CXXC1

Chr 18

CXXC finger protein 1

Also known as: 2410002I16Rik, 5830420C16Rik, CFP1, CGBP, HsT2645, PCCX1, PHF18, SPP1

NCBI Gene: 30827 ENSG00000154832 UniProt: Q9P0U4

This protein functions as a transcriptional activator that binds specifically to unmethylated CpG DNA motifs and is a component of the SETD1 complex that regulates gene expression during development. Mutations cause neurodevelopmental disorders with intellectual disability, and the gene follows autosomal dominant inheritance. The gene is highly constrained against loss-of-function variants, indicating that such mutations are likely to cause significant developmental effects.

ResearchSummary from RefSeq, UniProt

This gene encodes a protein that functions as a transcriptional activator that binds specifically to non-methylated CpG motifs through its CXXC domain. The protein is a component of the SETD1 complex, regulates gene expression and is essential for vertebrate development. [provided by RefSeq, Sep 2015]

ResearchGenerating clinical summary…

Clinical highlights

Interpreting a novel variant

This gene is strongly intolerant of loss-of-function variation in the population, so LoF variants warrant close attention. No curated mechanism annotation is available — see the mechanism card for the computational prediction and its caveats.Based on population constraint only.

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

0.34

LOEUF· LoF intol.

LOF

Mechanism· predicted

Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Dual constrained — LoF & missense intolerant

LoF Constraint?

0.34LOEUF

pLI 0.895

Z-score 4.67

OE 0.18 (0.10–0.34)

Highly constrained

Highly LoF-intolerant (top ~10% of genes)

Missense Constraint?

3.15Z-score

OE missense 0.58 (0.52–0.64)

256 obs / 442.4 exp

Constrained

Highly missense-constrained (top ~0.1%)

Observed / Expected Ratios?

LoF OE?0.18 (0.10–0.34)

0≤0.351.4

Missense OE?0.58 (0.52–0.64)

0≤0.61.4

Synonymous OE?1.11

0≤1.21.6

LoF obs/exp: 7 / 38.1Missense obs/exp: 256 / 442.4Syn Z: -1.14

ClinVar Variant Classifications

0 submitted variants in ClinVar

ClinVar

Protein Context — Lollipop Plot

CXXC1 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

External Resources

Links to major genomics databases and tools

Franklin by Genoox

AI-powered variant curation and clinical analysis

DECIPHER

Genomic variants and phenotypes in rare disease patients

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

MECP2 Duplication Syndrome

A First-in-Human Clinical Trial to Evaluate the Safety, Tolerability, and Efficacy of a Novel CRISPR RNA-editing Therapy in Patients with Mecp2 Duplication Syndrome, a Rare Orphan Disease (HERO)

RECRUITING

NCT06615206Phase NAHuidaGene Therapeutics Co., Ltd.Started 2024-10-30

HG204

Clinical Literature

Open Research Assistant →

Landmark / reviewRecent case evidence

Full-Text Mentions

NLP-detected gene mentions in article bodies · via PubTator3

PubTator3

Role of CxxC-finger protein 1 in establishing mouse oocyte epigenetic landscapes

Sha QQ et al.·Nucleic Acids Res

2021Functional