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t(3;9)(p13;q34.1) FOXP1/ABL1

Written2016-09Julie Sanford Biggerstaff
Idaho Cytogenetics Diagnostic Laboratory, Boise, ID 83706/

Abstract Review on t(3;9)(p13;q34.1) FOXP1/ABL1, with data on clinics, and the genes involved.

Keywords chromosome 3; chromosome 9; FOXP1; ABL1; B Cell Acute Lymphoblastic Leukemia; Follicular Lymphoma

(Note : for Links provided by Atlas : click)


ICD-Topo C420,C421,C424
ICD-Morpho 9811/3 B lymphoblastic leukaemia/lymphoma, NOS
ICD-Morpho 9690/3 Follicular lymphoma; Paediatric follicular lymphoma
Atlas_Id 1619

Clinics and Pathology

Disease Pre-B Cell Acute Lymphoblastic Leukemia/Lymphoma (ALL) and Follicular Lymphoma (Ernst et al., 2011; Koduru et al., 1997).
Note The FOXP1/ABL1 involvement was ascertained only in the B-ALL case. t(3;9) was found in a sub-clone and against the background of a complex karyotype and TP53 gene mutation in the follicular lymphoma case.
Phenotype / cell stem origin Pre-B cell.
Epidemiology 1 ALL case reported to date: a 16 yo female patient, and 1 follicular lymphoma case reported to date: a 52 yo male patient.
Cytology High leukocytosis (>50,000 x 109/L) at diagnosis.
Treatment For ALL: Standard COALL (German Cooperative Study Group) protocol for high-risk ALL followed by Allogeneic BMT; may be sensitive to treatment with first or 2nd generation tyrosine kinase inhibitors.
Prognosis Yet unknown; ALL patient was reported in remission 9 years post diagnosis, but after paternal origin haplo-identical BMT.


Probes ABL1 should show split signal using the standard DCDF BCR/ABL1 construct.

Genes involved and Proteins

Gene NameFOXP1 (Forkhead box P1)
Location 3p13
Note Member of forkhead box (FOX) subfamily P; transcription factor. These proteins play a role in cell- and tissue-specific gene transcription regulation.
  View of FOXP1 gene from UCSC genome browser
Dna / Rna Gene is 176,228 bp with 16 exons; transcribed from the - strand ; coding region is 171,437 bp with 14 exons.
Protein At least 12 protein isoforms produced; dimerizes with FOXP2 and FOXP4 using the leucine-zipper domain which is required for DNA binding capability. Protein locates to the nucleus.
Germinal mutations Germline mutations of FOXP1 are associated with autosomal dominant intellectual disability with language impairment, with or without autistic features (MIM phenotype 613670).
Gene NameABL1 (v-abl Abelson murine leukemia viral oncogene homolog 1)
Location 9q34.12
Dna / Rna Expressed as either 6- or 7-Kb transcript.
Protein Tyrosine kinase; located in either the nucleus (shorter transcript) or cytoplasm (longer transcript) depending on which splice variant is produced (Chissoe et al., 1995).

Result of the chromosomal anomaly

Hybrid gene
Note In the single patient characterized, the in-frame fusion was confirmed between FOXP1 exon 19 (ENST00000318789) and ABL1 exon 4 (ENST00000318560) (Ernst et al., 2011).
Description ABL1 exon 4 fused with FOXP1 alternative RNA isoform (NM_032682).
Detection RT-PCR

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.


Sequence and analysis of the human ABL gene, the BCR gene and regions involved in the Philadelphia chromosomal translocation
Chissoe SL, Bodenteich A, Wang YF, Wang YP, Burian D, Clifton SW, Crabtree J, Freeman A, Iyer K, Jian L, Ma Y, McLaury HL, Pan HQ, Sarhan OH, Toth S, Wang Z, Zhang G, Heisterkamp N, Droffen J, Roe BA.
Genomics. 1995 May 1;27:67-82.
PMID 7665185
Identification of FOXP1 and SNX2 as Novel ABL1 fusion partners in acute lymphoblastic leukaemia
Ernst, T, Score J, Deininger M, Hidalgo-Curtis C, Lackie P, Ershler WB, Goldman JM,Cross NC, Grand F.
Br J Haematol. 2011 Apr;153(1):43-6.doi:10.1111/j.1365-2141.2010.08457.x.Epub 2011 Feb 1.
PMID 21391972
De novo mutations in FOXP1 in cases with intellectual disability, autism and language impairment
Hamdan FF, Daoud H, Rochefort D, Piton A, Gauthier J, Langlois M, Foomani G, Dobrzeniecka S, Krebs M, Joober R, Lafreniere RG, Lacaille JC, Mottron L, Drapeau P, Beauchamp MH, Phillips M, Fombonne E, Rouleau GA, Michaud JL.
Am J Hum Genet 2010 Nov 12; 87(5):671-8. Doi: 10.1016/j.ajhg.2010.09.017.Epub 2010 Oct 14.
PMID 20950788
Correlation between mutation in P53, p53 expression, cytogenetics, histologic type, and survival in patients with B-cell non-Hodgkin's lymphoma.
Koduru PR, Raju K, Vadmal V, Menezes G, Shah S, Susin M, Kolitz J, Broome JD.
Blood. 1997 Nov 15:90(10)4078-91.
PMID 9354678


This paper should be referenced as such :
Julie Sanford Biggerstaff
t(3;9)(p13;q34.1) FOXP1/ABL1
Atlas Genet Cytogenet Oncol Haematol. 2017;21(7):263-264.
Free journal version : [ pdf ]   [ DOI ]
On line version :

Translocations implicated (Data extracted from papers in the Atlas)

 t(3;9)(p13;q34.1) FOXP1/ABL1

External links

Mitelman databaset(3;9)(p13;q34.1)
arrayMap (UZH-SIB Zurich)Morph ( 9811/3) -   [auto + random 100 samples .. if exist ]   [tabulated segments]
arrayMap (UZH-SIB Zurich)Morph ( 9690/3) -   [auto + random 100 samples .. if exist ]   [tabulated segments]
REVIEW articlesautomatic search in PubMed
Last year articlesautomatic search in PubMed
All articlesautomatic search in PubMed

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