HomeAboutRankingsData Sources
Β© 2026 GeneE
🧬
GeneE
10 sources retrieved Β· Most recent: April 2026 Β· Index updated 14 days ago
β“˜GeneE is for informational purposes only. It is not a substitute for professional medical advice, diagnosis, or treatment.
CRNKL1
crooked neck pre-mRNA splicing factor 1
Chromosome 20 Β· 20p11.23
NCBI Gene: 51340Ensembl: ENSG00000101343.15HGNC: HGNC:15762UniProt: Q5JY65
107PubMed Papers
20Diseases
0Drugs
3Pathogenic Variants
FUNCTIONAL ROLE
Hub Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
U2-type catalytic step 2 spliceosomeRNA bindingspliceosomal complexcatalytic step 2 spliceosomedengue diseaseAbnormality of the skeletal systemglomerulonephritistype 2 diabetes mellitus
✦AI Summary

CRNKL1 (crooked neck pre-mRNA splicing factor 1) is a component of the spliceosome machinery that plays critical roles in pre-mRNA splicing regulation and nuclear RNA retention. As part of the Prp19-associated complex, CRNKL1 is involved in both major and minor spliceosome-mediated splicing processes 1. A key function of CRNKL1 is the selective regulation of nuclear export for intron-retaining mRNAs, including HIV-1 unspliced transcripts and specific cellular mRNAs, effectively acting as a nuclear retention factor 1. Recent studies have identified CRNKL1 as essential for normal brain development, with pathogenic variants causing severe microcephaly, pontocerebellar hypoplasia, and seizures 2. The protein demonstrates tissue-specific regulatory functions despite its involvement in the ubiquitous splicing process. CRNKL1 dysregulation has significant clinical implications, serving as a prognostic biomarker in esophageal adenocarcinoma with high predictive accuracy 3. Environmental toxins like TCDD can alter CRNKL1 expression, contributing to splicing dysregulation 4. Additionally, genetic variants in CRNKL1 combined with cigarette smoking increase bladder cancer risk through m6A-mediated expression changes 5. These findings establish CRNKL1 as both a fundamental splicing regulator and a clinically relevant therapeutic target in multiple disease contexts.

Sources cited
1
CRNKL1 is part of the Prp19-associated complex and selectively regulates nuclear export of intron-retaining mRNAs including HIV-1 transcripts
PMID: 33468685
2
Pathogenic variants in CRNKL1 cause severe microcephaly, pontocerebellar hypoplasia, and seizures, demonstrating its essential role in brain development
PMID: 40857589
3
CRNKL1 serves as a prognostic biomarker in esophageal adenocarcinoma with high predictive accuracy
PMID: 28363284
4
Environmental toxin TCDD can alter CRNKL1 expression contributing to splicing dysregulation
PMID: 38346650
5
Genetic variants in CRNKL1 combined with cigarette smoking increase bladder cancer risk through m6A-mediated expression changes
PMID: 38270278
Disease Associationsβ“˜20
dengue diseaseOpen Targets
0.37Weak
Abnormality of the skeletal systemOpen Targets
0.32Weak
glomerulonephritisOpen Targets
0.31Weak
type 2 diabetes mellitusOpen Targets
0.21Weak
multiple myelomaOpen Targets
0.20Weak
esophageal adenocarcinomaOpen Targets
0.19Weak
acute myeloid leukemiaOpen Targets
0.19Weak
urinary bladder carcinomaOpen Targets
0.19Weak
hepatocellular carcinomaOpen Targets
0.19Weak
cervical squamous cell carcinomaOpen Targets
0.19Weak
small cell lung carcinomaOpen Targets
0.19Weak
cutaneous melanomaOpen Targets
0.19Weak
head and neck squamous cell carcinomaOpen Targets
0.19Weak
prostate adenocarcinomaOpen Targets
0.19Weak
esophageal squamous cell carcinomaOpen Targets
0.19Weak
bladder transitional cell carcinomaOpen Targets
0.18Weak
digestive system melanomaOpen Targets
0.18Weak
Endometrial Endometrioid AdenocarcinomaOpen Targets
0.18Weak
gastrointestinal stromal tumorOpen Targets
0.18Weak
nodular melanomaOpen Targets
0.18Weak
Pathogenic Variants3
NM_001278628.2(CRNKL1):c.317G>A (p.Arg106His)Pathogenic
Microcephaly, progressive, with simplified gyral pattern and cerebellar hypoplasia
β˜†β˜†β˜†β˜†2025β†’ Residue 106
NM_001278628.2(CRNKL1):c.316C>T (p.Arg106Cys)Pathogenic
Microcephaly, progressive, with simplified gyral pattern and cerebellar hypoplasia
β˜†β˜†β˜†β˜†2025β†’ Residue 106
NM_001278628.2(CRNKL1):c.418C>G (p.Arg140Gly)Pathogenic
Microcephaly, progressive, with simplified gyral pattern and cerebellar hypoplasia
β˜†β˜†β˜†β˜†2025β†’ Residue 140
View on ClinVar β†—
Related Genes
CDC5LProtein interaction100%FRG1Protein interaction100%MAGOHProtein interaction100%PLRG1Protein interaction100%PRCCProtein interaction100%SNRPA1Protein interaction100%
Tissue Expression6 tissues
Bone Marrow
100%
Brain
81%
Heart
66%
Ovary
51%
Liver
41%
Lung
40%
Gene Interaction Network
Click a node to explore
CRNKL1CDC5LFRG1MAGOHPLRG1PRCCSNRPA1
PROTEIN STRUCTURE
Preparing viewer…
PDB8C6J Β· 2.80 Γ… Β· EM
View on RCSB β†—
Constraintβ“˜
LOEUFβ“˜
0.45Moderately Constrained
pLIβ“˜
1.00Intolerant
Observed/Expected LoF0.32 [0.24–0.45]
RankingsWhere CRNKL1 stands among ~20K protein-coding genes
  • #4,429of 20,598
    Most Researched107 Β· top quartile
  • #3,983of 5,498
    Most Pathogenic Variants3
  • #2,458of 17,882
    Most Constrained (LOEUF)0.45 Β· top quartile
Genes detectedCRNKL1
Sources retrieved10 papers
Response timeβ€”
πŸ“„ Sources
10β–Ό
1
PMID: 40018934
Front Biosci (Landmark Ed) Β· 2025
1.00
2
Recurrent de novo variants in the spliceosomal factor CRNKL1 are associated with severe microcephaly and pontocerebellar hypoplasia with seizures.
PMID: 40857589
Am J Hum Genet Β· 2025
0.90
3
CRNKL1 Is a Highly Selective Regulator of Intron-Retaining HIV-1 and Cellular mRNAs.
PMID: 33468685
mBio Β· 2021
0.80
4
Protein coding gene CRNKL1 as a potential prognostic biomarker in esophageal adenocarcinoma.
PMID: 28363284
Artif Intell Med Β· 2017
0.70
5
Cigarette smoking combined with genetic variation regulates the m
PMID: 38270278
Environ Toxicol Β· 2024
0.60