Is CCND2 p.Thr115Ile (c.344C>T) pathogenic?

CCND2 p.Thr115Ile (c.344C>T) is classified Uncertain significance in CCND2 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-10-14). AlphaMissense: likely pathogenic (0.7645); Absent from gnomAD v4.1.

How common is CCND2 p.Thr115Ile (c.344C>T) in the general population?

CCND2 p.Thr115Ile (c.344C>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CCND2 p.Thr115Ile (c.344C>T)?

AlphaMissense predicts likely pathogenic (score 0.7645) — an in-silico prediction, not a clinical call.

CCND2 p.Thr115Ile

c.344C>T · rs762132499 · VCV2768438

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.7645 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

1/2 damaging

AlphaMissense, SaProt · REVEL no call

Computational evidence

Protein change
AlphaMissense	0.7645	likely pathogenic
REVEL	0.296	indeterminate
SaProt	LLR -8.56	tolerated
⇒ AlphaMissense calls this damaging; SaProt does not; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 5.9	GERP 1.2, phastCons 1
Regional constraint	o/e 0.55	unconstrained · MANE · 26 kb · p 7.7e-16 · regional, not allelic
Overall
CADD	27.5	PHRED · no single calibrated threshold — expert panels disagree

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: CCND2
Protein: p.Thr115Ile
Coding: c.344C>T
MANE Select: NM_001759
dbSNP: rs762132499
Type: single nucleotide variant
Location: chr12:4276153 (GRCh38)
Gene constraint: LOEUF 0.385 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 87.98 · 1 PDB
Residue 115: the cyclin n-terminal domain

Full CCND2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CCND2 p.Thr115Pro Uncertain significance ★ ⚠ same residue
CCND2 p.Thr115Ser Uncertain significance ★ ⚠ same residue
CCND2 p.Gln277Ter Pathogenic/Likely pathogenic ★★ same type
CCND2 p.Pro281Ala Pathogenic ★★ same type
CCND2 p.Pro281Ser Pathogenic/Likely pathogenic ★★ same type
CCND2 p.Ser271Ter Likely pathogenic ★★ same type
CCND2 p.Thr280Ala Pathogenic ★★ same type
CCND2 p.Thr280Asn Pathogenic/Likely pathogenic ★★ 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/ccnd2-p-thr115ile (accessed [today's date]).

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