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t(4;11)(q23;p15) NUP98/RAP1GDS1

Written2016-01Anwar N Mohamed
Cytogenetic laboratory, Pathology Department; Detroit Medical Center, Wayne State University School of Medicine, Detroit, USA
This article is an update of :
2002-07Franck Viguié
Laboratoire de Cytogenetique - Service d'Hematologie Biologique, Hopital Hotel-Dieu - 75181 Paris Cedex 04, France

(Note : for Links provided by Atlas : click)


ICD-Topo C420,C421,C424
ICD-Morpho 9837/3 T lymphoblastic leukaemia/lymphoma
ICD-Morpho 9861/3 AML with mutated NPM1; AML with mutated CEBPA; Acute myeloid leukaemia, NOS
Atlas_Id 1191
Note The t(4;11)(q23;q15) is a rare but recurrent translocation strongly associated with T-cell acute lymphoblastic leukemia (T-ALL). This translocation results in a novel gene fusion of NUP98/11p15 and RAP1GDS1/4q23 genes [Figure 1]. Therefore, t(4;11)(q23;p15) is NOT a variant of the t(4;11)(q21;q23) involving the AFF1 and KMT2A (MLL) genes, as previously presumed.
  Figure 1; Left; Partial karyotype showing t(4;11)(q23;p15), Right; FISH showing a double fusion pattern of NUP98-RAP1GDS1 genes.

Clinics and Pathology

Disease The t(4;11)(q23;p15) is mostly described in an early precursor T-cell ALL of thymic origin. Only two cases with acute myeloid leukemia (AML) were reported with this translocation; the t(4;11)(q?13;p15) with NUP98/RAP1GDS1 fusion expression was identified in a patient with AML-M0 at time of diagnosis. Whereas the second case was with AML-M4, in which the t(4;11)(q23;p15) was detected at relapse with a normal karyotype at diagnosis.
Phenotype / cell stem origin Bone marrows are hypercellular with a massive infiltration (~90%) with lymphoblasts of L1 or L2 morphology. Whereas different markers are tested for each case, leukemic cells are generally positive for CD3, CD5, CD7, CD10, TdT, and thymic associated marker CD1a, negative or partially expressing CD2, CD4, and CD8. One or more myeloid markers CD11b, CD13, and/or CD33 are co-expressed in some patients. This suggests that NUP98/RAP1GDS1 fusion occurs in subset of T-ALL originated from an early progenitor with a potential to express mature T-cell antigens as well as myeloid markers.
Epidemiology Patient's ages are ranged from 6 to 60 years, with a predominance of younger individuals (60% < = 25 years) as is classic for T-cell ALL. None of the patients with this translocation was an infant. The t(4;11)(q23;p15) seems to be extremely rare and its exact incidence in leukemia is difficult to establish. In large studies, t(4;11) was identified in approximately 2% adult and in 0.3% children with T-ALL while other studies have failed to detect a single case.
Clinics Most patients present with a high WBC counts with a high proportion of blasts, generalized lymphadenopathy and mediastinal mass but hepatospenomagaly is less frequent.
Prognosis The risk associated with t(4;11)(q23;p15.4) is not well determined due to low number of cases although most patients with this translocation had a short survival.


Note Karyotype is relatively simple with t(4;11)(q23;p15) a sole abnormality in 5/13 cases (Table 1).
Cytogenetics Morphological Table 1: Reported acute leukemia cases with t(4;11)(q21-q23;p15) and NUP98/RAP1GDS1 gene fusion.




WBC 109/L


Fusion Genes









Relapsed after 2 matched BMT; died 43 M

Hussey et al., 1999





46,XX,t(4;11)(q21;p14-15), del(12)(p13),+del(13)(q12q14)


Failure of induction; Died 1M later

Hussey et al., 1999







BM remission, early relapse, died 14 M

Hussey et al., 1999







CR, followed by BMT; 7 m+

Mecucci et al., 2000







CR, relapsed in 8 m; died after  BMT

Mecucci et al. 2000





46- t(4;11)(q1?3;p15),?der(8)(p?)


CR; relapsed and died 8m after diagnosis

van Zutven et al, 2006







CR obtained, survival 7M+

Present case, 2015

Additional anomalies One or two additional abnormalities were seen in 8/13 cases including del(12p) in two cases; del(5q), del(9p) , del(13q) , or trisomy 8 in a single case each.
Variants t(1;4;11)(p32;q21;p15) was reported in one case.

Genes involved and Proteins

Gene NameRAP1GDS1 (RAP1, GTP-GDP dissociation stimulator 1)
Location 4q23
Dna / Rna RAP1, GTP-GDP dissociation stimulator 1 (RAP1GDS1) is a gene that encodes a protein that functions as a stimulatory GDP/GTP exchange protein with GTPase activity. Fusions, missense mutations, nonsense mutations, silent mutations, frameshift deletions, and in-frame deletions are observed in cancers such as endometrial cancer , intestinal cancer, and skin cancer .
Protein RAP1GDS1 encodes a 558-amino acid protein with a molecular mass of 61.1 kD. The product of the RAP1GDS1 gene, usually referred to as smgGDS, has guanine nucleotide exchange factor activity. It stimulates the conversion of inactive GDP-bound from small GTPases to the active GTP-bound form. It has been speculated that smgGDS might also play a role in nucleocytoplasmic transport, as smgGDS is composed of multiple armadillo repeats that are thought to mediate protein-protein interactions.
SmgGDS has been described as a "master regulator" of small GTPases, such as RHOA , RAC1 , RAP1A , RAP1B , and KRAS . SmgGDS controls the activities of these GTPases through several mechanisms, most notably by controlling their prenylation and trafficking to cell membranes. The ability of smgGDS to regulate the cell cycle in multiple cancer cell lines with different mutational profiles indicates the importance of this protein as a key regulator of malignancy. SmgGDS is overexpressed in multiple types of cancer, including non-small cell lung carcinoma , prostate cancer , pancreatic cancer and breast cancer , making SmgGDS is an attractive target for cancer therapeutics.
Gene NameNUP98 (nucleoporin 98 kDa)
Location 11p15.4
Dna / Rna NUP98 is one of several genes located in the imprinted gene domain of chromosome 11p15. Combined haploinsufficiency of NUP98 and RAE1 has been shown to result in premature separation of sister chromatids, leading to severe aneuploidy. NUP98 plays roles in gene expression, mitotic spindle formation, and cell cycle progression.
NUP98 gene is fused to a large number of "partner genes" caused primarily by balanced translocations and inversions which are associated with a wide variety of hematological malignancies including AML and MDS (de novo and therapy related), CML-blast crisis, and pre T- ALL. To date, no NUP98 fusion gene has been described in B-cell malignancies. At least 30 different partner genes are reported to fuse with NUP98; 50% of which are homeobox genes. Approximately 10% of patients with NUP98 fusions have T-ALL; most commonly, these malignancies are associated with NUP98-RAP1GDS1 gene fusions. This suggests that different partner genes are associated with different leukemia, although such associations are rarely exclusive. Although NUP98 breakpoints in these translocations are variable located between introns 9 to 14, a chimeric transcript consisting of the 5' portion of NUP98 fused in-frame to the 3' portion of the partner genes is generated in all.
Protein NUP98 gene encodes two alternatively spliced mRNA variants: NUP98 and NUP98-NUP96 that are cleaved to produce two distinct nucleoporins, NUP98 and NUP96. The NUP98 is a 98 kDa protein component of the nuclear pore complex (NPC) family which is involved in the trafficking of RNA and protein between the nucleus and cytoplasm. The NUP98 protein contains two partially characterized functional domains: a GLFG repeat region, which serves as a nuclear transport receptor docking surface, and a GLEBS domain, which mediates the interaction with the RAE1 mRNA nuclear export factor. Both domains are located within the N-terminal portion of NUP98. The chimeric NUP98 protein that results from translocations always retains the intact N-terminal GLFG repeats of NUP98 and the C-terminal domain of the partner protein. NUP96 is a scaffold component of the NPC.

Result of the chromosomal anomaly

Hybrid gene
Note Of the 13 cases reported in the literature with t(4;11)(q23;q15); seven cases showed NUP98/RAP1GDS1 gene fusion while the status of these genes were not tested in the remaining five cases (Table 1).
Fusion Protein
Description T(4;11) generates two reciprocal chimeric products; chimeric 5'NUP98 -3'RAP1GDS1 transcript produces a novel protein composed of the N-terminal portion of the NUP98 protein and the entire smgGDS which is anticipated to promote leukemogenesis. However, the reciprocal 5' RAP1GDS1-3'NUP98 transcript is often but not always expressed.

To be noted

Additional cases are needed to delineate the epidemiology of this rare entity:
you are welcome to submit a paper to our new Case Report section.
Case Report T-cell acute lymphoblastic leukemia with t(4;11)(q23;p15) and NUP98/RAP1GDS1 gene fusion: Case report and review of literature.
Case Report t(4;11)(q23;p15) in paediatric early T cell precursor acute lymphoblastic leukemia


Molecular evaluation of the NUP98/RAP1GDS1 gene frequency in adults with T-acute lymphoblastic leukemia
Cimino G, Sprovieri T, Rapanotti MC, Foà R, Mecucci C, Mandelli F
Haematologica 2001 Apr;86(4):436-7
PMID 11325654
t(4;11)(q21;p15), including one complex translocation t(1;4;11)(p32;q21;p15), in adult T-cell acute lymphoblastic leukemia
Douet-Guilbert N, Morel F, Le Bris MJ, Herry A, Le Calvez G, Marion V, Berthou C, De Braekeleer M
Leuk Res 2003 Oct;27(10):965-7
PMID 12860018
NUP98 gene fusions and hematopoietic malignancies: common themes and new biologic insights
Gough SM, Slape CI, Aplan PD
Blood 2011 Dec 8;118(24):6247-57
PMID 21948299
The (4;11)(q21;p15) translocation fuses the NUP98 and RAP1GDS1 genes and is recurrent in T-cell acute lymphocytic leukemia
Hussey DJ, Nicola M, Moore S, Peters GB, Dobrovic A
Blood 1999 Sep 15;94(6):2072-9
PMID 10477737
A variant translocation between chromosomes 4 and 11, t(4q;11p) in a child with acute leukemia
Inoue S, Tyrkus M, Ravindranath Y, Gohle N
Am J Pediatr Hematol Oncol 1985 Summer;7(2):211-4
PMID 3842567
NUP98 gene fusions in hematologic malignancies
Lam DH, Aplan PD
Leukemia 2001 Nov;15(11):1689-95
PMID 11681408
t(4;11)(q21;p15) translocation involving NUP98 and RAP1GDS1 genes: characterization of a new subset of T acute lymphoblastic leukaemia
Mecucci C, La Starza R, Negrini M, Sabbioni S, Crescenzi B, Leoni P, Di Raimondo F, Krampera M, Cimino G, Tafuri A, Cuneo A, Vitale A, Foà R
Br J Haematol 2000 Jun;109(4):788-93
PMID 10929031
NUP98 fusion oncoproteins promote aneuploidy by attenuating the mitotic spindle checkpoint
Salsi V, Ferrari S, Gorello P, Fantini S, Chiavolelli F, Mecucci C, Zappavigna V
Cancer Res 2014 Feb 15;74(4):1079-90
PMID 24371226
SmgGDS-558 regulates the cell cycle in pancreatic, non-small cell lung, and breast cancers
Schuld NJ, Hauser AD, Gastonguay AJ, Wilson JM, Lorimer EL, Williams CL
Cell Cycle 2014;13(6):941-52
PMID 24552806
The role of NUP98 gene fusions in hematologic malignancy
Slape C, Aplan PD
Leuk Lymphoma 2004 Jul;45(7):1341-50
PMID 15359631
A t(4;11)(q21;p15) in a case of T-cell lymphoma and a case of acute myelogenous leukemia
Thangavelu M, Huang B, Lemieux M, Tom W, Richkind KE
Cancer Genet Cytogenet 2002 Jan 15;132(2):109-15
PMID 11850070
Identification of NUP98 abnormalities in acute leukemia: JARID1A (12p13) as a new partner gene
van Zutven LJ, Onen E, Velthuizen SC, van Drunen E, von Bergh AR, van den Heuvel-Eibrink MM, Veronese A, Mecucci C, Negrini M, de Greef GE, Beverloo HB
Genes Chromosomes Cancer 2006 May;45(5):437-46
PMID 16419055


This paper should be referenced as such :
Anwar N Mohamed
t(4;11)(q23;p15) NUP98/RAP1GDS1
Atlas Genet Cytogenet Oncol Haematol. 2016;20(11):579-582.
Free journal version : [ pdf ]   [ DOI ]
On line version :
History of this paper:
Viguié, F. t(4;11)(q21;p15). Atlas Genet Cytogenet Oncol Haematol. 2002;6(4):301-302.

Other genes implicated (Data extracted from papers in the Atlas) [ 2 ]

Genes NUP98 RAP1GDS1

Translocations implicated (Data extracted from papers in the Atlas)

 t(4;11)(q23;p15) NUP98/RAP1GDS1

External links

NUP98 (11p15.4) RAP1GDS1 (4q23)

NUP98 (11p15.4) RAP1GDS1 (4q23)

Mitelman databaset(4;11)(q23;p15)
arrayMap (UZH-SIB Zurich)Morph ( 9837/3) -   [auto + random 100 samples .. if exist ]   [tabulated segments]
arrayMap (UZH-SIB Zurich)Morph ( 9861/3) -   [auto + random 100 samples .. if exist ]   [tabulated segments]
Mitelman databaseNUP98/RAP1GDS1 [MCList]  NUP98 (11p15.4) RAP1GDS1 (4q23)
TICdbNUP98/RAP1GDS1  NUP98 (11p15.4) RAP1GDS1 (4q23)
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