Genetics

The Genetic Blueprint: Understanding the Deletion and Diagnosis

At a Glance

Jacobsen syndrome is diagnosed by identifying a missing piece of chromosome 11 (11q23 deletion) using tests like a chromosomal microarray. The symptoms occur because multiple adjacent genes are missing, including FLI1 (linked to bleeding disorders) and ETS1 (linked to heart defects).

The diagnosis of Jacobsen syndrome is confirmed through specialized genetic testing that identifies a missing piece of chromosome 11 ^[1]^[2]. Understanding the technical language in your child’s genetic report can help you better anticipate their specific needs and coordinate with their care team.

Diagnostic Tools: Karyotype vs. Microarray

There are two primary ways doctors find the deletion:

Karyotype: This is a traditional “map” of the chromosomes. It can see large deletions under a microscope ^[2]. A typical result might look like del(11)(q23), which means a deletion on the long arm (q) of chromosome 11, starting at position 23 ^[1].
Chromosomal Microarray (CMA): This is the modern “gold standard” ^[2]. It is much more precise and can identify the exact “breakpoints”—the precise start and end points of the missing section ^[3]. It can find “microdeletions” that a standard karyotype might miss ^[4].

Decoding the Language

In your report, you may see the term 11q23-qter.

11q: Refers to the long arm of chromosome 11.
23: Refers to a specific “neighborhood” or band on that arm.
qter: Short for “terminus,” meaning the deletion extends all the way to the very end of the chromosome ^[1]^[5]. This is called a terminal deletion ^[6]. If the deletion is a gap in the middle of the arm with the end still intact, it is called an interstitial deletion ^[7].

The Role of Key Genes

Because Jacobsen syndrome is a contiguous gene syndrome, the symptoms are caused by the loss of multiple genes located next to each other ^[8]. Some of the most important genes studied in this region include:

FLI1: Loss of this gene is the primary cause of Paris-Trousseau syndrome, the bleeding and platelet disorder common in Jacobsen syndrome ^[6]^[9].
ETS1: This gene is heavily linked to heart defects, immune system challenges, and specific facial features ^[3]^[10].
FEZ1: Deletion of this gene is often associated with motor-related developmental delays ^[11].
HEPACAM: Missing this gene can be linked to abnormalities in the brain’s white matter ^[12].

Differentiation from Other Syndromes

Jacobsen syndrome is often distinguished from other conditions by its unique “constellation” of symptoms. While it may share features with other disorders, specific clues help doctors tell them apart:

vs. Paris-Trousseau Syndrome: While both involve an 11q deletion and bleeding issues, Jacobsen syndrome is “broader,” involving many other organ systems like the heart and brain ^[6]^[5].
vs. Craniosynostosis Syndromes: Jacobsen syndrome can cause trigonocephaly (a pointed forehead), which is also seen in syndromes like Muenke or Saethre-Chotzen. However, those syndromes are usually caused by a mutation in a single gene (like FGFR), whereas Jacobsen syndrome involves an entire missing chromosomal section and the signature bleeding disorder ^[13]^[14].

Your Genetic Report Checklist

To ensure you have the most complete information for your child’s doctors, check that your report includes:

[ ] Genome Build: A reference number (like hg19 or hg38) that tells doctors which “map” was used ^[3].
[ ] Precise Coordinates: The exact start and stop numbers of the deletion (the “breakpoints”) ^[3].
[ ] Size of Deletion: Often measured in “Mb” (megabases) ^[2].
[ ] List of Missing Genes: A detailed list of the known genes located within the deleted section ^[15]^[3].
[ ] Inheritance Status: Whether the deletion is de novo (new) or inherited from a parent ^[16].

Common questions in this guide

What does an 11q23 deletion mean on a genetic report?

An 11q23 deletion means that a specific section on the long arm of chromosome 11 is missing. In Jacobsen syndrome, this missing section involves multiple adjacent genes that control normal development and organ function.

What is the difference between a karyotype and a microarray for diagnosing Jacobsen syndrome?

A karyotype is a traditional chromosome map that spots large deletions, while a chromosomal microarray (CMA) is much more precise. A microarray can identify the exact start and end points of the missing DNA section, including microdeletions a standard karyotype might miss.

What does terminal vs. interstitial deletion mean?

A terminal deletion means the missing DNA extends all the way to the end of the chromosome, which is often noted as 'qter' on a genetic report. An interstitial deletion means there is a missing gap in the middle of the chromosome arm, but the very end remains intact.

How does the FLI1 gene relate to Jacobsen syndrome?

The loss of the FLI1 gene is the primary cause of Paris-Trousseau syndrome, a bleeding and platelet disorder common in individuals with Jacobsen syndrome. If your child's report shows this gene is missing, doctors will typically recommend a hematology evaluation.

Why do geneticists check for the ETS1 gene in Jacobsen syndrome?

Heart defects and immune system challenges in Jacobsen syndrome are heavily linked to the loss of the ETS1 gene. Knowing whether this gene is included in your child's specific deletion helps doctors prioritize comprehensive cardiology and immunology evaluations.

Curated prompts to bring to your next appointment.

1.Does my child's report show a terminal or interstitial deletion, and how does this affect their specific prognosis?
2.Can you help me list every gene missing in the deleted region from my child's microarray results?
3.Based on the breakpoints in this report, is the FLI1 gene missing, and should we consult a hematologist for Paris-Trousseau syndrome?
4.Are there any genes in the deleted region, such as ETS1, that suggest we should prioritize a cardiology or immunology evaluation?
5.Was this testing done using the most recent genome build (like hg38), and does that change which genes are identified as missing?

Tap a prompt to share your answer — we'll use it plus this page's context to start a tailored conversation.

References (16)

1
A Case Report: Jacobsen Syndrome Complicated by Paris-Trousseau Syndrome and Shone's Complex.
Malia LA, Wolkoff LI, Mnayer L, et al.
Journal of pediatric hematology/oncology 2015; (37(7)):e429-32 doi:10.1097/MPH.0000000000000372.
PMID: 26056793
2
Jacobsen syndrome and neonatal bleeding: report on two unrelated patients.
Serra G, Memo L, Antona V, et al.
Italian journal of pediatrics 2021; (47(1)):147 doi:10.1186/s13052-021-01108-2.
PMID: 34210338
3
Partial Jacobsen syndrome phenotype in a patient with a de novo frameshift mutation in the ETS1 transcription factor.
Tootleman E, Malamut B, Akshoomoff N, et al.
Cold Spring Harbor molecular case studies 2019; (5(3)) doi:10.1101/mcs.a004010.
PMID: 31160359
4
Molecular cytogenetic characterization of Jacobsen syndrome (11q23.3-q25 deletion) in a fetus associated with double outlet right ventricle, hypoplastic left heart syndrome and ductus venosus agenesis on prenatal ultrasound.
Chen CP, Wang LK, Wu PC, et al.
Taiwanese journal of obstetrics & gynecology 2017; (56(1)):102-105 doi:10.1016/j.tjog.2016.12.004.
PMID: 28254208
5
Teaching NeuroImages: A rare case of Jacobsen syndrome with global diffuse hypomyelination of brain.
Patel H, Kumar A, Raymond G, Mainali G
Neurology 2019; (92(14)):e1665-e1666 doi:10.1212/WNL.0000000000007234.
PMID: 30936237
6
Recurrent Spontaneous Intracranial Hemorrhage in a Patient With Jacobsen Syndrome.
Suryadevara N, Ahmed R, El-Dokla A
Neurology. Clinical practice 2021; (11(4)):e598-e599 doi:10.1212/CPJ.0000000000000963.
PMID: 34484972
7
de novo interstitial deletions at the 11q23.3-q24.2 region.
Su J, Chen R, Luo J, et al.
Molecular cytogenetics 2016; (9()):39 doi:10.1186/s13039-016-0247-7.
PMID: 27158264
8
Jacobsen syndrome: Advances in our knowledge of phenotype and genotype.
Favier R, Akshoomoff N, Mattson S, Grossfeld P
American journal of medical genetics. Part C, Seminars in medical genetics 2015; (169(3)):239-50 doi:10.1002/ajmg.c.31448.
PMID: 26285164
9
Mice Haploinsufficient for Ets1 and Fli1 Display Middle Ear Abnormalities and Model Aspects of Jacobsen Syndrome.
Carpinelli MR, Kruse EA, Arhatari BD, et al.
The American journal of pathology 2015; (185(7)):1867-76.
PMID: 26093983
10
Gene-targeted deletion in mice of the Ets-1 transcription factor, a candidate gene in the Jacobsen syndrome kidney "critical region," causes abnormal kidney development.
Ye M, Xu L, Fu M, et al.
American journal of medical genetics. Part A 2019; (179(1)):71-77 doi:10.1002/ajmg.a.40481.
PMID: 30422383
11
Loss of FEZ1, a gene deleted in Jacobsen syndrome, causes locomotion defects and early mortality by impairing motor neuron development.
Gunaseelan S, Wang Z, Tong VKJ, et al.
Human molecular genetics 2021; (30(1)):5-20 doi:10.1093/hmg/ddaa281.
PMID: 33395696
12
Leukoencephalopathy associated with 11q24 deletion involving the gene encoding hepatic and glial cell adhesion molecule in two patients.
Yamamoto T, Shimada S, Shimojima K, et al.
European journal of medical genetics 2015; (58(9)):492-6.
PMID: 26193381
13
Jacobsen syndrome associated with Shone's complex: a case report.
Brum A, Laskoski LV, Matos FGOA, d'Arce LPG
Revista paulista de pediatria : orgao oficial da Sociedade de Pediatria de Sao Paulo 2025; (43()):e2024136 doi:10.1590/1984-0462/2025/43/2024136.
PMID: 39841699
14
Craniosynostosis as a clinical and diagnostic problem: molecular pathology and genetic counseling.
Kutkowska-Kaźmierczak A, Gos M, Obersztyn E
Journal of applied genetics 2018; (59(2)):133-147 doi:10.1007/s13353-017-0423-4.
PMID: 29392564
15
Case report: ETS1 gene deletion associated with a low number of recent thymic emigrants in three patients with Jacobsen syndrome.
Trachsel T, Prader S, Steindl K, Pachlopnik Schmid J
Frontiers in immunology 2022; (13()):867206 doi:10.3389/fimmu.2022.867206.
PMID: 36341443
16
Jacobsen Syndrome: Surgical Complications due to Unsuspected Diagnosis, the Importance of Molecular Studies in Patients with Craniosynostosis.
Linares Chávez EP, Toral López J, Valdés Miranda JM, et al.
Molecular syndromology 2016; (6(5)):229-35 doi:10.1159/000442477.
PMID: 26997943

This page explains Jacobsen syndrome genetic testing terminology for educational purposes. A medical geneticist is the best source for interpreting your child's specific microarray report.

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