Is CDKN1C p.Arg20Ser (c.58C>A) pathogenic?

CDKN1C p.Arg20Ser (c.58C>A) is classified Uncertain significance in CDKN1C (ClinVar, Multiple submitters, 4 submitters; last evaluated 2025-06-26). AlphaMissense: likely pathogenic (0.9955); Absent from gnomAD v4.1; Associated with Beckwith-Wiedemann syndrome.

What condition is associated with CDKN1C p.Arg20Ser (c.58C>A)?

CDKN1C p.Arg20Ser (c.58C>A) is associated with Beckwith-Wiedemann syndrome (ClinVar).

How common is CDKN1C p.Arg20Ser (c.58C>A) in the general population?

CDKN1C p.Arg20Ser (c.58C>A) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CDKN1C p.Arg20Ser (c.58C>A)?

AlphaMissense predicts likely pathogenic (score 0.9955) — an in-silico prediction, not a clinical call.

CDKN1C p.Arg20Ser

c.58C>A · rs1467420956 · VCV524716

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

AlphaMissense

likely pathogenic

0.9955 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,558,236)

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Beckwith-Wiedemann syndrome

Computational evidence

Protein change
AlphaMissense	0.9955	likely pathogenic · top 3% in CDKN1C
REVEL	0.826	moderately pathogenic-leaning
SaProt	LLR -13.09	damaging
⇒ AlphaMissense, REVEL and SaProt all call this damaging.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 11	GERP -2.3, phastCons 1
Overall
CADD	26.5	PHRED · no single calibrated threshold — expert panels disagree

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

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

⚠ Isoform check: AlphaMissense numbered on a different transcript (AM R31S vs ClinVar R20S) — verify the residue.

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,558,236). 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: CDKN1C
Protein: p.Arg20Ser
Coding: c.58C>A
MANE Select: NM_001122630
dbSNP: rs1467420956
Type: single nucleotide variant
Location: chr11:2885399 (GRCh38)
Gene constraint: LOEUF 1.943 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 63.93

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.Arg20Cys Uncertain significance ★ ⚠ same residue
CDKN1C p.Arg20His Uncertain significance ★ ⚠ same residue
CDKN1C p.Arg20Leu Uncertain significance ★ ⚠ same residue
CDKN1C p.Arg20= 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

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-arg20ser (accessed [today's date]).

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