Is CDKL5 p.Phe780Ser (c.2339T>C) pathogenic?

CDKL5 p.Phe780Ser (c.2339T>C) is classified Uncertain significance in CDKL5 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-06-30). AlphaMissense: likely pathogenic (0.9809); Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with CDKL5 p.Phe780Ser (c.2339T>C)?

CDKL5 p.Phe780Ser (c.2339T>C) is associated with Inborn genetic diseases (ClinVar).

How common is CDKL5 p.Phe780Ser (c.2339T>C) in the general population?

CDKL5 p.Phe780Ser (c.2339T>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CDKL5 p.Phe780Ser (c.2339T>C)?

AlphaMissense predicts likely pathogenic (score 0.9809) — an in-silico prediction, not a clinical call.

CDKL5 p.Phe780Ser

c.2339T>C · VCV4224729

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9809 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

1/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.9809	likely pathogenic
REVEL	0.445	indeterminate
SaProt	LLR -8.57	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 7.9	GERP 2.2, phastCons 1
Regional constraint	o/e 0.70	unconstrained · MANE · 30 kb · p 1.5e-11 · regional, not allelic
Overall
CADD	26.5	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: CDKL5
Protein: p.Phe780Ser
Coding: c.2339T>C
MANE Select: NM_001323289
Type: single nucleotide variant
Location: chrX:18619929 (GRCh38)
Structure: AlphaFold pLDDT 53.76 · 3 PDB
Residue 780: the 'disordered' region; a UniProt-annotated variant site (in dee2)

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-phe780ser (accessed [today's date]).

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