Is CDKL3 p.Arg101Gln (c.302G>A) pathogenic?

CDKL3 p.Arg101Gln (c.302G>A) is classified Uncertain significance in CDKL3 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-08-13). AlphaMissense: likely benign (0.2025); Very rare (popmax 0.00361%, amr).

How common is CDKL3 p.Arg101Gln (c.302G>A) in the general population?

CDKL3 p.Arg101Gln (c.302G>A) is very rare (popmax 0.00361%, amr) (gnomAD).

What do computational predictors say about CDKL3 p.Arg101Gln (c.302G>A)?

AlphaMissense predicts likely benign (score 0.2025) — an in-silico prediction, not a clinical call.

CDKL3 p.Arg101Gln

c.302G>A · VCV4224709

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.2025 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00361%, amr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.2025	likely benign
REVEL	0.173	moderately benign-leaning
SaProt	LLR -8.48	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 4.8	GERP 1.7, phastCons 1
Regional constraint	o/e 0.95	unconstrained · MANE · 68 kb · p 0.16 · regional, not allelic
Overall
CADD	26.8	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

Grpmax group 0.00361% Admixed American · 2/55,432 alleles

Filtering AF 0.000966% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000797%

Overall 0.00158% 25/1,584,874 alleles · very rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00361%	27,716
Remaining individualsnot grpmax-eligible	0.00326%	30,709
African / African-American	0.00268%	37,268
European (non-Finnish)	0.00155%	64,684
South Asian	0.00116%	86,554

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: CDKL3
Protein: p.Arg101Gln
Coding: c.302G>A
MANE Select: NM_001113575
Type: single nucleotide variant
Location: chr5:134359955 (GRCh38)
Gene constraint: LOEUF 1.523 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 64.87 · 1 PDB
Residue 101: the protein kinase domain; an α-helix

Full CDKL3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CDKL3 p.Ala195Thr Uncertain significance ★ ⚠ same type
CDKL3 p.Ala235Ser Uncertain significance ★ ⚠ same type
CDKL3 p.Arg111Pro Uncertain significance ★ ⚠ same type
CDKL3 p.Arg148Gln Uncertain significance ★ ⚠ same type
CDKL3 p.Arg164His Uncertain significance ★ ⚠ same type
CDKL3 p.Arg367Thr Uncertain significance ★ ⚠ same type
CDKL3 p.Arg463Ser Uncertain significance ★ ⚠ same type
CDKL3 p.Arg464Cys 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/cdkl3-p-arg101gln (accessed [today's date]).

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