Is CDK3 p.Pro95Arg (c.284C>G) pathogenic?

CDK3 p.Pro95Arg (c.284C>G) is classified Uncertain significance in CDK3 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-04-17). AlphaMissense: likely benign (0.1084); Absent from gnomAD v4.1.

How common is CDK3 p.Pro95Arg (c.284C>G) in the general population?

CDK3 p.Pro95Arg (c.284C>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CDK3 p.Pro95Arg (c.284C>G)?

AlphaMissense predicts likely benign (score 0.1084) — an in-silico prediction, not a clinical call.

CDK3 p.Pro95Arg

c.284C>G · VCV3265464

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1084 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1084	likely benign
REVEL	0.069	moderately benign-leaning
SaProt	LLR -6.47	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 3	GERP -0.079, phastCons 0.058
Regional constraint	o/e 0.92	unconstrained · MANE · 3,994 bp · p 0.11 · regional, not allelic
Overall
CADD	7.702	PHRED · no single calibrated threshold — expert panels disagree

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

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: CDK3
Protein: p.Pro95Arg
Coding: c.284C>G
MANE Select: NM_001258
Type: single nucleotide variant
Location: chr17:76002111 (GRCh38)
Gene constraint: LOEUF 1.082 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 86.31 · 2 PDB
Residue 95: the protein kinase domain; a turn

Full CDK3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CDK3 p.Ala170Ser Uncertain significance ★ ⚠ same type
CDK3 p.Ala282Asp Uncertain significance ★ ⚠ same type
CDK3 p.Arg126Gln Uncertain significance ★ ⚠ same type
CDK3 p.Arg150Cys Uncertain significance ★ ⚠ same type
CDK3 p.Arg150His Uncertain significance ★ ⚠ same type
CDK3 p.Arg199Gln Uncertain significance ★ ⚠ same type
CDK3 p.Arg214Cys Uncertain significance ★ ⚠ same type
CDK3 p.Arg217His Uncertain significance ★ ⚠ 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/cdk3-p-pro95arg (accessed [today's date]).

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