# NM_001323289.2(CDKL5):c.2556G>A (p.Pro852=)

https://sugi.bio/variant/cdkl5-p-pro852

## Summary

**CDKL5 p.Pro852= (c.2556G>A)** is classified **Likely benign** in CDKL5 (ClinVar, Expert panel, 3 submitters; last evaluated 2023-06-15). Ultra-rare (popmax 0.046%, mid); Associated with CDKL5 disorder.

**At a glance:** Likely benign · review: Expert panel · rsID rs748905018 · 3 submitters · 2 linked conditions · ultra-rare (popmax 0.046%, mid)

## For patients & families {#patients}

This is a change in the CDKL5 gene that is classified as likely benign — not considered disease-causing, submitted by 3 submitters, and is linked to CDKL5 disorder.

*Reference information, not medical advice, and not a prediction for any individual. A genetic counselor or clinician can interpret what it means for you and your family.*

|  |  |
| --- | --- |
| Clinical trials | 12 registered for this condition — see ClinicalTrials.gov |

**Support & next steps:** [Condition overview & support (NIH GARD)](https://rarediseases.info.nih.gov/diseases/0026021/index) · [Find a genetic counselor (NSGC)](https://findageneticcounselor.nsgc.org/).

## Identity {#identity}

| Field | Value |
| --- | --- |
| Gene | [CDKL5](https://sugi.bio/atlas/gene/CDKL5/) |
| Protein change (HGVS p.) | p.Pro852= |
| Coding change (HGVS c.) | c.2556G>A |
| MANE Select transcript | [NM_001323289](https://www.ncbi.nlm.nih.gov/nuccore/NM_001323289) |
| dbSNP | [rs748905018](https://www.ncbi.nlm.nih.gov/snp/rs748905018/) |
| Variant type | single nucleotide variant |
| Location | chrX:18628430-18628430 (GRCh38) |
| ClinVar | [VCV1046637](https://www.ncbi.nlm.nih.gov/clinvar/variation/1046637/) |

**All HGVS expressions:** `NC_000023.10:g.18646550G>A`, `NC_000023.11:g.18628430G>A`, `NG_008475.1:g.207826G>A`, `NM_001037343.2:c.2556G>A`, `NM_001323289.2:c.2556G>A`, `NM_003159.3:c.2556G>A`

## Computational & population evidence {#evidence}

**Concordance:** Mixed / partial computational evidence (see below).

- **Missense predictors (AlphaMissense/REVEL/SaProt) do not apply** to this variant type — they score amino-acid substitutions only. For non-missense variants the computational signal comes from conservation (below), not from a missing predictor score.
- Conservation: phyloP -1.643, GERP -4.42 — not a conserved position (phyloP < 0.1, ACGS BP7 cut)
- CADD: **PHRED 0.345**. No single ClinGen-calibrated threshold exists and the expert panels that use CADD disagree — GUCY2D/AIPL1 require ≥ 20.0 for an untranslated-region variant, ABCA4 ≥ 28.1 for a synonymous or indel variant, the Pulmonary Hypertension panel imports Pejaver 2022's missense-calibrated numbers, and the Antibody Deficiencies panel declines CADD entirely for PIK3CD. CADD v1.7 also incorporates Zoonomia phyloP, so it partly re-expresses the conservation above. *Descriptive; no threshold applied.*
- SpliceAI: **not assessed** — no allele at this position is in our SpliceAI release, either because it lies outside the scored MANE transcript scope or because every allele is below Δ0.2. We cannot tell which, so this claims neither; absence is not evidence against a splicing effect.
- Population frequency (gnomAD v4.1): grpmax **0.046%** (mid) · FAF95 0.00813% · FAF99 0.00373% · 2/4,348 in the highest group · 12/1,097,829 alleles overall — ultra-rare (popmax 0.046%, mid).

| Ancestry group | Allele frequency | 1 in |
| --- | --- | --- |
| Middle Eastern (grpmax) | 0.046% | 2,174 |
| East Asian | 0.0148% | 6,763 |
| South Asian | 0.00175% | 56,998 |
| European (non-Finnish) | 0.000447% | 223,780 |

*Computational predictors are not independent (ClinGen Variant Classification guidance): AlphaMissense (Cheng et al. 2023) carries the ACMG weight for missense and conservation (phyloP/GERP/phastCons) for non-missense; REVEL (Pejaver-2022 calibrated strength bands) and SaProt (Su et al. 2023, structure-aware, ClinVar-independent protein language model, raw LLR) are shown as orthogonal agreement signals, not additive. For frequency, the gnomAD v4.1 grpmax filtering allele frequency (FAF95) is ClinGen's designated BA1/BS1 input (gnomAD v4 guidance v3.0, June 2025); BA1/BS1 thresholds are disease-specific, not a blanket 5%. Predictions, not a clinical determination.*

## Gene constraint & dosage {#gene-context}


Curated gene–disease validity (ClinGen):

- **CDKL5 disorder** — Definitive (XL)

## Protein context {#protein}

Residue **852** lies in the 'disordered' region; a UniProt-annotated variant site (in dee2).

AlphaFold model confidence (whole protein): pLDDT 53.76, 23% of residues very-high.

**3 experimental structure(s)** (PDB): [4BGQ](https://www.rcsb.org/structure/4BGQ), [8CIE](https://www.rcsb.org/structure/8CIE), [9EPU](https://www.rcsb.org/structure/9EPU).

## What this gene does {#gene-function}

*Describes the biological roles of CDKL5 (the gene this variant disrupts) — not effects measured for this specific variant. A damaging variant is expected to affect these functions and pathways; the degree depends on the variant.*

**How this variant is thought to act:** CDKL5's established molecular role includes protein kinase activity. p.Pro852= falls in the disordered region.


### Molecular function & processes (GO — experimentally supported) {#go}

**Molecular function:** protein kinase activity, ATP binding, kinase activity.

**Biological process:** modulation of chemical synaptic transmission, regulation of postsynapse organization, regulation of cilium assembly.

## Clinical significance {#significance}

**Likely benign** — review status Expert panel *(reviewed by expert panel)*, last evaluated 2023-06-15.

**Submitter consensus:** unanimous (3/3 Likely benign).

**Submission history:** 3 submissions (2020–2024); classifications have been stable.

**ClinGen expert panel:** Likely Benign — Rett and Angelman-like Disorders VCEP (CDKL5 disorder). *Expert-panel curated (ACMG); the highest ClinVar review tier.*
**Applied ACMG criteria (met):** `BP7`, `BP4`.
*Considered but not met:* `BS1`.
Inheritance: X-linked inheritance.

> **Curation rationale (ClinGen, verbatim):** The c.2556G>A p.Pro852= variant in CDKL5 (NM_001323289.2) is present in 2 female individuals in gnomAD (0.0072%) (not sufficient to meet BS1 criteria). The silent p.Pro852= variant is not predicted to affect splicing using multiple computational tools and does not affect a highly conserved nucleotide (BP4, BP7). In summary, the p.Pro852= variant in CDKL5 is classified as Likely Benign based on the ACMG/AMP criteria (BP4, BP7).
*Source: https://cspec.clinicalgenome.org/cspec/ui/svi/affiliation/50022 · approved 2023-06-15 · [ClinGen Evidence Repository](https://erepo.genome.network/evrepo/ui/classification/e984a0f5-e529-4176-8c80-806fae84527e).*
*These are ClinGen's applied codes, reported verbatim — Sugi Variant does not re-tally or combine them into its own classification.*

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| GeneDx | Likely benign | criteria provided, single submitter | clinical testing | 2020-06-29 |
| ClinGen Rett and Angelman-like Disorders Variant Curation Expert Panel | Likely benign | reviewed by expert panel | curation | 2023-06-15 |
| Labcorp Genetics (formerly Invitae), Labcorp | Likely benign | criteria provided, single submitter | clinical testing | 2024-04-05 |

## Associated conditions {#conditions}

[CDKL5 disorder](https://sugi.bio/atlas/disease/cdkl5-disorder/), [developmental and epileptic encephalopathy, 2](https://sugi.bio/atlas/disease/developmental-and-epileptic-encephalopathy-2/).

**Reported phenotype names (ClinVar):** CDKL5 disorder, Angelman syndrome-like, Developmental and epileptic encephalopathy, 2, not provided, none provided, INFANTILE SPASM SYNDROME, X-LINKED 2, CDKL5 deficiency disorder.

## Similar variants {#similar}

Related CDKL5 variant pages (same residue, condition, or type): [CDKL5 p.Pro852Leu](/variant/cdkl5-p-pro852leu), [CDKL5 p.Pro852Arg](/variant/cdkl5-p-pro852arg), [CDKL5 c.146-1G>A](/variant/cdkl5-c-146-minus-1g-a), [CDKL5 p.Ala157Pro](/variant/cdkl5-p-ala157pro), [CDKL5 p.Ala157Val](/variant/cdkl5-p-ala157val), [CDKL5 p.Ala40Val](/variant/cdkl5-p-ala40val), [CDKL5 p.Arg178Gln](/variant/cdkl5-p-arg178gln), [CDKL5 p.Arg717=](/variant/cdkl5-p-arg717).

### Data sources & attribution {#sources}

ClinVar (NCBI — public domain, built 2026-10-11); gnomAD v4.1 (Broad Institute, built 2026-10-06); AlphaMissense (Cheng et al. 2023, © Google DeepMind — CC BY 4.0, built 2026-01-27); REVEL (Ioannidis et al. 2016 — ODbL, built 2026-07-13); SaProt (Su et al. 2023 — MIT, built 2026-07-14); SpliceAI (Illumina — free for non-commercial use, built 2026-10-13); CADD (Rentzsch et al. 2019, University of Washington — free for non-commercial use, built 2026-10-10); Conservation (phyloP/phastCons/GERP) (UCSC hg38 470-way mammal (Hiller Lab) + Ensembl Compara, built 2026-07-12); gnomAD Non-coding Constraint (Gnocchi) (Chen et al. 2024, Broad Institute — CC0, built 2026-10-11); gnomAD Regional Missense Constraint (Broad Institute — CC0, built 2026-10-13); Pangolin (Zeng & Li 2022 — CC BY 4.0, built 2026-10-11); Repeat regions (UCSC — RepeatMasker, TRF, segmental duplications, built 2026-10-11); ClinGen (ClinGen, built 2026-09-22); UniProt (CC BY 4.0); Reactome / GO (CC BY 4.0, built 2026-09-23); MaveDB (per-record license, built 2026-10-11); CIViC (CC0, built 2026-09-22); Orphanet (Orphanet, built 2026-06-12)

*Primary record: NCBI ClinVar (variation 1046637). Classifications reflect these databases as of the page's build date and may change. Free reference use — not medical advice; consult the primary submitters and a clinician.*