Is CDKN1C p.Pro153Leu (c.458C>T) pathogenic?

CDKN1C p.Pro153Leu (c.458C>T) is classified Uncertain significance in CDKN1C (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-11-08). AlphaMissense: likely benign (0.14); Very rare (popmax 0.00942%, nfe); Associated with Beckwith-Wiedemann syndrome.

What condition is associated with CDKN1C p.Pro153Leu (c.458C>T)?

CDKN1C p.Pro153Leu (c.458C>T) is associated with Beckwith-Wiedemann syndrome (ClinVar).

How common is CDKN1C p.Pro153Leu (c.458C>T) in the general population?

CDKN1C p.Pro153Leu (c.458C>T) is very rare (popmax 0.00942%, nfe) (gnomAD).

What do computational predictors say about CDKN1C p.Pro153Leu (c.458C>T)?

AlphaMissense predicts likely benign (score 0.14) — an in-silico prediction, not a clinical call.

CDKN1C p.Pro153Leu

c.458C>T · rs1315960524 · VCV454005

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.14 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00942%, nfe)

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Beckwith-Wiedemann syndrome

Computational evidence

Protein change
AlphaMissense	0.14	likely benign
REVEL	0.078	moderately benign-leaning
SaProt	LLR -11.27	damaging
⇒ SaProt calls this damaging; AlphaMissense and REVEL do not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.9	GERP 0.28, phastCons 0.022
Overall
CADD	17.34	PHRED · no single calibrated threshold — expert panels disagree

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

⚠ Isoform check: AlphaMissense numbered on a different transcript (AM P164L vs ClinVar P153L) — verify the residue.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00942% European (non-Finnish) · 86/912,840 alleles

Filtering AF 0.00781% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0072%

Overall 0.00778% 89/1,144,612 alleles · very rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.00942%	10,614
Remaining individualsnot grpmax-eligible	0.00473%	21,127
Admixed American	0.00441%	22,694

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: CDKN1C
Protein: p.Pro153Leu
Coding: c.458C>T
MANE Select: NM_001122630
dbSNP: rs1315960524
Type: single nucleotide variant
Location: chr11:2884999 (GRCh38)
Gene constraint: LOEUF 1.943 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 63.93
Residue 153: the 'disordered' region

Full CDKN1C gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Beckwith-Wiedemann syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

CDKN1C p.Pro153Ala Uncertain significance ★★ ⚠ same residue
CDKN1C p.Pro153Thr Uncertain significance ★ ⚠ same residue
CDKN1C p.Pro153= Likely benign ★ same residue
CDKN1C p.Asp263Asn Pathogenic ★★ ⚠ same condition
CDKN1C p.Cys19Ter Pathogenic/Likely pathogenic ★★ same condition
CDKN1C p.Gln219Ter Pathogenic ★★ same condition
CDKN1C p.Gln221Ter Pathogenic ★★ same condition
CDKN1C p.Gln230Ter 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/cdkn1c-p-pro153leu (accessed [today's date]).

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