Is CDKL5 p.Pro361= (c.1083T>C) pathogenic?

CDKL5 p.Pro361= (c.1083T>C) is classified Likely benign in CDKL5 (ClinVar, Single submitter, 1 submitter; last evaluated 2014-10-06). Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with CDKL5 p.Pro361= (c.1083T>C)?

CDKL5 p.Pro361= (c.1083T>C) is associated with Inborn genetic diseases (ClinVar).

How common is CDKL5 p.Pro361= (c.1083T>C) in the general population?

CDKL5 p.Pro361= (c.1083T>C) is absent from gnomAD v4.1 (gnomAD).

CDKL5 p.Pro361=

c.1083T>C · rs2518873560 · VCV1787115

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

Inborn genetic diseases

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 -0.25	GERP -4.2, phastCons 0.4
Overall
CADD	6.03	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: CDKL5
Protein: p.Pro361=
Coding: c.1083T>C
MANE Select: NM_001323289
dbSNP: rs2518873560
Type: single nucleotide variant
Location: chrX:18604007 (GRCh38)
Structure: AlphaFold pLDDT 53.76 · 3 PDB

Full CDKL5 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

CDKL5 c.2152+1G>A Pathogenic ★★ same condition
CDKL5 p.Gln605Ter Pathogenic ★★ same condition
CDKL5 p.Gln69Ter Pathogenic ★★ same condition
CDKL5 p.Gln865Ter Pathogenic ★★ same condition
CDKL5 p.Ala166Thr Uncertain significance ★★ ⚠ same condition
CDKL5 p.Arg81Gln Uncertain significance ★★ ⚠ same condition
CDKL5 p.Arg822Cys Uncertain significance ★★ ⚠ same condition
CDKL5 p.Asn325Asp Uncertain significance ★★ ⚠ 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/cdkl5-p-pro361 (accessed [today's date]).

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