Is CCND1 p.Val60= (c.180C>G) pathogenic?

CCND1 p.Val60= (c.180C>G) is classified Likely benign in CCND1 (ClinVar, Single submitter, 1 submitter; last evaluated 2018-08-08). Absent from gnomAD v4.1.

How common is CCND1 p.Val60= (c.180C>G) in the general population?

CCND1 p.Val60= (c.180C>G) is absent from gnomAD v4.1 (gnomAD).

CCND1 p.Val60=

c.180C>G · rs1590912454 · VCV761360

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 3.5	GERP -0.22, phastCons 1
Overall
CADD	12.12	PHRED · no single calibrated threshold — expert panels disagree

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: CCND1
Protein: p.Val60=
Coding: c.180C>G
MANE Select: NM_053056
dbSNP: rs1590912454
Type: single nucleotide variant
Location: chr11:69641493 (GRCh38)
Gene constraint: LOEUF 0.609 · pLI 0.72 (gnomAD)
Structure: AlphaFold pLDDT 87.31 · 11 PDB
Residue 60: the cyclin n-terminal domain; an α-helix

Full CCND1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CCND1 p.Ile251Met Uncertain significance ★★ ⚠ same type
CCND1 c.415-170G>C Benign ★★ same type
CCND1 c.575-120G>A Benign ★★ same type
CCND1 c.724-205A>G Benign ★★ same type
CCND1 c.724-26A>G Benign ★★ same type
CCND1 c.*65C>A Benign ★★ same type
CCND1 p.Arg245= Benign/Likely benign ★★ same type
CCND1 p.Phe223= Benign ★★ same type

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/ccnd1-p-val60 (accessed [today's date]).

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