Is CDKN1C p.Arg7fs (c.19del) pathogenic?

CDKN1C p.Arg7fs (c.19del) is classified Likely pathogenic in CDKN1C (ClinVar, Single submitter, 1 submitter). Absent from gnomAD v4.1; Associated with Beckwith-Wiedemann syndrome.

What condition is associated with CDKN1C p.Arg7fs (c.19del)?

CDKN1C p.Arg7fs (c.19del) is associated with Beckwith-Wiedemann syndrome (ClinVar).

How common is CDKN1C p.Arg7fs (c.19del) in the general population?

CDKN1C p.Arg7fs (c.19del) is absent from gnomAD v4.1 (gnomAD).

CDKN1C p.Arg7fs

c.19del · rs2494391145 · VCV3062304

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,548,240)

Conditions

Beckwith-Wiedemann syndrome

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-escape possible for C-terminal truncations
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 0.92	GERP -0.46, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,548,240). 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.Arg7fs
Coding: c.19del
MANE Select: NM_001122630
dbSNP: rs2494391145
Type: Deletion
Location: chr11:2885438 (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.Arg7Cys Uncertain significance ★ ⚠ same residue
CDKN1C p.Pro137fs Pathogenic ★★ same condition
CDKN1C p.Ser73fs Pathogenic/Likely pathogenic ★★ same condition
CDKN1C p.Val130fs Pathogenic/Likely pathogenic ★★ same condition
CDKN1C p.Ala246_Ala252del Uncertain significance ★★ same condition
CDKN1C p.Gly242_Ala245del Uncertain significance ★★ same condition
CDKN1C c.787+16_787+25del Likely benign ★★ same condition
CDKN1C p.168_169AP[5] Likely benign ★★ 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-arg7fs (accessed [today's date]).

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