.804 · pLI 0.24 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 71.08 · 19 PDB
Residue 43: an α-helix

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

Disease context

neuroendocrine neoplasm — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

CDKN1B p.Arg43fs Pathogenic ★ same residue
CDKN1B p.Arg43Gln Uncertain significance ★ ⚠ same residue
CDKN1B p.Arg43Trp Uncertain significance ★ ⚠ same residue
CDKN1B p.Arg43= Likely benign ★ same residue
CDKN1B p.Pro94fs Pathogenic ★ same condition
CDKN1B p.Ser112fs Likely pathogenic same condition
CDKN1B p.Leu84_Pro85delinsPheSer Uncertain significance ★★ same type
CDKN1B p.Val109Ser Uncertain significance ★★ 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/cdkn1b-p-arg43ter (accessed [today's date]).

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