Is CDKN1B p.Pro91His (c.272C>A) pathogenic?

CDKN1B p.Pro91His (c.272C>A) is classified Uncertain significance in CDKN1B (ClinVar, Multiple submitters, 2 submitters; last evaluated 2024-03-13). AlphaMissense: likely benign (0.183); Absent from gnomAD v4.1; Associated with hereditary neoplastic syndrome.

What condition is associated with CDKN1B p.Pro91His (c.272C>A)?

CDKN1B p.Pro91His (c.272C>A) is associated with hereditary neoplastic syndrome, multiple endocrine neoplasia type 4 (ClinVar).

How common is CDKN1B p.Pro91His (c.272C>A) in the general population?

CDKN1B p.Pro91His (c.272C>A) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CDKN1B p.Pro91His (c.272C>A)?

AlphaMissense predicts likely benign (score 0.183) — an in-silico prediction, not a clinical call.

CDKN1B p.Pro91His

c.272C>A · rs768793049 · VCV2059201

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.183 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/2 damaging

AlphaMissense, SaProt · REVEL indeterminate

Conditions

hereditary neoplastic syndrome

Computational evidence

Protein change
AlphaMissense	0.183	likely benign
REVEL	0.316	indeterminate
SaProt	LLR -9.75	tolerated
⇒ AlphaMissense and SaProt both call this tolerated; REVEL is indeterminate.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.6	GERP 1.6, phastCons 1
Regional constraint	o/e 1.29	unconstrained · MANE · 1,103 bp · p 3.6e-06 · regional, not allelic
Overall
CADD	26.2	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

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.Pro91His
Coding: c.272C>A
MANE Select: NM_004064
dbSNP: rs768793049
Type: single nucleotide variant
Location: chr12:12718111 (GRCh38)
Gene constraint: LOEUF 0.804 · pLI 0.24 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 71.08 · 19 PDB
Residue 91: the 'interaction with cdk2' region; the 'disordered' 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

Also linked: multiple endocrine neoplasia type 4

Similar variants

CDKN1B p.Pro91Ala Uncertain significance ★★ ⚠ same residue
CDKN1B p.Pro91Leu Uncertain significance ★★ ⚠ same residue
CDKN1B p.Pro91= Likely benign ★★ same residue
CDKN1B p.Pro91Arg Conflicting classifications of pathogenicity ★ ⚠ same residue
CDKN1B p.Pro91Ser Conflicting classifications of pathogenicity ★ ⚠ same residue
CDKN1B p.Pro91Thr Conflicting classifications of pathogenicity ★ ⚠ same residue
CDKN1B p.Pro91fs Pathogenic ★ same residue
CDKN1B p.Arg154Ter 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-pro91his (accessed [today's date]).

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