ClinGen Dosage Sensitivity Curation Page

NIPBL

  • Curation Status: Complete

Location Information

Select assembly: (NC_000005.9) (NC_000005.10)
Evidence for haploinsufficiency phenotype
PubMed ID Description
15146185 Tonkin et al (Nat Gen 2004) initially described the gene in several patients from their study with NIPBL variants (N = 10 patients, Table 1) detected by direct sequencing and heteroduplex analysis. The patients exhibited with a severe or mild (missense changes) Cornelia de Lange Syndrome (CdLS) phenotype. Phenotypic variation was noted but generally included characteristic face, severe growth restriction, feeding difficulty, and heart murmur. The alterations were small variants, splicing and/or nonsense changes. They were reported as either de novo or parental sample not available for testing.
15146186 Krantz et al. (Nat Gen 2004) identified stop gain, altered start codon, and splice site disruptions among 9 individuals across 12 families (table 2) with CdLS. A 1.1 Mb critical region involving NIPBL was delineated. All variants expected to result in a truncated protein and in three of the four sporadic cases for which samples were available from both parents, the detected variants were de novo.
15318302 Gills et al (AJHG 2004) evaluated 120 individuals with CdLS (including four previously reported, unrelated patients in PMID 15146186) for disruptions in the NIPBL gene. The entire NIPBL coding region (exons 2?47) was screened. The authors identified mutations in 56 patients with CdLS, of which 7 segregated in families and 49 were sporadic (i.e. 47% of tested probands, table 2 and fig. 1). In 25 of the 49 sporadic cases in which both parents were available for screening, all mutations were found to be de novo. The mutation spectrum comprised of 21 frameshift, 12 missense, 10 nonsense, and 8 splice-site mutations. The majority of identified variants were private.

Haploinsufficiency phenotype comments:

Additional study PMID: 31337854 (J of Human Gen 2019): Exome sequencing performed in 57 CdLS families examining several genes including NIPBL, SMC1A, SMC3, HDAC8, and RAD21 as major causes of CdLS. Pathogenic variants detected in 36 out of 57 families, with NIPBL being altered in 23 cases. NIPBL loss of function is a major causative gene for Cornelia de Lange syndrome (CdLS). To date over 80 pathogenic variants have been reported; including missense (~20%), frameshift (~40%), nonsense (~20%), and splice-site variants (~15%). Described in GeneReviews with highest loss of function pathogenic variants reported in NIPBL - Table 1 (https://www.ncbi.nlm.nih.gov/books/NBK1104/#cdls.Molecular_Genetics).

  • Triplosensitivity score: 1
  • Strength of Evidence (disclaimer): Little evidence for dosage pathogenicity
Evidence for triplosensitivity phenotype
PubMed ID Description
23085304 Novaro et al (EJMG 2012) performed aCGH (Agilent 180k microarray) and identified a 264kb duplication involving the entire NIPBL gene (no additional genes), confirmed by quantitative PCR . Coordinates (hg19) = chr5:36,809,705-37,073,754. This was indicated as a de novo occurrence following microsatellite analysis of the parents. The patient exhibits delay in psychomotor function, language, dysmorphic features of face, and extremities.
19052029 Yan et al (J Med Gen 2009) presented a study in which they comment on the dosage effect of 5p13 duplications. The patients, whose phenotype was assessed by medical geneticist, in their cohort shared common features including intellectual disability, developmental delay, sleep abnormalities, crainofacial obesity in some, and limb defects. The same systems are affected in CdLS, however clinical manifestations are distinct; namely the absence of the facial gestalt. The authors performed aCGH using a 244k oligo array (Agilent) Notable entry in this publication with respect to triplosensitivity: Patient 4 = 250 kb duplication containing only NIPBL (possibly smallest region of overlap reported). This individual also had a skull deformity. Whether this is a result of the duplication is difficult to assess and complicated the assessment of the phenotype. chr5:36870689-37120908 (hg18 coordinates). Converted to hg19: chr5:36,834,932-37,085,151 Of note, the gains were not detected in parental samples (both parents for two patients and 3 maternal samples for three patient). They were also not found in DGV and were confirmed by interphase FISH.

Triplosensitivity phenotype comment:

Additional cases of duplications including NIPBL (in addition to other genes) with overlapping clinical features have been reported, but are not counted as evidence here, since the effects of extra copies of those additional genes cannot be ruled out: PMID 19052029, Yan et al (J Med Gen 2009) above : Patients 1 and 2 = 390 kb duplication includes the NIPBL and exon 3 to the 3?UTR of the FLJ13231, a gene of unknown function. Patient 3 = 1.07 Mb duplication includes SLC1A3, NUP155, and exons 1 to 9 of the WDR70 gene in addition to the NIPBL and FLJ13231 genes. Patient 5 = 330 kb duplication includes exons 39 to 47 of NIPBL (partial duplication), FLJ13231, NUP155 and exons 1 and 2 of WDR70. PMID 21211577 : Oexle et al (European J. of Med Gen) report on a child with intellectual disability diagnosed at age 1.5 years, overweight (similar to phenotype in patient 1 of Yan et al). CNV analysis revealed a de novo 3.7 Mb duplication (fig. 3 for comparison to Yan et al study and some other ones with larger duplications Loscalzo 2008, Lorda-Sanch 1997) and confirmed by metaphase FISH. PMID: 22407779: Carrascosa Romero et al (AJMG 2011) describe a neonate with a broad forehead, craniosynostosis, hypertelorism, small low-set ears, mild retromicrognathia, large hands and feet, and hypoplastic corpus callosum. A 244k oligonucleotide array-CGH test detected a de novo 910 kb duplication spanning chr5:36255202-37167438 (Fig. 2, hg18). This duplication contained eight genes,