Is CDKN1B p.Ser7fs (c.18_23delinsT) pathogenic?

CDKN1B p.Ser7fs (c.1823delinsT) is classified Likely pathogenic in CDKN1B (ClinVar, Single submitter, 1 submitter; last evaluated 2023-07-20). No gnomAD frequency available for this variant; Associated with multiple endocrine neoplasia type 4.

What condition is associated with CDKN1B p.Ser7fs (c.18_23delinsT)?

CDKN1B p.Ser7fs (c.18_23delinsT) is associated with multiple endocrine neoplasia type 4 (ClinVar).

How common is CDKN1B p.Ser7fs (c.18_23delinsT) in the general population?

CDKN1B p.Ser7fs (c.18_23delinsT) is no gnomAD frequency available for this variant (gnomAD).

How is Multiple endocrine neoplasia type 4 inherited?

Typically Autosomal dominant, Not applicable (Orphanet). A genetic counselor can assess individual risk for a family.

CDKN1B p.Ser7fs

c.18_23delinsT · rs2497403627 · VCV2576587

Likely pathogenic Single submitter

Classification

Likely 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

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 2.1	GERP 0.45, 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.Ser7fs
Coding: c.18_23delinsT
MANE Select: NM_004064
dbSNP: rs2497403627
Type: Indel
Location: chr12:12717857 (GRCh38)
Gene constraint: LOEUF 0.804 · pLI 0.24 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 71.08 · 19 PDB
Residue 7: the 'disordered' region

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

Disease context

multiple endocrine neoplasia type 4 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Multiple endocrine neoplasia type 4 (Orphanet):

Inheritance: Autosomal dominant, Not applicable
Onset: Adult

Similar variants

CDKN1B p.Ser7Cys Uncertain significance ★★ ⚠ 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 c.476-6_476-5delinsAG Uncertain significance ★ same condition
CDKN1B p.Ala149Leu Uncertain significance ★ same condition
CDKN1B p.Ala55Val Uncertain significance ★ same condition
CDKN1B p.Gly143Arg 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-ser7fs (accessed [today's date]).

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