Entry - *606681 - NUCLEAR RECEPTOR-BINDING SET DOMAIN PROTEIN 1; NSD1 - OMIM
* 606681

NUCLEAR RECEPTOR-BINDING SET DOMAIN PROTEIN 1; NSD1


Alternative titles; symbols

NUCLEAR RECEPTOR-BINDING Su-var, ENHANCER OF ZESTE, AND TRITHORAX DOMAIN PROTEIN 1
SET DOMAIN PROTEIN 1
ANDROGEN RECEPTOR-ASSOCIATED COREGULATOR 267; ARA267


Other entities represented in this entry:

NSD1/NUP98 FUSION GENE, INCLUDED

HGNC Approved Gene Symbol: NSD1

Cytogenetic location: 5q35.3     Genomic coordinates (GRCh38): 5:177,131,798-177,300,213 (from NCBI)


Gene-Phenotype Relationships
Location Phenotype Phenotype
MIM number
Inheritance Phenotype
mapping key
5q35.3 Sotos syndrome 117550 AD 3


TEXT

Description

The androgen receptor (AR; 313700) is a member of the steroid receptor (SR) superfamily that interacts with DNA response elements. SRs may enhance or inhibit transcription by recruiting an array of coregulators, including NSD1, that interact with its N or C terminus.


Cloning and Expression

Jaju et al. (1999) identified a recurrent cryptic translocation, t(5;11)(q35;p15.5), associated with a deletion of the long arm of chromosome 5 in de novo childhood acute myeloid leukemia (AML; see 601626). Jaju et al. (2001) confirmed that the chromosome 11 breakpoint gene is NUP98 (601021) and reported the cloning of its novel chromosome 5 fusion partner, NSD1. Nucleotide 1552 of NUP98 was fused in-frame to nucleotide 3504 of NSD1. The full coding sequence of NSD1 encodes a deduced 2,596-amino acid protein. The human and mouse NSD1 proteins share 85% sequence identity and have the same domain structure including a conserved SET domain, a SET domain-associated cysteine-rich domain (SAC domain), and 5 PHD fingers. Northern blot analysis detected wide expression of 2 NSD1 transcripts of 10.5 and 12.0 kb in hematologic and other tissues, respectively.

Using a yeast 2-hybrid screen of a brain cDNA library with the ligand-binding domains (LBDs) of AR and TR4 (NR2C2; 601426) as bait, followed by 5-prime RACE on a testis cDNA library, Wang et al. (2001) isolated a cDNA encoding NSD1, which they called ARA267-alpha, encoding a. 2,427-amino acid protein with homology to other ARA coregulators. The protein possesses a SET domain, 2 LXXLL motifs, 3 nuclear translocation signals (NLSs), 4 plant homeodomain (PHD) finger regions, and a proline-rich region. The 4 PHD finger regions contain a cys-rich region, a ring finger, and a zinc finger. Wang et al. (2001) also identified an ARA267-beta isoform encoding a 2,696-amino acid protein that is 83% homologous to mouse Nsd1 and has 279 N-terminal residues that merge into the eleventh residue of ARA267-alpha. Northern blot analysis revealed expression of 13- and 10-kb transcripts in multiple cell lines. Dot blot analysis detected expression in most tissues, with highest expression in lymph node. Mutation and binding analyses indicated that the N- and C-terminal domains of ARA267 can interact with full-length or C-terminal AR, but not with N-terminal AR, suggesting that the LBD and DNA-binding domain of AR may be responsible for the interaction. Luciferase analysis demonstrated that ARA267, like other ARA coregulators, has little or no influence on the interaction of the N and C termini of AR.

Kurotaki et al. (2001) independently cloned the NSD1 gene and found that it is expressed in fetal/adult brain, skeletal muscle, kidney, spleen, and thymus, and faintly in lung.


Gene Function

Functional analysis by Wang et al. (2001) showed that ARA267-alpha enhances AR transactivation, and this enhancement could be increased further in the presence of other ARA coregulators, such as ARA24 (RAN; 601179) and PCAF (602303).

Weinberg et al. (2019) reported that NSD1-mediated H3K36me2 is required for the recruitment of DNMT3A (602769) and maintenance DNA methylation at intergenic regions. Genomewide analysis showed that the binding and activity of DNMT3A colocalized with H3K36me2 at noncoding regions of euchromatin. Genetic ablation of Nsd1 and its paralog Nsd2 in mouse cells resulted in a redistribution of Dnmt3A to H3K36me3-modified gene bodies and a reduction in the methylation of intergenic DNA. Blood samples from patients with Sotos syndrome (117550) and NSD1-mutant tumors also exhibited hypomethylation of intergenic DNA. The PWWP domain of DNMT3A showed dual recognition of H3K36me2 and H3K36me3 in vitro, with a higher binding affinity towards H3K36me2 that was abrogated by Tatton-Brown-Rahman syndrome (TBRS; 615879)-derived missense mutations. Weinberg et al. (2019) concluded that their study revealed a trans-chromatin regulatory pathway that connects aberrant intergenic CpG methylation to human neoplastic and developmental overgrowth.

Using genomewide profiling, Shirane et al. (2020) showed that Setd2 (612778) and H3K36me3 were dispensable for de novo DNA methylation (DNAme) in male mouse germline development. Instead, H3K36me2 was broadly correlated with DNAme. Nsd1 was required for DNAme in prenatal male germ cells and was essential for establishment of DNAme at H3K36me2-marked regions within paternal gametic differentially methylated regions. Furthermore, Nsd1 was required for survival of spermatogonia and spermatogenesis. Knockout of Nsd1 in prospermatogonia revealed that H3K36me2 deposited by Nsd1 impeded further deposition of H3K27me3 in prenatal male germline development in the absence of de novo DNAme, thereby safeguarding a subset of genes against H3K27me3-associated repression. In contrast, Setd2 was required not only for deposition of H3K36me3 in oocytes and de novo DNAme in transcribed regions, but also for deposition of the majority of H3K36me2 in oocytes.


Gene Structure

Kurotaki et al. (2001) determined that the NSD1 gene contains 23 exons.


Mapping

By FISH, Jaju et al. (2001) mapped the NSD1 gene to chromosome 5q35.


Molecular Genetics

Imaizumi et al. (2002) found a t(5;8)(q35;q24.1) translocation in a child with Sotos syndrome (SOTOS; 117550). Kurotaki et al. (2002) identified NSD1 as the gene disrupted by the 5q35 breakpoint.

Kurotaki et al. (2002) identified 4 different de novo point mutations in the NSD1 gene in 4 of 38 individuals with Sotos syndrome. These included 1 nonsense mutation, 2 frameshift mutations, and 1 splice site mutation. FISH analysis revealed a common 2.2-Mb deletion in 19 individuals and a smaller deletion in 1 individual from a total of 30 affected individuals whose metaphase or interphase cells were available. The deletions involved the entire NSD1 gene. Kurotaki et al. (2002) found that 77% of individuals with Sotos syndrome in their study had either deletions or point mutations in the NSD1 gene as the cause of Sotos syndrome. They concluded that haploinsufficiency of NSD1 is the major cause of Sotos syndrome.

Douglas et al. (2003) evaluated 75 patients with childhood overgrowth for intragenic mutations and large deletions in NSD1 of the type reported by Kurotaki et al. (2002) as the major cause of Sotos syndrome. Before molecular analyses, the patients were phenotypically scored into 4 groups: 37 patients comprising group 1 had a phenotype typical of Sotos syndrome; 13 patients comprising group 2 had a Sotos-like phenotype but with some atypical features; 7 patients comprising group 3 had been diagnosed with Weaver syndrome (WVS; 277590); and 18 patients comprising group 4 had an overgrowth condition that was neither Sotos nor Weaver syndrome. Douglas et al. (2003) detected 3 deletions and 32 mutations that were predicted to impair NSD1 functions. The truncating mutations were spread throughout NSD1, but there was evidence of clustering of missense mutations in highly conserved functional domains between exons 13 and 23. There was a strong correlation between presence of an NSD1 alteration and clinical phenotype, as 28 of 37 (76%) patients in group 1 had NSD1 mutations or deletions, whereas none of the patients in group 4 had abnormalities of NSD1. Three of the 7 patients who had been diagnosed with Weaver syndrome had NSD1 mutations, all between amino acids 2142 and 2184 (see 606681.0006). Tatton-Brown et al. (2005) reviewed the phenotype of the 3 patients who carried a diagnosis of Weaver syndrome and in whom Douglas et al. (2003) had identified mutations in the NSD1 gene, and on the basis of multiple pictures at different ages, reclassified 2 of them as having 'typical Sotos syndrome' and the third as 'possible Sotos syndrome.'

Nagai et al. (2003) analyzed the phenotypic findings of 5 patients with intragenic NSD1 mutations predicted to form a truncated NSD1 protein and in 21 patients with a fairly common deletion of approximately 2.2 Mb involving the entire NSD1 gene. Overgrowth and advanced maturation in infancy to early childhood, mental retardation, hypotonia, hyperreflexia, and characteristic minor anomalies were present in patients with mutations and deletions, whereas major anomalies in the central nervous system (agenesis or hypoplasia of the corpus callosum), cardiovascular system (patent ductus arteriosus and atrial septal defect), and urinary system (vesicoureteric reflux, hydronephrosis, and small kidney) were exclusively exhibited by patients with deletions. The results suggested that clinical features in Sotos syndrome can be classified into 2 major categories: those primarily caused by NSD1 haploinsufficiency and those primarily ascribed to some factors, such as the dosage effects of genes other than NSD1, involved in the deletion.

Turkmen et al. (2003) screened the NSD1 gene for mutations in 20 patients and 1 familial case with Sotos syndrome, 5 patients with Weaver syndrome, 6 patients with unclassified overgrowth and mental retardation, and 6 patients with macrocephaly and mental retardation. They identified 19 mutations, 17 previously undescribed, in 18 Sotos patients and the familial case (90%). The best correlation between the molecular and clinical findings was for facial gestalt in conjunction with overgrowth, macrocephaly, and developmental delay. Turkmen et al. (2003) found no mutations of the NSD1 gene in the patients with Weaver syndrome or other overgrowth phenotypes and concluded that the great majority of patients with Sotos syndrome have mutations in NSD1.

Kurotaki et al. (2003) found 50 microdeletions (606681.0001) among 112 cases of Sotos syndrome and suggested that low copy repeats (LCRs) possibly mediate the common deletion. As pointed out by Visser and Matsumoto (2003), intragenic mutations prevail in Caucasian Sotos syndrome patients, whereas Japanese patients with this disorder more frequently harbor a microdeletion. Each deletion breakpoint is located in either of the 2 flanking LCRs. Most meiotic rearrangements seem to be of intrachromosomal origin and show a preference for the paternally derived chromosome.

In light of accumulated evidence, Sotos syndrome can be added to the list of genomic disorders (Shaw and Lupski, 2004), defined as pathologic conditions in which the gain, loss, or disruption of dosage-sensitive gene(s) results in a recognized phenotype (Lupski, 1998). Unequal rearrangement (nonallelic homologous recombination) between regions of high homology (i.e., LCRs) is the most common mechanism. Visser et al. (2005) found a heterozygous inversion of the interval between the LCRs in all fathers of children carrying a deletion in the paternally derived chromosome. Segmental duplications of the primate genome played a major role in chromosomal evolution. Evolutionary studies by Visser et al. (2005) showed that the duplication of the Sotos syndrome LCRs occurred 23.3 to 47.6 million years ago, before the divergence of Old World monkeys.

Kurotaki et al. (2005) characterized 2 complex mosaic low-copy repeats (LCRs) that are centromeric and telomeric to NSD1, which they designated proximal Sos-REP (Sos-PREP, approximately 390 kb) and distal Sos-REP (Sos-DREP, approximately 429 kb), respectively. Sos-PREP and Sos-DREP are composed of 6 subunits termed A to F. All but one homologous subunit was located in an inverted orientation, and the order of subunits was different between the 2 Sos-REPs. Only the subunit C-prime in Sos-DREP was oriented directly with respect to the subunit C in Sos-PREP. Among 8 Sotos patients with a common deletion, an approximately 550-kb junction fragment was detected that was generated by nonallelic homologous recombination (NAHR) between Sos-PREP C and Sos-DREP C-prime subunits. This patient-specific junction fragment was not present in 51 Japanese and non-Japanese controls. Kurotaki et al. (2005) identified a 2.5-kb unequal crossover hotspot region in 6 of 9 analyzed Sotos patients with the common deletion.

Melchior et al. (2005) developed a denaturing high-performance liquid chromatography (DHPLC) screening protocol for mutation detection in NSD1 and identified 9 novel mutations among 33 patients, an efficiency of mutation detection comparable to that achieved by direct sequencing. In 2 patients, NSD1 deletions were identified. A summary of over 100 NSD1 mutations was provided.

Through analyses of 530 individuals with diverse phenotypes, Tatton-Brown et al. (2005) identified 266 individuals with intragenic NSD1 mutations or 5q35 microdeletions encompassing the NSD1 gene. Of 166 patients with NSD1 abnormalities for whom photographs were available, Sotos syndrome was clinically diagnosed in 164 (99%) independent of the molecular analysis, indicating that NSD1 aberrations are essentially specific to this condition. Analysis of 124 patients from the United Kingdom suggested that 93% of patients who have been clinically diagnosed with Sotos syndrome have identifiable NSD1 abnormalities, of which 83% are intragenic mutations and 10% are 5q35 microdeletions. Tatton-Brown et al. (2005) reviewed the clinical phenotype of 239 individuals with NSD1 abnormalities and observed that individuals with identical mutations had different phenotypes, that all features present in patients with microdeletions were also observed in patients with mutations, and that there was no correlation between deletion size and clinical phenotype. Tatton-Brown et al. (2005) identified only 13 familial cases and noted that familial cases were more likely than nonfamilial cases to carry missense mutations (p = 0.005), suggesting that the underlying NSD1 mutation mechanism in Sotos syndrome may influence reproductive fitness.

Van Haelst et al. (2005) reported a 3-generation family with gigantism (Sotos syndrome) in whom they identified a missense mutation in the NSD1 gene (C2202Y; 606681.0013).

Cecconi et al. (2005) identified mutations in the NSD1 gene in 17 (71%) of 24 patients with classic Sotos syndrome. All patients with a mutant NSD1 genotype showed the typical facial gestalt; however, not all patients showed height above the 97th percentile, absolute macrocephaly, or advanced bone age. No genotype/phenotype correlations were observed. NSD1 mutations were not identified in 9 patients with a Sotos-like phenotype, 2 patients with Weaver syndrome, or 24 additional patients with nonspecific overgrowth, suggesting that mutations in the NSD1 gene are specific for Sotos syndrome.

Kanemoto et al. (2006) reported a female infant with features of both Sotos syndrome and Nevo syndrome (see 225400) in whom they identified a heterozygous 2.2-Mb deletion (606681.0001) encompassing the NSD1 gene.

Saugier-Veber et al. (2007) identified 69 different point mutations, including 48 novel mutations, in the NSD1 gene in 104 patients from 102 families with Sotos syndrome. Point mutations were detected in 80%, large deletions removing the entire NSD1 gene in 14%, and intragenic NSD1 rearrangements in 6%. The large deletions ranged in size from 1 to 4.5 Mb. Patients with truncating mutations had a more severe phenotype than those with nontruncating mutations. No NSD1 mutations were identified in 12 additional patients with a clinical diagnosis of Sotos syndrome.

Tatton-Brown and Rahman (2013) reviewed the similarities and differences between the NSD1 and EZH2 (601573) genes, which cause the overgrowth Sotos and Weaver syndromes, respectively. The authors noted that although the NSD1-associated phenotype has been well characterized with many hundreds of reported cases, it is not yet understood what factors determine the variability of the Sotos syndrome phenotype, in which unrelated individuals with the same recurrent mutation exhibit differing degrees of intellectual disability and frequencies of associated medical issues such as cardiac and renal anomalies, seizures, and scoliosis.

In 7 patients with Sotos syndrome with hyperinsulinemic hypoglycemia with persistence beyond a year of age in at least 3 patients, Grand et al. (2019) identified point mutations in the NSD1 gene. The mutations included 4 nonsense, 3 missense, and 1 frameshift. The authors noted that these patients disprove the hypothesis that hyperinsulinemic hypoglycemia is due to deletion of nearby genes in the 5q35 deleted region and suggest a role for NSD1 in glucose homeostasis.


ALLELIC VARIANTS ( 13 Selected Examples):

.0001 SOTOS SYNDROME

NSD1, 1.9-MB DEL
   RCV003231075

In 19 of 30 Japanese individuals with Sotos syndrome (SOTOS; 117550), Kurotaki et al. (2002) identified a 2.2-Mb deletion on chromosome 5q35 leading to complete deletion of the NSD1 gene.

Haploinsufficiency of the NSD1 gene owing to either intragenic mutations or microdeletions is the major cause of Sotos syndrome. The common microdeletion of approximately 2.2 Mb encompasses the whole NSD1 gene and neighboring genes and is flanked by low-copy repeats (LCRs). Visser et al. (2005) identified a 3.0-kb major recombination hotspot within these LCRs, in which they mapped deletion breakpoints in 78.7% (37/47) of patients with Sotos syndrome who carried the common microdeletion. They were able to refine the size of the deletion to 1.9 Mb. Sequencing of breakpoint fragments from all 37 patients revealed junctions between a segment of the proximal LCR (PLCR-B) and the corresponding region of the distal LCR (DLCR-2B). Visser et al. (2005) found that PLCR-B and DLCR-2B are the only directly oriented regions, whereas the remaining regions of the PLCR and DLCR are in inverted orientation. PLCR and DLCR showed high overall homology (approximately 98.5%), with an increased sequence similarity (approximately 99.4%) within the 3.0-kb breakpoint cluster.

In a female infant with features of both Sotos syndrome and Nevo syndrome (225400), Kanemoto et al. (2006) identified heterozygosity for a 2.2-Mb deletion encompassing the NSD1 gene.


.0002 SOTOS SYNDROME

NSD1, SER437TER
  
RCV003231076...

In a patient with sporadic Sotos syndrome (SOTOS; 117550), Kurotaki et al. (2002) identified a C-to-G transversion at nucleotide 1310 leading to a ser437-to-ter substitution at codon 437 on 1 allele of the NSD1 gene. This patient with the S437X nonsense mutation was 1 of 5 in whom the phenotype was analyzed by Nagai et al. (2003).


.0003 SOTOS SYNDROME

NSD1, 1-BP DEL, 3536A
  
RCV003231078

In a patient with sporadic Sotos syndrome (SOTOS; 117550), Kurotaki et al. (2002) identified a deletion of a single basepair at nucleotide 3536 of the NSD1 gene. This patient was 1 of 5 in whom the phenotype was analyzed by Nagai et al. (2003).


.0004 SOTOS SYNDROME

NSD1, 1-BP INS, 5998T
  
RCV003231079

In a patient with sporadic Sotos syndrome (SOTOS; 117550), Kurotaki et al. (2002) identified an insertion of a thymidine at nucleotide 5998 in the NSD1 gene. This patient was 1 of 5 in whom the phenotype was analyzed by Nagai et al. (2003).


.0005 SOTOS SYNDROME

NSD1, IVS20DS, G-A, +1
  
RCV001818128...

In a patient with sporadic Sotos syndrome (SOTOS; 117550), Kurotaki et al. (2002) identified a splice site mutation at the splice donor site of intron 20 leading to a premature termination codon only 9 amino acids thereafter. This patient was 1 of 5 in whom the phenotype was analyzed by Nagai et al. (2003).


.0006 SOTOS SYNDROME

NSD1, HIS2143GLN
  
RCV003231081

In a patient originally diagnosed with Weaver syndrome, Douglas et al. (2003) identified a heterozygous mutation in exon 22 of the NSD1 gene, resulting in a his2143-to-glu substitution. The patient was later diagnosed with Sotos syndrome (SOTOS; 117550) by Tatton-Brown et al. (2005) after review of patient photographs at different ages and the mutation was corrected to his2143-to-gln (H2143Q). See online Table 2 in Tatton-Brown et al. (2005).


.0007 SOTOS SYNDROME

NSD1, CYS2183SER
  
RCV003231082

In a patient originally diagnosed with Weaver syndrome, Douglas et al. (2003) identified a heterozygous mutation in exon 23 of the NSD1 gene, resulting in a cys2183-to-ser (C2183S) substitution. The patient was later diagnosed with Sotos syndrome (SOTOS; 117550) by Tatton-Brown et al. (2005) after review of patient photographs at different ages.


.0008 SOTOS SYNDROME

NSD1, 1-BP INS, 6450C
  
RCV003231083

In a patient originally diagnosed with Weaver syndrome, Douglas et al. (2003) identified a heterozygous 1-bp insertion (6450insC) in exon 22 of the NSD1, resulting in a frameshift and a termination at codon 2165. The patient was later diagnosed with Sotos syndrome (SOTOS; 117550) by Tatton-Brown et al. (2005) after review of patient photographs at different ages.


.0009 SOTOS SYNDROME

NSD1, 1-BP DEL, 896C
  
RCV003231084

In a Finnish father and son with Sotos syndrome (SOTOS; 117550), Hoglund et al. (2003) identified a heterozygous 1-bp deletion (896delC) in exon 2 of the NSD1 gene, resulting in a truncation of 88% of the predicted polypeptide. The mutation was not detected in the unaffected mother or in 94 unrelated Finnish individuals. Hoglund et al. (2003) noted that the findings in this family confirm that familial Sotos syndrome is caused by mutation in the NSD1 gene.


.0010 SOTOS SYNDROME

NSD1, ARG1320TER
  
RCV000487238...

One of the 5 patients with Sotos syndrome (SOTOS; 117550) and intragenic mutations of the NSD1 gene studied by Nagai et al. (2003) had a novel nonsense mutation in exon 7 of the NSD1 gene: 3958C-T, arg1320 to stop (R1320X).


.0011 SOTOS SYNDROME

NSD1, 1-BP INS, 4976G
  
RCV003231086

In a patient (PB) with Sotos syndrome (SOTOS; 117550), who had a clinical diagnosis of Beckwith-Wiedemann syndrome (130650), Baujat et al. (2004) identified a de novo 1-bp insertion, 4976insG, in exon 14 of the NSD1 gene. Features consistent with BWS included large umbilical hernia and left-sided hemihypertrophy.


.0012 SOTOS SYNDROME

NSD1, 4-BP DEL, 7968GACA
  
RCV003231087

In a patient (BA) with Sotos syndrome (SOTOS; 117550), who had a clinical diagnosis of Beckwith-Wiedemann syndrome (130650), Baujat et al. (2004) identified a de novo 4-bp deletion, 7968delGACA, in exon 23 of the NSD1 gene.


.0013 SOTOS SYNDROME

NSD1, CYS2202TYR
  
RCV001813734...

In affected members of a 3-generation family with Sotos syndrome (SOTOS; 117550), van Haelst et al. (2005) identified a 6605G-A transition in the NSD1 gene, resulting in a cys2202-to-tyr (C2202Y) substitution.


REFERENCES

  1. Baujat, G., Rio, M., Rossignol, S., Sanlaville, D., Lyonnet, S., Le Merrer, M., Munnich, A., Gicquel, C., Cormier-Daire, V., Colleaux, L. Paradoxical NSD1 mutations in Beckwith-Wiedemann syndrome and 11p15 anomalies in Sotos syndrome. Am. J. Hum. Genet. 74: 715-720, 2004. [PubMed: 14997421, images, related citations] [Full Text]

  2. Cecconi, M., Forzano, F., Milani, D., Cavani, S., Baldo, C., Selicorni, A., Pantaleoni, C., Silengo, M., Ferrero, G. B., Scarano, G., Della Monica, M., Fischetto, R., and 10 others. Mutation analysis of the NSD1 gene in a group of 59 patients with congenital overgrowth. Am. J. Med. Genet. 134A: 247-253, 2005. [PubMed: 15742365, related citations] [Full Text]

  3. Douglas, J., Hanks, S., Temple, I. K., Davies, S., Murray, A., Upadhyaya, M., Tomkins, S., Hughes, H. E., Cole, T. R. P., Rahman, N. NSD1 mutations are the major cause of Sotos syndrome and occur in some cases of Weaver syndrome but are rare in other overgrowth phenotypes. Am. J. Hum. Genet. 72: 132-143, 2003. [PubMed: 12464997, images, related citations] [Full Text]

  4. Grand, K., Gonzalez-Gandolfi, C., Ackermann, A. M., Aljeaid, D., Bedoukian, E., Bird, L. M., De Leon, D. D., Diaz, J., Hopkin, R. J., Kadakia, S. P., Keena, B., Klein, K. O., and 11 others. Hyperinsulinemic hypoglycemia in seven patients with de novo NSD1 mutations. Am. J. Med. Genet. 179A: 542-551, 2019. [PubMed: 30719864, images, related citations] [Full Text]

  5. Hoglund, P., Kurotaki, N., Kytola, S., Miyake, N., Somer, M., Matsumoto, N. Familial Sotos syndrome is caused by a novel 1 bp deletion of the NSD1 gene. (Letter) J. Med. Genet. 40: 51-54, 2003. [PubMed: 12525543, related citations] [Full Text]

  6. Imaizumi, K., Kimura, J., Matsuo, M., Kurosawa, K., Masuno, M., Niikawa, N., Kuroki, Y. Sotos syndrome associated with a de novo balanced reciprocal translocation t(5;8)(q35;q24.1). Am. J. Med. Genet. 107: 58-60, 2002. [PubMed: 11807869, related citations] [Full Text]

  7. Jaju, R. J., Fidler, C., Haas, O. A., Strickson, A. J., Watkins, F., Clark, K., Cross, N. C. P., Cheng, J.-F., Aplan, P. D., Kearney, L., Boultwood, J., Wainscoat, J. S. A novel gene, NSD1, is fused to NUP98 in the t(5;11)(q35;p15.5) in de novo childhood acute myeloid leukemia. Blood 98: 1264-1267, 2001. [PubMed: 11493482, related citations] [Full Text]

  8. Jaju, R. J., Haas, O. A., Neat, M., Harbott, J., Saha, V., Boultwood, J., Brown, J. M., Pirc-Danoewinata, H., Krings, B. W., Muller, U., Morris, S. W., Wainscoat, J. S., Kearney, L. A new recurrent translocation, t(5;11)(q35p15.5), associated with del(5q) in childhood acute myeloid leukemia. Blood 94: 773-780, 1999. [PubMed: 10397745, related citations]

  9. Kanemoto, N., Kanemoto, K., Nishimura, G., Kamoda, T., Visser, R., Shimokawa, O., Matsumoto, N. Nevo syndrome with an NSD1 deletion: a variant of Sotos syndrome? Am. J. Med. Genet. 140A: 70-73, 2006. [PubMed: 16329110, related citations] [Full Text]

  10. Kurotaki, N., Harada, N., Shimokawa, O., Miyake, N., Kawame, H., Uetake, K., Makita, Y., Kondoh, T., Ogata, T., Hasegawa, T., Nagai, T., Ozaki, T., and 22 others. Fifty microdeletions among 112 cases of Sotos syndrome: low copy repeats possibly mediate the common deletion. Hum. Mutat. 22: 378-387, 2003. [PubMed: 14517949, related citations] [Full Text]

  11. Kurotaki, N., Harada, N., Yoshiura, K., Sugano, S., Niikawa, N., Matsumoto, N. Molecular characterization of NSD1, a human homologue of the mouse Nsd1 gene. Gene 279: 197-204, 2001. [PubMed: 11733144, related citations] [Full Text]

  12. Kurotaki, N., Imaizumi, K., Harada, N., Masuno, M., Kondoh, T., Nagai, T., Ohashi, H., Naritomi, K., Tsukahara, M., Makita, Y., Sugimoto, T., Sonoda, T., and 11 others. Haploinsufficiency of NSD1 causes Sotos syndrome. Nature Genet. 30: 365-366, 2002. [PubMed: 11896389, related citations] [Full Text]

  13. Kurotaki, N., Stankiewicz, P., Wakui, K., Niikawa, N., Lupski, J. R. Sotos syndrome common deletion is mediated by directly oriented subunits within inverted Sos-REP low-copy repeats. Hum. Molec. Genet. 14: 535-542, 2005. [PubMed: 15640245, related citations] [Full Text]

  14. Lupski, J. R. Genomic disorders: structural features of the genome can lead to DNA rearrangements and human disease traits. Trends Genet. 14: 417-422, 1998. [PubMed: 9820031, related citations] [Full Text]

  15. Melchior, L., Schwartz, M., Duno, M. dHPLC screening of the NSD1 gene identifies nine novel mutations--summary of the first 100 Sotos syndrome mutations. Ann. Hum. Genet. 69: 222-226, 2005. [PubMed: 15720303, related citations] [Full Text]

  16. Nagai, T., Matsumoto, N., Kurotaki, N., Harada, N., Niikawa, N., Ogata, T., Imaizumi, K., Kurosawa, K., Kondoh, T., Ohashi, H., Tsukahara, M., Makita, Y., Sugimoto, T., Sonoda, T., Yokoyama, T., Uetake, K., Sakazume, S., Fukushima, Y., Naritomi, K. Sotos syndrome and haploinsufficiency of NSD1: clinical features of intragenic mutations and submicroscopic deletions. J. Med. Genet. 40: 285-289, 2003. [PubMed: 12676901, related citations] [Full Text]

  17. Saugier-Veber, P., Bonnet, C., Afenjar, A., Drouin-Garraud, V., Coubes, C., Fehrenbach, S., Holder-Espinasse, M., Roume, J., Malan, V., Portnoi, M.-F., Jeanne, N., Baumann, C., and 9 others. Heterogeneity of NSD1 alterations in 116 patients with Sotos syndrome. Hum. Mutat. 28: 1098-1107, 2007. [PubMed: 17565729, related citations] [Full Text]

  18. Shaw, C. J., Lupski, J. R. Implications of human genome architecture for rearrangement-based disorders: the genomic basis of disease. Hum. Molec. Genet. 13 Spec. No. 1: R57-R64, 2004. [PubMed: 14764619, related citations] [Full Text]

  19. Shirane, K., Miura, F., Ito, T., Lorincz, M. C. NSD1-deposited H3K36me2 directs de novo methylation in the mouse male germline and counteracts Polycomb-associated silencing. Nature Genet. 52: 1088-1098, 2020. [PubMed: 32929285, related citations] [Full Text]

  20. Tatton-Brown, K., Douglas, J., Coleman, K., Baujat, G., Cole, T. R. P., Das, S., Horn, D., Hughes, H. E., Temple, I. K., Faravelli, F., Waggoner, D., Turkmen, S., Cormier-Daire, V., Irrthum, A., Rahman, N. Genotype-phenotype associations in Sotos syndrome: an analysis of 266 individuals with NSD1 aberrations. Am. J. Hum. Genet. 77: 193-204, 2005. [PubMed: 15942875, images, related citations] [Full Text]

  21. Tatton-Brown, K., Rahman, N. The NSD1 and EZH2 overgrowth genes, similarities and differences. Am. J. Med. Genet. 163C: 86-91, 2013. [PubMed: 23592277, images, related citations] [Full Text]

  22. Turkmen, S., Gillessen-Kaesbach, G., Meinecke, P., Albrecht, B., Neumann, L. M., Hesse, V., Palanduz, S., Balg, S., Majewski, F., Fuchs, S., Zschieschang, P., Greiwe, M., Mennicke, K., Kreuz, F. R., Dehmel, H. J., Rodeck, B., Kunze, J., Tinschert, S., Mundlos, S., Horn, D. Mutations in NSD1 are responsible for Sotos syndrome, but are not a frequent finding in other overgrowth phenotypes. Europ. J. Hum. Genet. 11: 858-865, 2003. [PubMed: 14571271, related citations] [Full Text]

  23. van Haelst, M. M., Hoogeboom, J. J. M., Baujat, G., Bruggenwirth, H. T., Van de Laar, I., Coleman, K., Rahman, N., Niermeijer, M. F., Drop, S. L. S., Scambler, P. J. Familial gigantism caused by an NSD1 mutation. Am. J. Med. Genet. 139A: 40-44, 2005. [PubMed: 16222665, related citations] [Full Text]

  24. Visser, R., Matsumoto, N. Genetics of Sotos syndrome. Curr. Opin. Pediat. 15: 598-606, 2003. [PubMed: 14631206, related citations] [Full Text]

  25. Visser, R., Shimokawa, O., Harada, N., Kinoshita, A., Ohta, T., Niikawa, N., Matsumoto, N. Identification of a 3.0-kb major recombination hotspot in patients with Sotos syndrome who carry a common 1.9-Mb microdeletion. Am. J. Hum. Genet. 76: 52-67, 2005. [PubMed: 15580547, images, related citations] [Full Text]

  26. Wang, X., Yeh, S., Wu, G., Hsu, C.-L., Wang, L., Chiang, T., Yang, Y., Guo, Y., Chang, C. Identification and characterization of a novel androgen receptor coregulator ARA267-alpha in prostate cancer cells. J. Biol. Chem. 276: 40417-40423, 2001. [PubMed: 11509567, related citations] [Full Text]

  27. Weinberg, D. N., Papillon-Cavanagh, S., Chen, H., Yue, Y., Chen, X., Rajagopalan, K. N., Horth, C., McGuire, J. T., Xu, X., Nikbakht, H., Lemiesz, A. E., Marchione, D. M., and 13 others. The histone mark H3K36me2 recruits DNMT3A and shapes the intergenic DNA methylation landscape. Nature 573: 281-286, 2019. [PubMed: 31485078, images, related citations] [Full Text]


Sonja A. Rasmussen - updated : 05/19/2022
Bao Lige - updated : 02/04/2021
Ada Hamosh - updated : 11/15/2019
Marla J. F. O'Neill - updated : 5/2/2013
George E. Tiller - updated : 1/3/2008
Cassandra L. Kniffin - updated : 11/13/2007
Cassandra L. Kniffin - updated : 10/2/2006
Marla J. F. O'Neill - updated : 1/25/2006
Marla J. F. O'Neill - updated : 11/17/2005
Marla J. F. O'Neill - updated : 8/30/2005
Victor A. McKusick - updated : 5/11/2005
Victor A. McKusick - updated : 12/15/2004
Marla J. F. O'Neill - updated : 5/14/2004
Victor A. McKusick - updated : 4/21/2004
Victor A. McKusick - updated : 1/22/2004
Cassandra L. Kniffin - updated : 12/9/2003
Victor A. McKusick - updated : 1/22/2003
Ada Hamosh - updated : 3/29/2002
Paul J. Converse - updated : 3/13/2002
Creation Date:
Victor A. McKusick : 2/7/2002
carol : 05/19/2022
carol : 01/26/2022
mgross : 02/04/2021
alopez : 11/15/2019
carol : 09/25/2017
carol : 04/19/2017
carol : 10/18/2016
carol : 12/28/2015
carol : 5/2/2013
carol : 1/4/2013
carol : 8/7/2012
carol : 3/12/2012
carol : 1/10/2012
wwang : 6/10/2010
terry : 6/9/2010
wwang : 5/27/2009
wwang : 1/17/2008
terry : 1/3/2008
wwang : 12/14/2007
ckniffin : 11/13/2007
wwang : 10/9/2006
ckniffin : 10/2/2006
wwang : 9/21/2006
wwang : 2/2/2006
terry : 1/25/2006
wwang : 11/22/2005
terry : 11/17/2005
wwang : 8/30/2005
wwang : 5/12/2005
terry : 5/11/2005
alopez : 12/16/2004
terry : 12/15/2004
carol : 5/18/2004
terry : 5/14/2004
tkritzer : 4/22/2004
terry : 4/21/2004
cwells : 1/27/2004
terry : 1/22/2004
carol : 12/12/2003
ckniffin : 12/9/2003
tkritzer : 1/31/2003
tkritzer : 1/23/2003
terry : 1/22/2003
carol : 3/29/2002
mgross : 3/29/2002
terry : 3/13/2002
terry : 3/8/2002
carol : 3/4/2002
carol : 2/11/2002
carol : 2/11/2002

* 606681

NUCLEAR RECEPTOR-BINDING SET DOMAIN PROTEIN 1; NSD1


Alternative titles; symbols

NUCLEAR RECEPTOR-BINDING Su-var, ENHANCER OF ZESTE, AND TRITHORAX DOMAIN PROTEIN 1
SET DOMAIN PROTEIN 1
ANDROGEN RECEPTOR-ASSOCIATED COREGULATOR 267; ARA267


Other entities represented in this entry:

NSD1/NUP98 FUSION GENE, INCLUDED

HGNC Approved Gene Symbol: NSD1

SNOMEDCT: 75968004;   ICD10CM: Q87.3;  


Cytogenetic location: 5q35.3     Genomic coordinates (GRCh38): 5:177,131,798-177,300,213 (from NCBI)


Gene-Phenotype Relationships

Location Phenotype Phenotype
MIM number
Inheritance Phenotype
mapping key
5q35.3 Sotos syndrome 117550 Autosomal dominant 3

TEXT

Description

The androgen receptor (AR; 313700) is a member of the steroid receptor (SR) superfamily that interacts with DNA response elements. SRs may enhance or inhibit transcription by recruiting an array of coregulators, including NSD1, that interact with its N or C terminus.


Cloning and Expression

Jaju et al. (1999) identified a recurrent cryptic translocation, t(5;11)(q35;p15.5), associated with a deletion of the long arm of chromosome 5 in de novo childhood acute myeloid leukemia (AML; see 601626). Jaju et al. (2001) confirmed that the chromosome 11 breakpoint gene is NUP98 (601021) and reported the cloning of its novel chromosome 5 fusion partner, NSD1. Nucleotide 1552 of NUP98 was fused in-frame to nucleotide 3504 of NSD1. The full coding sequence of NSD1 encodes a deduced 2,596-amino acid protein. The human and mouse NSD1 proteins share 85% sequence identity and have the same domain structure including a conserved SET domain, a SET domain-associated cysteine-rich domain (SAC domain), and 5 PHD fingers. Northern blot analysis detected wide expression of 2 NSD1 transcripts of 10.5 and 12.0 kb in hematologic and other tissues, respectively.

Using a yeast 2-hybrid screen of a brain cDNA library with the ligand-binding domains (LBDs) of AR and TR4 (NR2C2; 601426) as bait, followed by 5-prime RACE on a testis cDNA library, Wang et al. (2001) isolated a cDNA encoding NSD1, which they called ARA267-alpha, encoding a. 2,427-amino acid protein with homology to other ARA coregulators. The protein possesses a SET domain, 2 LXXLL motifs, 3 nuclear translocation signals (NLSs), 4 plant homeodomain (PHD) finger regions, and a proline-rich region. The 4 PHD finger regions contain a cys-rich region, a ring finger, and a zinc finger. Wang et al. (2001) also identified an ARA267-beta isoform encoding a 2,696-amino acid protein that is 83% homologous to mouse Nsd1 and has 279 N-terminal residues that merge into the eleventh residue of ARA267-alpha. Northern blot analysis revealed expression of 13- and 10-kb transcripts in multiple cell lines. Dot blot analysis detected expression in most tissues, with highest expression in lymph node. Mutation and binding analyses indicated that the N- and C-terminal domains of ARA267 can interact with full-length or C-terminal AR, but not with N-terminal AR, suggesting that the LBD and DNA-binding domain of AR may be responsible for the interaction. Luciferase analysis demonstrated that ARA267, like other ARA coregulators, has little or no influence on the interaction of the N and C termini of AR.

Kurotaki et al. (2001) independently cloned the NSD1 gene and found that it is expressed in fetal/adult brain, skeletal muscle, kidney, spleen, and thymus, and faintly in lung.


Gene Function

Functional analysis by Wang et al. (2001) showed that ARA267-alpha enhances AR transactivation, and this enhancement could be increased further in the presence of other ARA coregulators, such as ARA24 (RAN; 601179) and PCAF (602303).

Weinberg et al. (2019) reported that NSD1-mediated H3K36me2 is required for the recruitment of DNMT3A (602769) and maintenance DNA methylation at intergenic regions. Genomewide analysis showed that the binding and activity of DNMT3A colocalized with H3K36me2 at noncoding regions of euchromatin. Genetic ablation of Nsd1 and its paralog Nsd2 in mouse cells resulted in a redistribution of Dnmt3A to H3K36me3-modified gene bodies and a reduction in the methylation of intergenic DNA. Blood samples from patients with Sotos syndrome (117550) and NSD1-mutant tumors also exhibited hypomethylation of intergenic DNA. The PWWP domain of DNMT3A showed dual recognition of H3K36me2 and H3K36me3 in vitro, with a higher binding affinity towards H3K36me2 that was abrogated by Tatton-Brown-Rahman syndrome (TBRS; 615879)-derived missense mutations. Weinberg et al. (2019) concluded that their study revealed a trans-chromatin regulatory pathway that connects aberrant intergenic CpG methylation to human neoplastic and developmental overgrowth.

Using genomewide profiling, Shirane et al. (2020) showed that Setd2 (612778) and H3K36me3 were dispensable for de novo DNA methylation (DNAme) in male mouse germline development. Instead, H3K36me2 was broadly correlated with DNAme. Nsd1 was required for DNAme in prenatal male germ cells and was essential for establishment of DNAme at H3K36me2-marked regions within paternal gametic differentially methylated regions. Furthermore, Nsd1 was required for survival of spermatogonia and spermatogenesis. Knockout of Nsd1 in prospermatogonia revealed that H3K36me2 deposited by Nsd1 impeded further deposition of H3K27me3 in prenatal male germline development in the absence of de novo DNAme, thereby safeguarding a subset of genes against H3K27me3-associated repression. In contrast, Setd2 was required not only for deposition of H3K36me3 in oocytes and de novo DNAme in transcribed regions, but also for deposition of the majority of H3K36me2 in oocytes.


Gene Structure

Kurotaki et al. (2001) determined that the NSD1 gene contains 23 exons.


Mapping

By FISH, Jaju et al. (2001) mapped the NSD1 gene to chromosome 5q35.


Molecular Genetics

Imaizumi et al. (2002) found a t(5;8)(q35;q24.1) translocation in a child with Sotos syndrome (SOTOS; 117550). Kurotaki et al. (2002) identified NSD1 as the gene disrupted by the 5q35 breakpoint.

Kurotaki et al. (2002) identified 4 different de novo point mutations in the NSD1 gene in 4 of 38 individuals with Sotos syndrome. These included 1 nonsense mutation, 2 frameshift mutations, and 1 splice site mutation. FISH analysis revealed a common 2.2-Mb deletion in 19 individuals and a smaller deletion in 1 individual from a total of 30 affected individuals whose metaphase or interphase cells were available. The deletions involved the entire NSD1 gene. Kurotaki et al. (2002) found that 77% of individuals with Sotos syndrome in their study had either deletions or point mutations in the NSD1 gene as the cause of Sotos syndrome. They concluded that haploinsufficiency of NSD1 is the major cause of Sotos syndrome.

Douglas et al. (2003) evaluated 75 patients with childhood overgrowth for intragenic mutations and large deletions in NSD1 of the type reported by Kurotaki et al. (2002) as the major cause of Sotos syndrome. Before molecular analyses, the patients were phenotypically scored into 4 groups: 37 patients comprising group 1 had a phenotype typical of Sotos syndrome; 13 patients comprising group 2 had a Sotos-like phenotype but with some atypical features; 7 patients comprising group 3 had been diagnosed with Weaver syndrome (WVS; 277590); and 18 patients comprising group 4 had an overgrowth condition that was neither Sotos nor Weaver syndrome. Douglas et al. (2003) detected 3 deletions and 32 mutations that were predicted to impair NSD1 functions. The truncating mutations were spread throughout NSD1, but there was evidence of clustering of missense mutations in highly conserved functional domains between exons 13 and 23. There was a strong correlation between presence of an NSD1 alteration and clinical phenotype, as 28 of 37 (76%) patients in group 1 had NSD1 mutations or deletions, whereas none of the patients in group 4 had abnormalities of NSD1. Three of the 7 patients who had been diagnosed with Weaver syndrome had NSD1 mutations, all between amino acids 2142 and 2184 (see 606681.0006). Tatton-Brown et al. (2005) reviewed the phenotype of the 3 patients who carried a diagnosis of Weaver syndrome and in whom Douglas et al. (2003) had identified mutations in the NSD1 gene, and on the basis of multiple pictures at different ages, reclassified 2 of them as having 'typical Sotos syndrome' and the third as 'possible Sotos syndrome.'

Nagai et al. (2003) analyzed the phenotypic findings of 5 patients with intragenic NSD1 mutations predicted to form a truncated NSD1 protein and in 21 patients with a fairly common deletion of approximately 2.2 Mb involving the entire NSD1 gene. Overgrowth and advanced maturation in infancy to early childhood, mental retardation, hypotonia, hyperreflexia, and characteristic minor anomalies were present in patients with mutations and deletions, whereas major anomalies in the central nervous system (agenesis or hypoplasia of the corpus callosum), cardiovascular system (patent ductus arteriosus and atrial septal defect), and urinary system (vesicoureteric reflux, hydronephrosis, and small kidney) were exclusively exhibited by patients with deletions. The results suggested that clinical features in Sotos syndrome can be classified into 2 major categories: those primarily caused by NSD1 haploinsufficiency and those primarily ascribed to some factors, such as the dosage effects of genes other than NSD1, involved in the deletion.

Turkmen et al. (2003) screened the NSD1 gene for mutations in 20 patients and 1 familial case with Sotos syndrome, 5 patients with Weaver syndrome, 6 patients with unclassified overgrowth and mental retardation, and 6 patients with macrocephaly and mental retardation. They identified 19 mutations, 17 previously undescribed, in 18 Sotos patients and the familial case (90%). The best correlation between the molecular and clinical findings was for facial gestalt in conjunction with overgrowth, macrocephaly, and developmental delay. Turkmen et al. (2003) found no mutations of the NSD1 gene in the patients with Weaver syndrome or other overgrowth phenotypes and concluded that the great majority of patients with Sotos syndrome have mutations in NSD1.

Kurotaki et al. (2003) found 50 microdeletions (606681.0001) among 112 cases of Sotos syndrome and suggested that low copy repeats (LCRs) possibly mediate the common deletion. As pointed out by Visser and Matsumoto (2003), intragenic mutations prevail in Caucasian Sotos syndrome patients, whereas Japanese patients with this disorder more frequently harbor a microdeletion. Each deletion breakpoint is located in either of the 2 flanking LCRs. Most meiotic rearrangements seem to be of intrachromosomal origin and show a preference for the paternally derived chromosome.

In light of accumulated evidence, Sotos syndrome can be added to the list of genomic disorders (Shaw and Lupski, 2004), defined as pathologic conditions in which the gain, loss, or disruption of dosage-sensitive gene(s) results in a recognized phenotype (Lupski, 1998). Unequal rearrangement (nonallelic homologous recombination) between regions of high homology (i.e., LCRs) is the most common mechanism. Visser et al. (2005) found a heterozygous inversion of the interval between the LCRs in all fathers of children carrying a deletion in the paternally derived chromosome. Segmental duplications of the primate genome played a major role in chromosomal evolution. Evolutionary studies by Visser et al. (2005) showed that the duplication of the Sotos syndrome LCRs occurred 23.3 to 47.6 million years ago, before the divergence of Old World monkeys.

Kurotaki et al. (2005) characterized 2 complex mosaic low-copy repeats (LCRs) that are centromeric and telomeric to NSD1, which they designated proximal Sos-REP (Sos-PREP, approximately 390 kb) and distal Sos-REP (Sos-DREP, approximately 429 kb), respectively. Sos-PREP and Sos-DREP are composed of 6 subunits termed A to F. All but one homologous subunit was located in an inverted orientation, and the order of subunits was different between the 2 Sos-REPs. Only the subunit C-prime in Sos-DREP was oriented directly with respect to the subunit C in Sos-PREP. Among 8 Sotos patients with a common deletion, an approximately 550-kb junction fragment was detected that was generated by nonallelic homologous recombination (NAHR) between Sos-PREP C and Sos-DREP C-prime subunits. This patient-specific junction fragment was not present in 51 Japanese and non-Japanese controls. Kurotaki et al. (2005) identified a 2.5-kb unequal crossover hotspot region in 6 of 9 analyzed Sotos patients with the common deletion.

Melchior et al. (2005) developed a denaturing high-performance liquid chromatography (DHPLC) screening protocol for mutation detection in NSD1 and identified 9 novel mutations among 33 patients, an efficiency of mutation detection comparable to that achieved by direct sequencing. In 2 patients, NSD1 deletions were identified. A summary of over 100 NSD1 mutations was provided.

Through analyses of 530 individuals with diverse phenotypes, Tatton-Brown et al. (2005) identified 266 individuals with intragenic NSD1 mutations or 5q35 microdeletions encompassing the NSD1 gene. Of 166 patients with NSD1 abnormalities for whom photographs were available, Sotos syndrome was clinically diagnosed in 164 (99%) independent of the molecular analysis, indicating that NSD1 aberrations are essentially specific to this condition. Analysis of 124 patients from the United Kingdom suggested that 93% of patients who have been clinically diagnosed with Sotos syndrome have identifiable NSD1 abnormalities, of which 83% are intragenic mutations and 10% are 5q35 microdeletions. Tatton-Brown et al. (2005) reviewed the clinical phenotype of 239 individuals with NSD1 abnormalities and observed that individuals with identical mutations had different phenotypes, that all features present in patients with microdeletions were also observed in patients with mutations, and that there was no correlation between deletion size and clinical phenotype. Tatton-Brown et al. (2005) identified only 13 familial cases and noted that familial cases were more likely than nonfamilial cases to carry missense mutations (p = 0.005), suggesting that the underlying NSD1 mutation mechanism in Sotos syndrome may influence reproductive fitness.

Van Haelst et al. (2005) reported a 3-generation family with gigantism (Sotos syndrome) in whom they identified a missense mutation in the NSD1 gene (C2202Y; 606681.0013).

Cecconi et al. (2005) identified mutations in the NSD1 gene in 17 (71%) of 24 patients with classic Sotos syndrome. All patients with a mutant NSD1 genotype showed the typical facial gestalt; however, not all patients showed height above the 97th percentile, absolute macrocephaly, or advanced bone age. No genotype/phenotype correlations were observed. NSD1 mutations were not identified in 9 patients with a Sotos-like phenotype, 2 patients with Weaver syndrome, or 24 additional patients with nonspecific overgrowth, suggesting that mutations in the NSD1 gene are specific for Sotos syndrome.

Kanemoto et al. (2006) reported a female infant with features of both Sotos syndrome and Nevo syndrome (see 225400) in whom they identified a heterozygous 2.2-Mb deletion (606681.0001) encompassing the NSD1 gene.

Saugier-Veber et al. (2007) identified 69 different point mutations, including 48 novel mutations, in the NSD1 gene in 104 patients from 102 families with Sotos syndrome. Point mutations were detected in 80%, large deletions removing the entire NSD1 gene in 14%, and intragenic NSD1 rearrangements in 6%. The large deletions ranged in size from 1 to 4.5 Mb. Patients with truncating mutations had a more severe phenotype than those with nontruncating mutations. No NSD1 mutations were identified in 12 additional patients with a clinical diagnosis of Sotos syndrome.

Tatton-Brown and Rahman (2013) reviewed the similarities and differences between the NSD1 and EZH2 (601573) genes, which cause the overgrowth Sotos and Weaver syndromes, respectively. The authors noted that although the NSD1-associated phenotype has been well characterized with many hundreds of reported cases, it is not yet understood what factors determine the variability of the Sotos syndrome phenotype, in which unrelated individuals with the same recurrent mutation exhibit differing degrees of intellectual disability and frequencies of associated medical issues such as cardiac and renal anomalies, seizures, and scoliosis.

In 7 patients with Sotos syndrome with hyperinsulinemic hypoglycemia with persistence beyond a year of age in at least 3 patients, Grand et al. (2019) identified point mutations in the NSD1 gene. The mutations included 4 nonsense, 3 missense, and 1 frameshift. The authors noted that these patients disprove the hypothesis that hyperinsulinemic hypoglycemia is due to deletion of nearby genes in the 5q35 deleted region and suggest a role for NSD1 in glucose homeostasis.


ALLELIC VARIANTS 13 Selected Examples):

.0001   SOTOS SYNDROME

NSD1, 1.9-MB DEL
ClinVar: RCV003231075

In 19 of 30 Japanese individuals with Sotos syndrome (SOTOS; 117550), Kurotaki et al. (2002) identified a 2.2-Mb deletion on chromosome 5q35 leading to complete deletion of the NSD1 gene.

Haploinsufficiency of the NSD1 gene owing to either intragenic mutations or microdeletions is the major cause of Sotos syndrome. The common microdeletion of approximately 2.2 Mb encompasses the whole NSD1 gene and neighboring genes and is flanked by low-copy repeats (LCRs). Visser et al. (2005) identified a 3.0-kb major recombination hotspot within these LCRs, in which they mapped deletion breakpoints in 78.7% (37/47) of patients with Sotos syndrome who carried the common microdeletion. They were able to refine the size of the deletion to 1.9 Mb. Sequencing of breakpoint fragments from all 37 patients revealed junctions between a segment of the proximal LCR (PLCR-B) and the corresponding region of the distal LCR (DLCR-2B). Visser et al. (2005) found that PLCR-B and DLCR-2B are the only directly oriented regions, whereas the remaining regions of the PLCR and DLCR are in inverted orientation. PLCR and DLCR showed high overall homology (approximately 98.5%), with an increased sequence similarity (approximately 99.4%) within the 3.0-kb breakpoint cluster.

In a female infant with features of both Sotos syndrome and Nevo syndrome (225400), Kanemoto et al. (2006) identified heterozygosity for a 2.2-Mb deletion encompassing the NSD1 gene.


.0002   SOTOS SYNDROME

NSD1, SER437TER
SNP: rs121908067, ClinVar: RCV003231076, RCV003231077

In a patient with sporadic Sotos syndrome (SOTOS; 117550), Kurotaki et al. (2002) identified a C-to-G transversion at nucleotide 1310 leading to a ser437-to-ter substitution at codon 437 on 1 allele of the NSD1 gene. This patient with the S437X nonsense mutation was 1 of 5 in whom the phenotype was analyzed by Nagai et al. (2003).


.0003   SOTOS SYNDROME

NSD1, 1-BP DEL, 3536A
SNP: rs1562213381, ClinVar: RCV003231078

In a patient with sporadic Sotos syndrome (SOTOS; 117550), Kurotaki et al. (2002) identified a deletion of a single basepair at nucleotide 3536 of the NSD1 gene. This patient was 1 of 5 in whom the phenotype was analyzed by Nagai et al. (2003).


.0004   SOTOS SYNDROME

NSD1, 1-BP INS, 5998T
SNP: rs1562295135, ClinVar: RCV003231079

In a patient with sporadic Sotos syndrome (SOTOS; 117550), Kurotaki et al. (2002) identified an insertion of a thymidine at nucleotide 5998 in the NSD1 gene. This patient was 1 of 5 in whom the phenotype was analyzed by Nagai et al. (2003).


.0005   SOTOS SYNDROME

NSD1, IVS20DS, G-A, +1
SNP: rs1562296511, ClinVar: RCV001818128, RCV003231080

In a patient with sporadic Sotos syndrome (SOTOS; 117550), Kurotaki et al. (2002) identified a splice site mutation at the splice donor site of intron 20 leading to a premature termination codon only 9 amino acids thereafter. This patient was 1 of 5 in whom the phenotype was analyzed by Nagai et al. (2003).


.0006   SOTOS SYNDROME

NSD1, HIS2143GLN
SNP: rs121908068, gnomAD: rs121908068, ClinVar: RCV003231081

In a patient originally diagnosed with Weaver syndrome, Douglas et al. (2003) identified a heterozygous mutation in exon 22 of the NSD1 gene, resulting in a his2143-to-glu substitution. The patient was later diagnosed with Sotos syndrome (SOTOS; 117550) by Tatton-Brown et al. (2005) after review of patient photographs at different ages and the mutation was corrected to his2143-to-gln (H2143Q). See online Table 2 in Tatton-Brown et al. (2005).


.0007   SOTOS SYNDROME

NSD1, CYS2183SER
SNP: rs121908069, ClinVar: RCV003231082

In a patient originally diagnosed with Weaver syndrome, Douglas et al. (2003) identified a heterozygous mutation in exon 23 of the NSD1 gene, resulting in a cys2183-to-ser (C2183S) substitution. The patient was later diagnosed with Sotos syndrome (SOTOS; 117550) by Tatton-Brown et al. (2005) after review of patient photographs at different ages.


.0008   SOTOS SYNDROME

NSD1, 1-BP INS, 6450C
SNP: rs864309639, ClinVar: RCV003231083

In a patient originally diagnosed with Weaver syndrome, Douglas et al. (2003) identified a heterozygous 1-bp insertion (6450insC) in exon 22 of the NSD1, resulting in a frameshift and a termination at codon 2165. The patient was later diagnosed with Sotos syndrome (SOTOS; 117550) by Tatton-Brown et al. (2005) after review of patient photographs at different ages.


.0009   SOTOS SYNDROME

NSD1, 1-BP DEL, 896C
SNP: rs1562099585, ClinVar: RCV003231084

In a Finnish father and son with Sotos syndrome (SOTOS; 117550), Hoglund et al. (2003) identified a heterozygous 1-bp deletion (896delC) in exon 2 of the NSD1 gene, resulting in a truncation of 88% of the predicted polypeptide. The mutation was not detected in the unaffected mother or in 94 unrelated Finnish individuals. Hoglund et al. (2003) noted that the findings in this family confirm that familial Sotos syndrome is caused by mutation in the NSD1 gene.


.0010   SOTOS SYNDROME

NSD1, ARG1320TER
SNP: rs121908070, ClinVar: RCV000487238, RCV003231085

One of the 5 patients with Sotos syndrome (SOTOS; 117550) and intragenic mutations of the NSD1 gene studied by Nagai et al. (2003) had a novel nonsense mutation in exon 7 of the NSD1 gene: 3958C-T, arg1320 to stop (R1320X).


.0011   SOTOS SYNDROME

NSD1, 1-BP INS, 4976G
SNP: rs1562269320, ClinVar: RCV003231086

In a patient (PB) with Sotos syndrome (SOTOS; 117550), who had a clinical diagnosis of Beckwith-Wiedemann syndrome (130650), Baujat et al. (2004) identified a de novo 1-bp insertion, 4976insG, in exon 14 of the NSD1 gene. Features consistent with BWS included large umbilical hernia and left-sided hemihypertrophy.


.0012   SOTOS SYNDROME

NSD1, 4-BP DEL, 7968GACA
SNP: rs1562312238, ClinVar: RCV003231087

In a patient (BA) with Sotos syndrome (SOTOS; 117550), who had a clinical diagnosis of Beckwith-Wiedemann syndrome (130650), Baujat et al. (2004) identified a de novo 4-bp deletion, 7968delGACA, in exon 23 of the NSD1 gene.


.0013   SOTOS SYNDROME

NSD1, CYS2202TYR
SNP: rs121908071, ClinVar: RCV001813734, RCV003231088

In affected members of a 3-generation family with Sotos syndrome (SOTOS; 117550), van Haelst et al. (2005) identified a 6605G-A transition in the NSD1 gene, resulting in a cys2202-to-tyr (C2202Y) substitution.


REFERENCES

  1. Baujat, G., Rio, M., Rossignol, S., Sanlaville, D., Lyonnet, S., Le Merrer, M., Munnich, A., Gicquel, C., Cormier-Daire, V., Colleaux, L. Paradoxical NSD1 mutations in Beckwith-Wiedemann syndrome and 11p15 anomalies in Sotos syndrome. Am. J. Hum. Genet. 74: 715-720, 2004. [PubMed: 14997421] [Full Text: https://doi.org/10.1086/383093]

  2. Cecconi, M., Forzano, F., Milani, D., Cavani, S., Baldo, C., Selicorni, A., Pantaleoni, C., Silengo, M., Ferrero, G. B., Scarano, G., Della Monica, M., Fischetto, R., and 10 others. Mutation analysis of the NSD1 gene in a group of 59 patients with congenital overgrowth. Am. J. Med. Genet. 134A: 247-253, 2005. [PubMed: 15742365] [Full Text: https://doi.org/10.1002/ajmg.a.30492]

  3. Douglas, J., Hanks, S., Temple, I. K., Davies, S., Murray, A., Upadhyaya, M., Tomkins, S., Hughes, H. E., Cole, T. R. P., Rahman, N. NSD1 mutations are the major cause of Sotos syndrome and occur in some cases of Weaver syndrome but are rare in other overgrowth phenotypes. Am. J. Hum. Genet. 72: 132-143, 2003. [PubMed: 12464997] [Full Text: https://doi.org/10.1086/345647]

  4. Grand, K., Gonzalez-Gandolfi, C., Ackermann, A. M., Aljeaid, D., Bedoukian, E., Bird, L. M., De Leon, D. D., Diaz, J., Hopkin, R. J., Kadakia, S. P., Keena, B., Klein, K. O., and 11 others. Hyperinsulinemic hypoglycemia in seven patients with de novo NSD1 mutations. Am. J. Med. Genet. 179A: 542-551, 2019. [PubMed: 30719864] [Full Text: https://doi.org/10.1002/ajmg.a.61062]

  5. Hoglund, P., Kurotaki, N., Kytola, S., Miyake, N., Somer, M., Matsumoto, N. Familial Sotos syndrome is caused by a novel 1 bp deletion of the NSD1 gene. (Letter) J. Med. Genet. 40: 51-54, 2003. [PubMed: 12525543] [Full Text: https://doi.org/10.1136/jmg.40.1.51]

  6. Imaizumi, K., Kimura, J., Matsuo, M., Kurosawa, K., Masuno, M., Niikawa, N., Kuroki, Y. Sotos syndrome associated with a de novo balanced reciprocal translocation t(5;8)(q35;q24.1). Am. J. Med. Genet. 107: 58-60, 2002. [PubMed: 11807869] [Full Text: https://doi.org/10.1002/ajmg.10080]

  7. Jaju, R. J., Fidler, C., Haas, O. A., Strickson, A. J., Watkins, F., Clark, K., Cross, N. C. P., Cheng, J.-F., Aplan, P. D., Kearney, L., Boultwood, J., Wainscoat, J. S. A novel gene, NSD1, is fused to NUP98 in the t(5;11)(q35;p15.5) in de novo childhood acute myeloid leukemia. Blood 98: 1264-1267, 2001. [PubMed: 11493482] [Full Text: https://doi.org/10.1182/blood.v98.4.1264]

  8. Jaju, R. J., Haas, O. A., Neat, M., Harbott, J., Saha, V., Boultwood, J., Brown, J. M., Pirc-Danoewinata, H., Krings, B. W., Muller, U., Morris, S. W., Wainscoat, J. S., Kearney, L. A new recurrent translocation, t(5;11)(q35p15.5), associated with del(5q) in childhood acute myeloid leukemia. Blood 94: 773-780, 1999. [PubMed: 10397745]

  9. Kanemoto, N., Kanemoto, K., Nishimura, G., Kamoda, T., Visser, R., Shimokawa, O., Matsumoto, N. Nevo syndrome with an NSD1 deletion: a variant of Sotos syndrome? Am. J. Med. Genet. 140A: 70-73, 2006. [PubMed: 16329110] [Full Text: https://doi.org/10.1002/ajmg.a.30776]

  10. Kurotaki, N., Harada, N., Shimokawa, O., Miyake, N., Kawame, H., Uetake, K., Makita, Y., Kondoh, T., Ogata, T., Hasegawa, T., Nagai, T., Ozaki, T., and 22 others. Fifty microdeletions among 112 cases of Sotos syndrome: low copy repeats possibly mediate the common deletion. Hum. Mutat. 22: 378-387, 2003. [PubMed: 14517949] [Full Text: https://doi.org/10.1002/humu.10270]

  11. Kurotaki, N., Harada, N., Yoshiura, K., Sugano, S., Niikawa, N., Matsumoto, N. Molecular characterization of NSD1, a human homologue of the mouse Nsd1 gene. Gene 279: 197-204, 2001. [PubMed: 11733144] [Full Text: https://doi.org/10.1016/s0378-1119(01)00750-8]

  12. Kurotaki, N., Imaizumi, K., Harada, N., Masuno, M., Kondoh, T., Nagai, T., Ohashi, H., Naritomi, K., Tsukahara, M., Makita, Y., Sugimoto, T., Sonoda, T., and 11 others. Haploinsufficiency of NSD1 causes Sotos syndrome. Nature Genet. 30: 365-366, 2002. [PubMed: 11896389] [Full Text: https://doi.org/10.1038/ng863]

  13. Kurotaki, N., Stankiewicz, P., Wakui, K., Niikawa, N., Lupski, J. R. Sotos syndrome common deletion is mediated by directly oriented subunits within inverted Sos-REP low-copy repeats. Hum. Molec. Genet. 14: 535-542, 2005. [PubMed: 15640245] [Full Text: https://doi.org/10.1093/hmg/ddi050]

  14. Lupski, J. R. Genomic disorders: structural features of the genome can lead to DNA rearrangements and human disease traits. Trends Genet. 14: 417-422, 1998. [PubMed: 9820031] [Full Text: https://doi.org/10.1016/s0168-9525(98)01555-8]

  15. Melchior, L., Schwartz, M., Duno, M. dHPLC screening of the NSD1 gene identifies nine novel mutations--summary of the first 100 Sotos syndrome mutations. Ann. Hum. Genet. 69: 222-226, 2005. [PubMed: 15720303] [Full Text: https://doi.org/10.1046/j.1529-8817.2004.00150.x]

  16. Nagai, T., Matsumoto, N., Kurotaki, N., Harada, N., Niikawa, N., Ogata, T., Imaizumi, K., Kurosawa, K., Kondoh, T., Ohashi, H., Tsukahara, M., Makita, Y., Sugimoto, T., Sonoda, T., Yokoyama, T., Uetake, K., Sakazume, S., Fukushima, Y., Naritomi, K. Sotos syndrome and haploinsufficiency of NSD1: clinical features of intragenic mutations and submicroscopic deletions. J. Med. Genet. 40: 285-289, 2003. [PubMed: 12676901] [Full Text: https://doi.org/10.1136/jmg.40.4.285]

  17. Saugier-Veber, P., Bonnet, C., Afenjar, A., Drouin-Garraud, V., Coubes, C., Fehrenbach, S., Holder-Espinasse, M., Roume, J., Malan, V., Portnoi, M.-F., Jeanne, N., Baumann, C., and 9 others. Heterogeneity of NSD1 alterations in 116 patients with Sotos syndrome. Hum. Mutat. 28: 1098-1107, 2007. [PubMed: 17565729] [Full Text: https://doi.org/10.1002/humu.20568]

  18. Shaw, C. J., Lupski, J. R. Implications of human genome architecture for rearrangement-based disorders: the genomic basis of disease. Hum. Molec. Genet. 13 Spec. No. 1: R57-R64, 2004. [PubMed: 14764619] [Full Text: https://doi.org/10.1093/hmg/ddh073]

  19. Shirane, K., Miura, F., Ito, T., Lorincz, M. C. NSD1-deposited H3K36me2 directs de novo methylation in the mouse male germline and counteracts Polycomb-associated silencing. Nature Genet. 52: 1088-1098, 2020. [PubMed: 32929285] [Full Text: https://doi.org/10.1038/s41588-020-0689-z]

  20. Tatton-Brown, K., Douglas, J., Coleman, K., Baujat, G., Cole, T. R. P., Das, S., Horn, D., Hughes, H. E., Temple, I. K., Faravelli, F., Waggoner, D., Turkmen, S., Cormier-Daire, V., Irrthum, A., Rahman, N. Genotype-phenotype associations in Sotos syndrome: an analysis of 266 individuals with NSD1 aberrations. Am. J. Hum. Genet. 77: 193-204, 2005. [PubMed: 15942875] [Full Text: https://doi.org/10.1086/432082]

  21. Tatton-Brown, K., Rahman, N. The NSD1 and EZH2 overgrowth genes, similarities and differences. Am. J. Med. Genet. 163C: 86-91, 2013. [PubMed: 23592277] [Full Text: https://doi.org/10.1002/ajmg.c.31359]

  22. Turkmen, S., Gillessen-Kaesbach, G., Meinecke, P., Albrecht, B., Neumann, L. M., Hesse, V., Palanduz, S., Balg, S., Majewski, F., Fuchs, S., Zschieschang, P., Greiwe, M., Mennicke, K., Kreuz, F. R., Dehmel, H. J., Rodeck, B., Kunze, J., Tinschert, S., Mundlos, S., Horn, D. Mutations in NSD1 are responsible for Sotos syndrome, but are not a frequent finding in other overgrowth phenotypes. Europ. J. Hum. Genet. 11: 858-865, 2003. [PubMed: 14571271] [Full Text: https://doi.org/10.1038/sj.ejhg.5201050]

  23. van Haelst, M. M., Hoogeboom, J. J. M., Baujat, G., Bruggenwirth, H. T., Van de Laar, I., Coleman, K., Rahman, N., Niermeijer, M. F., Drop, S. L. S., Scambler, P. J. Familial gigantism caused by an NSD1 mutation. Am. J. Med. Genet. 139A: 40-44, 2005. [PubMed: 16222665] [Full Text: https://doi.org/10.1002/ajmg.a.30973]

  24. Visser, R., Matsumoto, N. Genetics of Sotos syndrome. Curr. Opin. Pediat. 15: 598-606, 2003. [PubMed: 14631206] [Full Text: https://doi.org/10.1097/00008480-200312000-00010]

  25. Visser, R., Shimokawa, O., Harada, N., Kinoshita, A., Ohta, T., Niikawa, N., Matsumoto, N. Identification of a 3.0-kb major recombination hotspot in patients with Sotos syndrome who carry a common 1.9-Mb microdeletion. Am. J. Hum. Genet. 76: 52-67, 2005. [PubMed: 15580547] [Full Text: https://doi.org/10.1086/426950]

  26. Wang, X., Yeh, S., Wu, G., Hsu, C.-L., Wang, L., Chiang, T., Yang, Y., Guo, Y., Chang, C. Identification and characterization of a novel androgen receptor coregulator ARA267-alpha in prostate cancer cells. J. Biol. Chem. 276: 40417-40423, 2001. [PubMed: 11509567] [Full Text: https://doi.org/10.1074/jbc.M104765200]

  27. Weinberg, D. N., Papillon-Cavanagh, S., Chen, H., Yue, Y., Chen, X., Rajagopalan, K. N., Horth, C., McGuire, J. T., Xu, X., Nikbakht, H., Lemiesz, A. E., Marchione, D. M., and 13 others. The histone mark H3K36me2 recruits DNMT3A and shapes the intergenic DNA methylation landscape. Nature 573: 281-286, 2019. [PubMed: 31485078] [Full Text: https://doi.org/10.1038/s41586-019-1534-3]


Contributors:
Sonja A. Rasmussen - updated : 05/19/2022
Bao Lige - updated : 02/04/2021
Ada Hamosh - updated : 11/15/2019
Marla J. F. O'Neill - updated : 5/2/2013
George E. Tiller - updated : 1/3/2008
Cassandra L. Kniffin - updated : 11/13/2007
Cassandra L. Kniffin - updated : 10/2/2006
Marla J. F. O'Neill - updated : 1/25/2006
Marla J. F. O'Neill - updated : 11/17/2005
Marla J. F. O'Neill - updated : 8/30/2005
Victor A. McKusick - updated : 5/11/2005
Victor A. McKusick - updated : 12/15/2004
Marla J. F. O'Neill - updated : 5/14/2004
Victor A. McKusick - updated : 4/21/2004
Victor A. McKusick - updated : 1/22/2004
Cassandra L. Kniffin - updated : 12/9/2003
Victor A. McKusick - updated : 1/22/2003
Ada Hamosh - updated : 3/29/2002
Paul J. Converse - updated : 3/13/2002

Creation Date:
Victor A. McKusick : 2/7/2002

Edit History:
carol : 05/19/2022
carol : 01/26/2022
mgross : 02/04/2021
alopez : 11/15/2019
carol : 09/25/2017
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carol : 12/28/2015
carol : 5/2/2013
carol : 1/4/2013
carol : 8/7/2012
carol : 3/12/2012
carol : 1/10/2012
wwang : 6/10/2010
terry : 6/9/2010
wwang : 5/27/2009
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ckniffin : 11/13/2007
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carol : 5/18/2004
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carol : 12/12/2003
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carol : 3/4/2002
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