NIPBL

Chr 5AD

NIPBL cohesin loading factor

Also known as: CDLS, CDLS1, IDN3, IDN3-B, Scc2

The protein functions as a cohesin loading factor that facilitates sister chromatid cohesion and enables enhancer-promoter communication for proper developmental gene regulation. Loss-of-function mutations cause Cornelia de Lange syndrome 1, an autosomal dominant disorder characterized by distinctive facial features, growth delay, limb defects, and intellectual disability. The high intolerance to loss-of-function variants (pLI=1) reflects the protein's essential role in chromatin organization and gene expression during development.

OMIMResearchSummary from RefSeq, OMIM, UniProt, Mechanism
LOFmechanismADLOEUF 0.031 OMIM phenotype
Clinical SummaryNIPBL
🧬
Gene-Disease Validity (ClinGen)
Cornelia de Lange syndrome · ADDefinitive

Definitive — sufficient evidence for diagnostic panels

Population Constraint (gnomAD)
Highly constrained gene — heterozygous loss-of-function variants are very rare in the population (pLI 1.00). One damaged copy is likely sufficient to cause disease.
💊
Clinical Trials
1 active or recruiting trial — potential therapeutic options may be available

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

Dual constrained — LoF & missense intolerant
LoF Constraint
0.03LOEUF
pLI 1.000
Z-score 11.29
OE 0.01 (0.000.03)
Highly constrained

Among the most LoF-intolerant genes (~top 3%)

Missense Constraint
5.57Z-score
OE missense 0.59 (0.550.62)
846 obs / 1441.5 exp
Constrained

Extremely missense-constrained (top ~0.01%)

Observed / Expected Ratios
LoF OE0.01 (0.000.03)
00.351.4
Missense OE0.59 (0.550.62)
00.61.4
Synonymous OE1.00
01.21.6
LoF obs/exp: 1 / 150.3Missense obs/exp: 846 / 1441.5Syn Z: -0.04
Curated Mechanism (G2P)Gene2Phenotype (DDG2P) ↗
definitiveNIPBL-related Cornelia de Lange syndromeLOFAD
DN
0.16100th %ile
GOF
0.14100th %ile
LOF
0.90top 5%

The highest-scoring mechanism for this gene is loss-of-function (haploinsufficiency).

LOFprediction above median · 1 literature citation · LOEUF 0.03

Literature Evidence

LOFHowever, the effect of NIPBL haploinsufficiency on cohesin binding, and how this relates to the clinical presentation of CdLS, has not been fully investigated.PMID:28855971

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312. Mechanism ranking also informed by gnomAD constraint, ClinVar, and ClinGen data.

ClinVar Variant Classifications

0 submitted variants in ClinVar

Protein Context — Lollipop Plot

NIPBL · protein map & ClinVar variants

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

3D Protein StructureAlphaFold
Clinical Literature
Open Research Assistant →
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
NIPBL and cohesin: new take on a classic tale.
Alonso-Gil D et al.·Trends Cell Biol
2023
NIPBL::NACC1 Fusion Hepatic Carcinoma.
Hissong E et al.·Am J Surg Pathol
2023
Malignant Bone-Forming Neoplasm With NIPBL::BEND2 Fusion.
Dashti NK et al.·Genes Chromosomes Cancer
2024
[Hepatic carcinoma with NIPBL::NACC1 fusion: report of a case].
Zhang YD et al.·Zhonghua Bing Li Xue Za Zhi
2025
Top 5 full-text resultsSearch PubTator3 ↗