HomeAboutRankingsData Sources
Β© 2026 GeneE
🧬
GeneE
25 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.
NIPBL
NIPBL cohesin loading factor
Chromosome 5 Β· 5p13.2
NCBI Gene: 25836Ensembl: ENSG00000164190.19HGNC: HGNC:28862UniProt: A0A590UJS4
198PubMed Papers
21Diseases
0Drugs
587Pathogenic Variants
FUNCTIONAL ROLE
Highly ConstrainedHub GeneTranscription Factor
RESEARCH IMPACT
TrendingVariant-Rich
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
cellular response to X-raytranscription corepressor activityprotein bindingmaintenance of mitotic sister chromatid cohesionCornelia de Lange syndromegenetic disorderDislocated radial headIntellectual disability
✦AI Summary

NIPBL is a cohesin loading factor essential for genome organization and developmental processes. Its primary function involves forming a heterodimeric complex with MAU2 to load cohesin onto chr5, enabling DNA loop extrusion at rates up to 2.1 kilobase pairs per second 1. NIPBL activates the cohesin ATPase required for topological entrapment of sister DNAs and fuels dynamic loop extrusion, while also regulating conformational switches of the cohesin complex 2. Beyond cohesion, NIPBL recruits histone deacetylase to modulate gene expression through chr5 remodeling and interacts with transcriptional machinery to regulate developmental genes 3. During DNA damage response, NIPBL is recruited to double-strand breaks and UV-induced lesions through CBX3-, RNF8-, and RNF168-dependent mechanisms [UniProt]. NIPBL mutations cause Cornelia de Lange Syndrome (CdLS), accounting for >60% of cases and representing the only gene definitively associated with severe CdLS phenotypes 4. CdLS manifests as a multisystem developmental disorder featuring growth and developmental delays, craniofacial abnormalities, cardiac defects including ventricular septal defects, and gastrointestinal involvement 5. NIPBL interactions with BRD4 and other chr5 regulators are critical for proper genome folding during neural crest and cardiac development, with imbalances in cohesin activity disrupting these processes 6.

Sources cited
1
NIPBL-MAU2 mediates DNA loop extrusion by cohesin at rates up to 2.1 kilobase pairs per second
PMID: 31753851
2
NIPBL activates cohesin ATPase activity required for topological entrapment and DNA loop extrusion, and regulates conformational switches of the complex
PMID: 37062615
3
NIPBL recruits histone deacetylase, interacts with cohesin and CTCF, and regulates gene expression through dynamic alterations of genome organization
PMID: 30096364
4
NIPBL mutations account for >60% of Cornelia de Lange Syndrome cases and are the only gene causing severe/classic CdLS phenotypes
PMID: 37377026
5
CdLS, caused by NIPBL mutations, is associated with cardiac defects including ventricular septal defects as part of multisystem developmental involvement
PMID: 38884729
6
NIPBL interacts with BRD4 to stabilize NIPBL occupancy on chromatin and maintain proper genome folding during neural crest and smooth muscle differentiation
PMID: 34611363
Disease Associationsβ“˜21
Cornelia de Lange syndromeOpen Targets
0.86Strong
genetic disorderOpen Targets
0.54Moderate
Dislocated radial headOpen Targets
0.46Moderate
Intellectual disabilityOpen Targets
0.38Weak
low grade gliomaOpen Targets
0.37Weak
microcephalyOpen Targets
0.34Weak
cleft palateOpen Targets
0.34Weak
Abnormal brain morphologyOpen Targets
0.34Weak
Tetralogy of FallotOpen Targets
0.34Weak
septic shockOpen Targets
0.32Weak
liver diseaseOpen Targets
0.32Weak
MyoclonusOpen Targets
0.31Weak
Global developmental delayOpen Targets
0.29Weak
hypertrophic cardiomyopathyOpen Targets
0.28Weak
sensory perception of smellOpen Targets
0.28Weak
Abnormality of the skeletal systemOpen Targets
0.27Weak
vesicoureteral refluxOpen Targets
0.27Weak
adolescent idiopathic scoliosisOpen Targets
0.27Weak
Neurodevelopmental disorderOpen Targets
0.27Weak
fetal growth restrictionOpen Targets
0.27Weak
Cornelia de Lange syndrome 1UniProt
Pathogenic Variants587
NM_133433.4(NIPBL):c.2521C>T (p.Arg841Ter)Pathogenic
Cornelia de Lange syndrome 1
β˜…β˜…β˜†β˜†2026β†’ Residue 841
NM_133433.4(NIPBL):c.7301A>G (p.Asn2434Ser)Likely pathogenic
Cornelia de Lange syndrome 1|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 2434
NM_133433.4(NIPBL):c.2479_2480del (p.Arg827fs)Pathogenic
not provided|Cornelia de Lange syndrome 1
β˜…β˜…β˜†β˜†2025β†’ Residue 827
NM_133433.4(NIPBL):c.6620T>C (p.Met2207Thr)Pathogenic
Cornelia de Lange syndrome 1|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 2207
NM_133433.4(NIPBL):c.3855+5G>APathogenic
Cornelia de Lange syndrome 1
β˜…β˜…β˜†β˜†2025
NM_133433.4(NIPBL):c.7141G>A (p.Gly2381Ser)Likely pathogenic
Cornelia de Lange syndrome 1
β˜…β˜…β˜†β˜†2025β†’ Residue 2381
NM_133433.4(NIPBL):c.64+1G>APathogenic
Cornelia de Lange syndrome 1|Adrenocortical carcinoma, hereditary
β˜…β˜…β˜†β˜†2025
NM_133433.4(NIPBL):c.6647ATA[2] (p.Asn2218del)Pathogenic
Cornelia de Lange syndrome 1|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 2218
NM_133433.4(NIPBL):c.2466_2469del (p.Gln822fs)Likely pathogenic
Cornelia de Lange syndrome 1|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 822
NM_133433.4(NIPBL):c.6892C>T (p.Arg2298Cys)Pathogenic
Cornelia de Lange syndrome 1|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 2298
NM_133433.4(NIPBL):c.1447_1448del (p.Glu483fs)Pathogenic
Cornelia de Lange syndrome 1
β˜…β˜…β˜†β˜†2025β†’ Residue 483
NM_133433.4(NIPBL):c.6697G>A (p.Val2233Met)Pathogenic
Cornelia de Lange syndrome 1|NIPBL-related disorder
β˜…β˜…β˜†β˜†2025β†’ Residue 2233
NM_133433.4(NIPBL):c.43G>A (p.Gly15Arg)Pathogenic
not provided|Cornelia de Lange syndrome 1
β˜…β˜…β˜†β˜†2025β†’ Residue 15
NM_133433.4(NIPBL):c.8326dup (p.Ile2776fs)Pathogenic
Cornelia de Lange syndrome 1|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 2776
NM_133433.4(NIPBL):c.133C>T (p.Arg45Ter)Pathogenic
Cornelia de Lange syndrome 1|not provided|NIPBL-related disorder
β˜…β˜…β˜†β˜†2025β†’ Residue 45
NM_133433.4(NIPBL):c.6763+1G>APathogenic
Cornelia de Lange syndrome 1|not provided
β˜…β˜…β˜†β˜†2025
NM_133433.4(NIPBL):c.3060_3063del (p.Glu1021fs)Pathogenic
Cornelia de Lange syndrome 1|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 1021
NM_133433.4(NIPBL):c.5862+1G>APathogenic
Cornelia de Lange syndrome 1
β˜…β˜…β˜†β˜†2025
NM_133433.4(NIPBL):c.2389C>T (p.Arg797Ter)Pathogenic
Cornelia de Lange syndrome 1|not provided
β˜…β˜…β˜†β˜†2024β†’ Residue 797
NM_133433.4(NIPBL):c.771+1G>APathogenic
Cornelia de Lange syndrome 1|not provided|Inborn genetic diseases
β˜…β˜…β˜†β˜†2024
View on ClinVar β†—
Related Genes
SMC1BProtein interaction100%ESPL1Protein interaction98%SMC4Protein interaction98%STAG1Protein interaction98%CTCFProtein interaction98%STAG3Protein interaction98%
Tissue Expression6 tissues
Bone Marrow
100%
Ovary
50%
Lung
45%
Heart
37%
Brain
36%
Liver
27%
Gene Interaction Network
Click a node to explore
NIPBLSMC1BESPL1SMC4STAG1CTCFSTAG3
PROTEIN STRUCTURE
Preparing viewer…
PDB6WGE Β· 3.90 Γ… Β· EM
View on RCSB β†—
Constraintβ“˜
LOEUFβ“˜
0.06Highly Constrained
pLIβ“˜
1.00Intolerant
Observed/Expected LoF0.03 [0.02–0.06]
RankingsWhere NIPBL stands among ~20K protein-coding genes
  • #2,142of 20,598
    Most Researched198 Β· top quartile
  • #85of 5,498
    Most Pathogenic Variants587 Β· top 5%
  • #9of 17,882
    Most Constrained (LOEUF)0.06 Β· top 1%
Genes detectedNIPBL
Sources retrieved25 papers
Response timeβ€”
πŸ“„ Sources
25β–Ό
1
DNA loop extrusion by human cohesin.
PMID: 31753851
Science Β· 2019
1.00
2
Human Genetics of Ventricular Septal Defect.
PMID: 38884729
Adv Exp Med Biol Β· 2024
0.90
3
The expanding phenotypes of cohesinopathies: one ring to rule them all!
PMID: 31516082
Cell Cycle Β· 2019
0.80
4
The cancer driver genes IDH1/2, JARID1C/ KDM5C, and UTX/ KDM6A: crosstalk between histone demethylation and hypoxic reprogramming in cancer metabolism.
PMID: 31221981
Exp Mol Med Β· 2019
0.76
5
Genomic analyses in Cornelia de Lange Syndrome and related diagnoses: Novel candidate genes, genotype-phenotype correlations and common mechanisms.
PMID: 37377026
Am J Med Genet A Β· 2023
0.70