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Chromosome 11
Unusually gene-dense - includes the β-globin cluster (sickle-cell disease, β-thalassaemia), WT1, and ATM.
Schematic of chromosome 11 showing the short (p) and long (q) arms. Arm ratio per GRCh38 - banding schematic.
Available at Jeen Health
Clinical tests that include this
Overview
Chromosome 11 is a submetacentric chromosome, meaning that its centromere sits somewhat off-centre, creating a shorter p (short) arm and a longer q (long) arm. At 135.1 million base pairs, it represents about 4% of the total human genome yet encodes over 1,300 protein-coding genes, making it one of the most gene-dense chromosomes in the human karyotype. This high gene density translates into clinical significance: chromosome 11 harbours genes involved in oxygen transport, DNA repair, kidney and reproductive development, cardiac electrical activity, and tumour suppression.
Clinically, chromosome 11 is perhaps best known for the β-globin gene cluster at 11p15.4, mutations in which underlie sickle-cell disease and the β-thalassaemias, two of the most common inherited blood disorders worldwide. The short arm also contains the WT1 gene, pathogenic variants in which cause Wilms tumour and a spectrum of kidney-and-genital developmental syndromes. On the long arm, ATM encodes a master regulator of the DNA-damage response, and inherited ATM variants cause ataxia-telangiectasia and contribute to hereditary breast-cancer risk. The diversity of functions encoded by chromosome 11 means that both germline mutations and somatic rearrangements affecting this chromosome contribute to a broad range of paediatric and adult disease.
Structure
Like all chromosomes, chromosome 11 consists of a single, immensely long DNA molecule packaged into chromatin. The DNA double helix wraps around histone proteins to form nucleosomes, which in turn coil and fold into higher-order chromatin fibres. At metaphase, when the chromosome condenses for cell division, the full 135.1 million base pairs compact into a recognisable rod-shaped structure roughly a few micrometres in length. The centromere of chromosome 11 lies off-centre, creating a short p arm and a longer q arm, a configuration known as submetacentric. This asymmetry is visible under the microscope during karyotyping and provides a key landmark for identifying the chromosome and mapping structural abnormalities.
The p arm of chromosome 11 is particularly notable for its density of clinically important genes, especially in the distal band 11p15, which contains both the β-globin cluster and a major imprinted region (the Beckwith-Wiedemann locus). The q arm stretches from the centromere to the telomere and includes multiple tumour-suppressor genes, DNA-repair genes, and metabolic-enzyme genes distributed across its length. Both arms contain interspersed repetitive elements, gene deserts, and clusters of highly conserved regulatory sequences that coordinate gene expression across development and in response to environmental signals.
Video: What is a karyotype?
Notable regions
The 11p15.4 band, near the tip of the short arm, contains the β-globin gene cluster (HBB, HBD, HBG1, HBG2, HBE1), a tightly regulated array of genes that encode the beta chains of haemoglobin. Single-nucleotide variants in HBB can result in sickle-cell disease (a structural haemoglobin variant) or β-thalassaemia (reduced or absent β-globin production). These conditions are among the most common monogenic disorders globally, particularly in populations with historic malaria exposure. Carrier screening for haemoglobinopathies is routinely offered through NHS antenatal and newborn programmes, and diagnosis is confirmed by haemoglobin electrophoresis, high-performance liquid chromatography, and increasingly by genomic sequencing.
Just proximal to the β-globin cluster, at 11p15.5, lies the Beckwith-Wiedemann imprinted region, a complex locus containing the maternally expressed genes H19 and CDKN1C alongside the paternally expressed growth factor IGF2. Dysregulation of this region, whether through loss of methylation, uniparental disomy, or structural rearrangement, can result in Beckwith-Wiedemann syndrome, characterised by overgrowth, abdominal-wall defects, and an increased risk of childhood tumours such as Wilms tumour and hepatoblastoma. Genomic imprinting means that the parent of origin for a mutation or chromosomal abnormality matters, and molecular testing for Beckwith-Wiedemann typically includes methylation analysis at multiple imprinting centres in this region.
Moving inward along the short arm, the 11p13 band contains WT1, a transcription factor essential for kidney and gonadal development. Pathogenic variants in WT1 are associated with a spectrum of overlapping syndromes: WAGR syndrome (a contiguous gene deletion including WT1 and PAX6, causing Wilms tumour, aniridia, genitourinary anomalies, and intellectual disability), Denys-Drash syndrome (early-onset nephrotic syndrome and Wilms tumour risk), and Frasier syndrome (later-onset kidney disease and gonadal dysgenesis). WT1 testing is standard in children presenting with Wilms tumour or unexplained kidney disease, and results guide surveillance protocols for tumour risk.
On the long arm, the 11q22.3 band houses ATM, encoding a serine-threonine kinase that senses DNA double-strand breaks and orchestrates repair. Biallelic loss-of-function variants cause ataxia-telangiectasia, a childhood-onset neurodegenerative and immunodeficiency disorder with high cancer susceptibility. Heterozygous carriers of ATM pathogenic variants face a modestly increased risk of breast cancer, and ATM is now included in many hereditary-cancer gene panels offered through NHS genetics services. The 11q13.1 region contains MEN1, mutations in which cause multiple endocrine neoplasia type 1, a tumour-predisposition syndrome affecting the parathyroid glands, pancreatic islets, and pituitary.
Notable genes
Beyond the β-globin cluster and WT1, chromosome 11 encodes several other genes of major clinical importance. ATM is central to genome stability and cancer prevention, and its loss underpins both a devastating childhood syndrome and a contributor to hereditary breast cancer. MEN1, though less commonly discussed outside endocrinology, is the prototypic example of a multiple-endocrine-neoplasia gene, and carriers require lifelong biochemical and imaging surveillance for hormone-secreting tumours. KCNQ1, located at 11p15.5, encodes a cardiac potassium-channel subunit; variants cause long QT syndrome type 1 and, when combined with variants in KCNE1, Jervell and Lange-Nielsen syndrome (long QT with congenital deafness). To clarify, biallelic variants in either KCNQ1 or KCNE1 cause Jervell and Lange-Nielsen syndrome. MYBPC3, on the other hand, encodes cardiac myosin-binding protein C, and pathogenic variants are one of the most frequent causes of hypertrophic cardiomyopathy, a common inherited heart-muscle disorder.
Other medically important genes on chromosome 11 include SDHD and SDHAF2 (both involved in mitochondrial energy metabolism and associated with hereditary paraganglioma-phaeochromocytoma syndromes), SMPD1 (mutations cause Niemann-Pick disease types A and B), HMBS (acute intermittent porphyria), and SLC39A13 (spondylodysplastic Ehlers-Danlos syndrome). The concentration of so many disease genes on a single chromosome reflects both the high gene density of chromosome 11 and the broad range of cellular processes those genes regulate.
Chromosomal disorders
Unlike some chromosomes (notably 13, 18, and 21), whole-chromosome aneuploidies of chromosome 11 (trisomy 11 or monosomy 11) are generally not viable and are extremely rare in liveborn individuals. Most cases of trisomy 11 are confined to mosaic forms detected prenatally or in tumour samples, and complete trisomy 11 typically results in early pregnancy loss. As a result, there is no recognised clinical syndrome analogous to Down or Edwards syndrome for chromosome 11.
Instead, the clinically relevant chromosomal disorders involving chromosome 11 tend to be microdeletions, microduplications, and disturbances of genomic imprinting. The WAGR syndrome, mentioned earlier, arises from a contiguous gene deletion at 11p13 encompassing WT1, PAX6, and sometimes adjacent genes; it is detectable by chromosomal microarray or targeted fluorescence in-situ hybridisation and presents with a recognisable constellation of Wilms tumour, aniridia, genitourinary anomalies, and variable intellectual disability. Beckwith-Wiedemann syndrome, though often caused by epigenetic changes (loss of methylation at imprinting control regions) or uniparental disomy of chromosome 11p15, can also result from paternal duplication or maternal deletion of this region. The syndrome is characterised by macrosomia (large birth weight), macroglossia (enlarged tongue), abdominal-wall defects such as exomphalos, and an elevated risk of embryonal tumours in early childhood. Children with Beckwith-Wiedemann are enrolled in abdominal-ultrasound surveillance programmes to detect Wilms tumour and hepatoblastoma at an early, treatable stage. The majority of Beckwith-Wiedemann cases are sporadic, caused by epigenetic changes or somatic events, while a minority result from inherited genetic or epigenetic variants.
Uniparental disomy of chromosome 11 (where both copies are inherited from one parent) can lead to disease if the duplicated region includes imprinted genes. Paternal uniparental disomy of 11p15 can produce Beckwith-Wiedemann syndrome, while maternal uniparental disomy of the same region can result in Silver-Russell syndrome (characterised by growth restriction and asymmetry). These disorders illustrate the importance of parental origin in gene regulation and underscore why some chromosome-11 abnormalities require specialised molecular-genetic testing beyond standard karyotyping.
Prenatal screening & diagnosis
Antenatal screening for chromosome-11 disorders is not part of the standard non-invasive prenatal testing (NIPT) menu in the NHS, which focuses on the common autosomal trisomies (13, 18, 21) and sex-chromosome aneuploidies. However, certain ultrasound findings can prompt targeted investigation. For example, foetuses with exomphalos, macroglossia, or polyhydramnios may be assessed for Beckwith-Wiedemann syndrome through detailed anomaly scanning and, if indicated, diagnostic testing such as amniocentesis with chromosomal microarray and methylation studies of the 11p15 region. Similarly, aniridia detected on foetal magnetic-resonance imaging might raise suspicion for WAGR syndrome and lead to targeted genetic testing for an 11p13 deletion.
For families with a known pathogenic variant in a chromosome-11 gene (for instance, a familial ATM, WT1, or MEN1 variant), preimplantation genetic testing or prenatal diagnosis via chorionic-villus sampling or amniocentesis can be offered. Carrier screening for haemoglobinopathies (HBB variants) is routine in the NHS for at-risk ethnic groups and is typically performed before pregnancy or in early antenatal care. If both parents are carriers of a β-thalassaemia or sickle-cell variant, prenatal diagnosis is available, and results inform parental choice and preparation for postnatal management.
Chromosomal microarray is first-line for postnatal investigation of unexplained developmental delay or congenital anomalies, and is also used prenatally when structural abnormalities are detected on ultrasound. It will detect pathogenic deletions and duplications across chromosome 11, including WAGR deletions and Beckwith-Wiedemann duplications. Karyotyping remains useful for identifying balanced translocations involving chromosome 11, which may be relevant in recurrent-miscarriage workup or if a parent carries a rearrangement that increases the risk of unbalanced offspring.
Inheritance & recurrence
Most disease-causing variants in chromosome-11 genes follow Mendelian inheritance patterns. ATM-related ataxia-telangiectasia and many cases of β-thalassaemia are autosomal recessive, meaning both parents are typically unaffected carriers, and the recurrence risk for each subsequent pregnancy is 25%. Conditions such as hereditary breast cancer due to heterozygous ATM variants, long QT syndrome type 1 (KCNQ1), hypertrophic cardiomyopathy (MYBPC3), and multiple endocrine neoplasia type 1 (MEN1) are autosomal dominant; an affected parent has a 50% chance of passing the pathogenic variant to each child, though penetrance and expressivity vary.
Wilms tumour caused by WT1 variants can be inherited in an autosomal-dominant pattern with incomplete penetrance, but many cases arise de novo. WAGR syndrome, being a deletion, is usually sporadic, though rare familial cases due to parental mosaicism or balanced rearrangements have been reported. Beckwith-Wiedemann syndrome is more complex: the majority of cases are sporadic, caused by epigenetic changes or somatic events occurring after conception. A minority of cases result from inherited genetic or epigenetic variants, and recurrence risk depends on the specific molecular mechanism. Families affected by any chromosome-11 disorder are typically referred to NHS clinical genetics services for personalised risk assessment, carrier testing of relatives where appropriate, and discussion of reproductive options including preimplantation genetic testing.
Frequently asked questions
Why is chromosome 11 considered particularly important clinically?
Chromosome 11 is unusually gene-rich and contains numerous genes implicated in common and rare inherited conditions. The β-globin cluster underlies sickle-cell disease and β-thalassaemia, two of the most prevalent monogenic disorders worldwide. It also encodes tumour suppressors such as WT1 and MEN1, DNA-repair coordinators like ATM, and cardiac genes including KCNQ1 and MYBPC3, making it relevant across haematology, oncology, cardiology, and nephrology.
Can chromosome 11 trisomy or monosomy occur, and what are the outcomes?
Complete trisomy 11 or monosomy 11 is almost always lethal in early development and extremely rare in liveborn babies. Mosaic trisomy 11, where only some cells carry an extra copy, has occasionally been reported but is not associated with a recognisable clinical syndrome. Unlike chromosomes 13, 18, and 21, chromosome 11 aneuploidies do not form part of routine antenatal screening.
What is Beckwith-Wiedemann syndrome, and how does it relate to chromosome 11?
Beckwith-Wiedemann syndrome is an overgrowth disorder caused by dysregulation of imprinted genes in the 11p15.5 region, including H19, IGF2, and CDKN1C. Most cases result from loss of methylation at imprinting centres or paternal uniparental disomy, rather than large deletions or duplications. Affected children have an increased risk of Wilms tumour and hepatoblastoma and are monitored with regular abdominal ultrasound scans.
If I carry a pathogenic variant in a chromosome-11 gene, what is the chance my children will inherit it?
That depends on the inheritance pattern. For autosomal-dominant conditions (such as long QT syndrome type 1 or multiple endocrine neoplasia type 1), each child has a 50% chance of inheriting the variant. For autosomal-recessive conditions (such as ataxia-telangiectasia), both parents must be carriers, and each child has a 25% risk of being affected. An NHS clinical genetics appointment will provide tailored risk figures and discuss options such as preimplantation or prenatal diagnosis.
How are chromosome-11 deletions and duplications detected?
Chromosomal microarray analysis is the first-line test for detecting microdeletions and microduplications, including those affecting chromosome 11 such as WAGR deletions or Beckwith-Wiedemann duplications. Traditional karyotyping can identify larger structural rearrangements, and targeted tests (such as fluorescence in-situ hybridisation or methylation assays) are used when a specific syndrome is suspected. Many of these tests are available through NHS genetics laboratories.
Launch-set genes on chromosome 11
Genes on this chromosome that currently have dedicated pages in the library. This list grows as we publish more.