Fanconi anemia

What every physician needs to know:

Fanconi anemia is a recessively inherited disorder classically characterized by bone marrow failure, congenital anomalies, and cancer predisposition. Malignancies typically include acute myeloid leukemia, squamous cell carcinoma (oral, esophageal, vulvar), and hepatocellular carcinomas. Additionally, patients can develop liver adenomas.

The clinical phenotype of Fanconi anemia is broad. The absence of physical stigmata does not rule out the diagnosis of Fanconi anemia. For this reason, Fanconi anemia should be considered in patients presenting with aplastic anemia, squamous cell carcinomas presenting at an unusually young age, excessive side effects from chemotherapy or radiation, a personal or family history of cancer predisposition, a family history of cytopenias, or cytopenias together with congenital anomalies. Patients may present in adulthood with previously undiagnosed Fanconi anemia.

The diagnosis of Fanconi anemia is made by the demonstration of increased chromosomal breakage in the presence of clastogens such as mitomycin C (MMC) or diepoxybutane (DEB). Although the test is usually sent on a blood sample, testing of skin fibroblasts may be necessary to rule out somatic mosaicism in patients with a high clinical suspicion for Fanconi anemia.

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The Fanconi anemia molecular pathway functions in DNA repair. Patients with Fanconi anemia are exquisitely sensitive to DNA damaging agents such as chemotherapy or radiation. For this reason, diagnosis prior to initiating treatments for malignancies or bone marrow transplant is critical, as patients require reduced intensity regimens.

Aplastic anemia in Fanconi anemia patients is not responsive to anti-thymocyte globulin (ATG) and cyclosporin. Patients may respond to androgens.

Currently the only curative therapy for the hematological complications of Fanconi anemia (aplastic anemia, myelodysplastic syndrome, leukemia) is a hematopoietic stem cell transplant. Hematopoietic stem cell transplant does not cure the non-hematological complications of Fanconi anemia.

Are you sure your patient has Fanconi anemia? What should you expect to find?

Patients may present with physical stigmata of Fanconi anemia, though the absence of physical findings does not rule out the diagnosis.

Physical findings in Fanconi anemia, listed in approximate order of frequency:

  • Short stature
  • Skin pigmentation

– Hyperpigmentation (café au lait spots) or hypopigmented spots

  • Skeletal

– Thumbs: absent, hypoplastic, bifid, duplicated, triphalangeal, floating (pouce flottant), elongated, low set

– Arms: Absent, hypoplastic, or dysmorphic, absent or weak pulse

– Hands: Hypoplastic thenar eminence, absent first metacarpal, clinodactyly, polydactyly

– Head : Microcephaly, hydrocephaly

– Face: dysmorphic, micrognathia, mid-face hypoplasia

– Neck: Sprengel’s deformity, Klippel-Feil, short, low hairline, webbed

– Spine: Spina bifida, scoliosis, hemivertebrae, abnormal ribs, coccygeal aplasia

– Feet: Toe syndactyly, club feet

– Legs: Congenital hip dislocation

  • Eyes

– Microcephaly, strabismus, epicanthal folds, hypotelorism, hypertelorism, cataracts, ptosis.

  • Renal

– Horseshoe, ectopic or pelvic, abnormal, hypoplastic or dysplastic, absent, hydronephrosis or hydroureter.

  • Gonads

– Male: Hypogenitalia, undescended testes, hypospadias, micropenis, absent testes.

– Female: Hypogenitalia, bicornuate uterus, malposition, small ovaries.

  • Developmental delay (uncommon)

– Mental retardation, developmental delay.

  • Ears

– Deaf (typically conductive), dysplastic, atretic, narrow ear canal, abnormal middle ear.

  • Cardiopulmonary

– Patent ductus arteriosus, atrial septal defect, ventricular septal defect, coarctation, situs inversus, truncus arteriosus.

  • Gastrointestinal

– Atresia (esophagus, duodenum, jejunum), imperforate anus, tracheoesophageal fistula, annular pancreas, malrotation.

  • Central nervous system

– Small pituitary, pituitary stalk interruption syndrome, absent corpus callosum, cerebellar hypoplasia, hydrocephalus, dilated ventricles.

Fanconi anemia should be considered in patients with congenital anomalies, together with unexplained cytopenias or macrocytosis.

Patients may present with symptoms of cytopenias:

  • Thrombocytopenia

– Petechiae, bruising, bleeding.

  • Anemia

– Fatigue, shortness of breath, lack of energy, exercise intolerance, lightheadedness, pallor.

  • Neutropenia

– Fevers, infections, mouth sores.

Hypoproductive cytopenias may involve single or multiple hematopoietic lineages. Cytopenias may be present at birth but typically develop with age. An increased erythrocyte mean cell volume (MCV) is often found. Hemoglobin F may be elevated. Cytopenias may wax and wane or may be progressive. Not all patients develop severe aplastic anemia.

Patients may present with MDS or leukemia, typically acute myeloid leukemia. Malignancy may present without an antecedent history of marrow failure.

Patients may present with solid tumors, typically squamous cell carcinomas of the head and neck, liver tumors or vulvar/vaginal squamous cell carcinomas. Solid tumors present at an unusually young age in the absence of typical risk factors such as smoking or alcohol use. Tumors may be single, multifocal or recurrent. Solid tumors may be the first presentation of Fanconi anemia without antecedent marrow failure.

The Fanconi anemia group D1 (FANCD1)/breast cancer 2 susceptibility protein (BRCA2) subtype of FA may present with AML at a very young age, brain tumors, or Wilms tumor. VACTERL-H (vertebral, anal atresia, cardiac, trachea-esophageal fistula, renal, limb, +/- hydrocephalus) congenital anomalies are common in this Fanconi anemia subtype.

Beware of other conditions that can mimic Fanconi anemia:

Other inherited marrow failure syndromes may present with similar clinical features including congenital anomalies, cancer predisposition, and cytopenias. These include: dyskeratosis congenita, Diamond-Blackfan anemia, Shwachman-Diamond syndrome, Nijmegen breakage syndrome (NBS), and Seckel syndrome.

Increased chromosomal breakage with MMC or DEB may be seen in NBS. Patients may be distinguished by testing for mutations in the NBS1 gene. The clinical spectrum of NBS includes severe microcephaly, immunodeficiencies, developmental delay, and predisposition to lymphoid malignancies (lymphomas, acute lymphocytic leukemias), brain tumors, and rhabdomyosarcoma. Patients with NBS are radiosensitive and may require reduced intensity radiotherapy.

Fanconi anemia may be mistaken for congenital syndromes such as VATER (vertebral anomalies, anal atresia, tracheoesophageal fistula, renal anomalies) or VACTERL (VATER plus cardiac and limb anomalies).

Which individuals are most at risk for developing Fanconi anemia:

Fanconi anemia is found in both genders and has no racial predilection. Specific Fanconi anemia subtypes may be more prevalent in certain ethnic groups.

Recent reports describe an increased risk of squamous cell carcinomas following human papillomavirus (HPV) infection in cellular and animal models of Fanconi anemia.

What laboratory studies should you order to help make the diagnosis and how should you interpret the results?

The diagnostic test for Fanconi anemia is increased chromosomal breakage following exposure to a clastogen such as mitomycin C (MMC) or diepoxybutane (DEB). An increased number of radial forms (triradials or quadriradials: see arrows in Figure 1 [figure courtesy of Lisa Moreau, Dana Farber Cancer Institute] are typically observed. Testing is typically performed on peripheral blood lymphocytes.

Figure 1.
Fanconi anemia chromosomal breakage test

A subset of patients may undergo somatic reversion to wild-type in the peripheral blood lymphocytes. This reversion confers a growth advantage over the non-reverted Fanconi anemia lymphocytes. In such cases, testing may appear normal, or reveal only a small subpopulation of cells with increased chromosomal breakage. The molecular mechanisms of reversion include back-mutation, compensatory frameshift mutation, or recombination/gene conversion between compound heterozygous alleles. For this reason, if there is a strong clinical suspicion for Fanconi anemia despite a negative blood test, chromosomal breakage may be tested in fibroblasts obtained from a skin biopsy.

As noted above, NBS is another chromosomal breakage syndrome that may also manifest increased chromosomal breakage with MMC or DEB. The diagnosis of NBS is confirmed by genetic testing for mutations in the NBS1 gene.

Flow cytometry to detect a pause in the G2/M phase of the cell cycle after culture with a clastogen treatment has been used as a diagnostic screen for Fanconi anemia in some centers. The sensitivity and specificity of this assay as a diagnostic test for Fanconi anemia has not been validated.

Western blots to detect the ubiquitination of the Fanconi anemia group D2 (FANCD2) protein can detect patients with defects in the Fanconi anemia core complex which includes the Fanconi anemia gene products FANCA, FANCB, FANCC, FANCE, FANCF, FANCG, FANCL, and FANCM. See “Pathophysiology” below.

There are 164 different Fanconi anemia subtypes caused by mutations in 164 different genes (see “Pathophysiology” below). Complementation analysis may be performed for subtype identification. Complementation testing typically involves introducing individual wild-type Fanconi anemia genes to see which one corrects the Fanconi anemia cellular phenotype. Once a complementation group is identified, the corresponding gene may be sequenced to identify the specific mutations. Mutation testing allows for carrier detection, assists with family planning, and allow preimplantation genetic testing.

Among Fanconi anemia subtypes, FANCD1/BRCA2 and FANCN/PALB2 subtypes, carry a higher risk of malignancy, further characterized by younger age at presentation and a unique spectrum of cancer not typically seen in the other subtypes (e.g. medulloblastoma, neuroblastoma, and Wilms tumor).

What imaging studies (if any) will be helpful in making or excluding the diagnosis of Fanconi anemia?

Ultrasound of the urinary tract to look for malformations.

Pelvic ultrasound for female patients to assess for malformations of the reproductive tract.

Additional recommended exams:

  • Ophthalmology examination
  • Audiology examination
  • Otolaryngology examination for head and neck cancer starting around age 10
  • Gynecological examinations beginning at appropriate age

If you decide the patient has Fanconi anemia, what therapies should you initiate immediately?

If a patient with Fanconi anemia presents with severe or symptomatic cytopenias, appropriate supportive care should be instituted as clinically indicated:

  • Anemia

– Red cell transfusion support.

  • Thrombocytopenia

– Platelet transfusion support, antifibrinolytic medications (for example, aminocaproic acid).

  • Neutropenia

– Granulocyte colony-stimulating factor (G-CSF) (filgrastim).

Note: Blood donations from family members should be avoided to minimize the risk of allosensitization prior to potential bone marrow transplant.

For patients with chronically severe or symptomatic cytopenias and who are not candidates for a bone marrow transplant (see below), androgens such as oxymetholone or danazol may improve the blood counts.

Androgen therapy can in rare cases cause hepatic peliosis, a pathological entity characterized by multiple blood-filled cavities in the liver parenchyma. Androgens are often avoided or interrupted in patients preparing for hematopoietic stem cell transplantation.

The usual starting dose of oxymetholone is 2 to 5mg/kg/day, followed by a slow taper to the minimal required dose. Improvements in the red cell lineage are most pronounced, though the neutrophil and platelet counts may also rise. Side effects of androgens include virilization, premature epiphyseal closure, hypertension, labile mood, cholestatic jaundice, transaminitis, peliosis hepatis, and liver tumors. Regular monitoring of liver functions tests and liver ultrasounds are recommended.

A retrospective study of 8 Fanconi anemia patients whose baseline hemoglobin and platelet counts were <8 g/dL and <30,000/uL, respectively, reported that the values of both parameters rose on average >50% within 6 months of treatment with the synthetic androgen, danazol. As long-term danazol treatment for other disorders is very well-tolerated and generally associated with only minor androgenic side-effects, danazol is a promising treatment particularly for female Fanconi anemia patients.

More definitive therapies?

The only curative therapy for the hematological complications of Fanconi anemia (aplastic anemia, myelodysplastic syndrome, leukemia) is a hematopoietic stem cell transplant. Patients require reduced intensity regimens given their underlying sensitivity to chemotherapy or radiation used in conditioning regimens. Referral to a transplant center experienced with Fanconi anemia is recommended.

Leukemias arising in patients with Fanconi anemia are generally not cured with standard chemotherapy regimens. In addition, patients with Fanconi anemia may experience prolonged, life-threatening cytopenias following standard chemotherapy or radiotherapy dosing. Data are scarce regarding the role of pre-transplant cytoreduction for leukemia in Fanconi anemia.

What other therapies are helpful for reducing complications?

Regular surveillance for marrow failure, myelodysplastic syndrome, leukemia, and solid tumors are critical to successful outcomes.

Early complete surgical excision of solid tumors offers the best chance of cure. Suspicious lesions should be biopsied immediately.

Preemptive transplant prior to development of severe marrow failure or MDS/leukemia is not currently recommended, since only a subset of patients will develop these complications during their lifetimes.

Barrier measures to avoid sexually transmitted diseases such as HPV are recommended.

Administration of the HPV vaccine is recommended according to standard guidelines. Data are currently lacking as to whether Fanconi anemia patients might benefit from administration of the HPV vaccine at an earlier age.

To minimize the risk of squamous cell cancer, maintain good oral hygiene, and avoid alcohol or tobacco.

Where possible, the use of imaging modalities that do not involve ionizing radiation is preferred (for example, ultrasound, magnetic resonance imaging (MRI), particularly when serial imaging is necessary. However, X-rays or computed tomography (CT) scans may be utilized as clinically required for patient care.

What should you tell the patient and the family about prognosis?

The major causes of mortality are severe aplastic anemia, leukemia, or solid tumors.

Bone marrow transplant outcomes are excellent for matched sibling transplants performed for aplastic anemia following the introduction of fludarabine, a highly immunosuppressive and myelosuppressive nucleotide analog with minimal organ toxicity, which has allowed the reduction or elimination of other genotoxic conditioning agents, without increasing engraftment failure. Disease-free survival is generally lower for patients transplanted with leukemia.

The clinical spectrum of Fanconi anemia is broad. Information regarding natural history and outcomes is limited by small patient numbers.

“What if” scenarios.

Patients with Fanconi anemia presenting with cytopenias should be evaluated for potentially treatable causes such as infection, medications, nutritional deficiencies (for example, iron, B12, folate), or antibody-mediated destruction.

Marrow cellularity is not uniform, and must be interpreted within the context of the peripheral blood counts. Patients may maintain adequate blood counts, despite seemingly low marrow cellularity due to sampling bias.

Early human leukocyte antigen (HLA) testing of the patient and siblings allow advance planning in the event a hematopoietic stem cell transplant is warranted. This also allows families to make informed decisions regarding family planning. Some families choose to pursue preimplantation genetic diagnosis or prenatal testing. Families should be referred for genetic counseling.


Fanconi anemia is a multigenic disorder. Currently, 16 genes have been identified, with each corresponding to a distinct complementation group/subtype as follows: A, B, C, D1 (BRCA2), D2, E, F, G, I, J (BACH1/BRIP1), L, M, N (PALB2 [partner and localizer of BRCA2]), O (RAD51C), P (SLX4), and Q (XPF/ERCC4). See Table I.

The most common subtype is A, constituting around two thirds of all Fanconi anemia patients. Subtypes C and G are the next most common, with around 10% of Fanconi anemia patients falling into each of these subtypes. The remaining patients are distributed among the remaining rare subtypes.

The Fanconi anemia group B protein (FANCB) gene is located on the X chromosome and is inherited in an X-linked manner. The remaining Fanconi anemia genes are inherited in an autosomal recessive fashion.

The Fanconi anemia genes function coordinately to promote DNA interstrand crosslink repair.

The Fanconi anemia proteins FANCA, FANCB, FANCC, FANCE, FANCF, FANCG, FANCL, and FANCM, form a ubiquitin ligase complex that, when activated by DNA breaks or by S phase of the cell cycle, mono-ubiquitinates the FANCD2 and FANCI proteins. FANCL is an E3 ubiquitin ligase. FANCM may function as a translocase, to move the Fanconi anemia repair complex along the DNA. Mono-ubiquitination of FANCD2/FANCI is required for their localization to nuclear foci containing FANCD1/ BRCA2, FANCN/partner and localizer of BRCA2 (PALB2), BRCA1, and RAD51 (which functions in homologous recombination). FANCD2 also colocalizes with NBS1 and FANCJ. FANCD1, FANCJ, FANCN, FANCO, and FANCP function downstream of FANCD2/FANCI monoubiquitination.

Some of the Fanconi anemia proteins, such as FANCA, FANCG, and FANCD2, are also regulated by phosphorylation through interactions with other DNA repair pathways including ataxia telangiectasia mutated (ATM), serine/threonine-protein kinase ATR (ATR), and serine/threonine-protein kinase Chk1 (CHK1). Phosphorylation of FANCD2 has been implicated in the S-phase cell cycle checkpoint. FANCD1 is also known as BRCA2, the breast cancer susceptibility gene involved in homologous recombination. FANCN (PALB2, partner and localizer of BRCA2) binds and stabilizes FANCD1. FANCP/SLX4 is an endonuclease and interacts with FANCQ. This complex is believed to play a role in resolving the repaired crosslink intermediate.

Fanconi anemia proteins may also function in cellular stress signaling and regulate proinflammatory and proapoptotic cytokine signaling.

A role for the Fanconi anemia complex in resolving internuclear DNA bridges during chromosomal segregation and cytokinesis has also been described.

In a current model, Fanconi cells suffer unresolved cellular stress and DNA damage that result in a heightened p53 DNA damage response, which in turn drives the progressive elimination of hematopoietic stem and progenitor cells (HSPC). This manifests clinically as progressive bone marrow failure. P21 does not appear to act as the primary mediator of this p53-driven HSPC elimination.

Recent in vivo murine studies show that aldehydes produced endogenously as by-products of cellular metabolism (or exogenously supplied, i.e. by ethanol catabolism) mediate the initial genotoxic insult that leads to hematopoietic failure, and also contribute to abnormal development and cancer predisposition in Fanconi anemia. Hematopoietic stem and progenitor cells appear especially sensitive to aldehyde-mediated genotoxicity.

Intriguingly, a large percentage of East Asian populations (Japanese, Taiwanese, Chinese) express a dominant-negative allele of the aldehyde-catalysing enzyme, aldehyde dehydrogenase 2 (ALDH2), and this variant is associated with accelerated progression of bone marrow failure among Japanese Fanconi anemia patients (Hira A. et al. Blood 2012:122). These studies provide compelling data to explain, at least in part, the hematopoietic phenotype in Fanconi anemia and may inform future therapeutic approaches.

What other clinical manifestations may help me to diagnose Fanconi anemia?

A careful family history may provide clues to the diagnosis of Fanconi anemia. A family history of cytopenias, congenital anomalies, cancers at an unusually young age, or excessive toxicity to chemotherapy or radiation, warrant consideration of an underlying marrow failure syndrome.

All siblings of a patient with Fanconi anemia should be tested for Fanconi anemia, regardless of clinical findings.

See “Are you sure your patient has Fanconi Anemia?” above for physical findings that have been reported with Fanconi anemia; however, this list is not exhaustive. Any patient with unexplained marrow failure or macrocytosis, together with physical anomalies, warrants consideration of an underlying marrow failure syndrome.

The absence of physical findings does not rule out the diagnosis of Fanconi anemia. Fanconi anemia testing is recommended for pediatric patients presenting with aplastic anemia. Adults may also present with previously undiagnosed Fanconi anemia.

pWhat other additional laboratory studies may be ordered?


Blood counts may show decreased numbers of neutrophils, red blood cells, or platelets caused by decreased blood cell production. Thrombocytopenia is often the earliest cytopenia to develop. Blood counts may fall over time, but the absence of cytopenias does not rule out the diagnosis of Fanconi anemia. Red cell macrocytosis is common.

The bone marrow is usually hypocellular. Mild dysplastic features may be seen, including micromegakaryocytes, irregular red cell nuclei, and Pelger-Huet morphology. Clonal cytogenetic abnormalities of unclear clinical significance may arise and bear close observation for potential progression to myelodysplasia or leukemia.

Patients require regular monitoring of blood counts and bone marrow examinations by a hematologist experienced in the care of Fanconi anemia.

Other baseline blood tests:

  • Liver: Aspartate aminotransferase (AST), alanine aminotransferase (ALT), gamma-glutamyl transpeptidase (GGT), bilirubin
  • Renal: Serum electrolytes, blood urea nitrogen (BUN), creatinine
  • Endocrine: Thyroid stimulating hormone (TSH), free thyroxine (T4), glucose, glucose tolerance, lipid assessment.
Other tests

Some physicians recommend a bone density evaluation.

Gastrointestinal abnormalities are common in Fanconi anemia. Evaluation by a gastroenterologist is recommended.

What’s the evidence?

Eiler, ME, Frohnmayer, D, Frohnmayer, L, Larsen, K, Owen, J. “Fanconi Anemia Guidelines for Diagnosis and Management”. 2008. (Summary of clinical consensus conference for the clinical care of patients with Fanconi anemia)

Wagner, JE, Tolar, J, Levran, O. “Germline mutations in BRCA2: shared genetic susceptibility to breast cancer, early onset leukemia, and Fanconi anemia”. . vol. 103. 2004. pp. 3226-9. (Report of distinct phenotypic characteristics of the FANCD1/BRCA2 subtypes.)

Alter, BP, Rosenberg, PS, Brody, LC. “Clinical and molecular features associated with biallelic mutations in FANCD1/BRCA2”. . vol. 44. 2007. pp. 1-9. (Report of distinct phenotypic characteristics of the FANCD1/BRCA2 subtypes.)

Scheckenbach, K, Morgan, M, Filger-Brillinger, J. “Treatment of the bone marrow failure in Fanconi anemia patients with danazol”. . vol. 48. 2011. pp. 128-131. (Retrospective study of danazol to treat marrow failure in Fanconi anemia.)

Cioc, AM, Wagner, JE, MacMillan, ML, DeFor, T, Hirsch, B. “Diagnosis of myelodysplastic syndrome among a cohort of 119 patients with Fanconi anemia: morphologic and cytogenetic characteristics”. . vol. 133. 2010. pp. 92-100. (Study of marrow morphology and cytogenetic findings in 119 patients with Fanconi anemia referred for marrow transplant.)

Kottemann, MC, Smogorzewska, A. “Fanconi anemia and the repair of Watson and Crick crosslinks”. Nature. vol. 493. 2013. pp. 356-363. (Recent comprehensive review of the Fanconi anemia molecular pathway.)

Garaycoechea, J, Patel, KJ. “Why does the bone marrow fail in Fanconi anemia”. Blood. vol. 123. 2013. pp. 26-34. (Recent comprehensive review of the Fanconi anemia molecular pathway.)

Ceccaldi, R. “Bone marrow failure in Fanconi anemia is triggered by an exacerbated p53/p21 DNA damage response that impairs hematopoietic stem and progenitor cells”. Cell Stem Cell. vol. 11. 2012. pp. 36-49. (Important study that highlights a central role of p53 activation in response to DNA damage as a central mechanism of bone marrow failure in Fanconi anemia.)

Garaycoechea, J. “Genotoxic consequences of endogenous aldehydes on mouse haematopoietic stem cell function”. Nature. vol. 489. 2012. pp. 571-575. (First study to identify an inciting agent that drives the Fanconi anemia haematological phenotype – endogenous aldehyde-mediated genotoxicity restricted to hematopoietic stem and progenitor cells.)

Lo Ten Foe, JR, Kwee, ML, Rooimans, MA. “Somatic mocaicism in Fanconi anemia: molecular basis and clinical significance”. . vol. 5. 1997. pp. 137-48. (Report of the molecular basis of somatic mosaicism in Fanconi anemia.)

Gross, M, Hanenberg, H, Lobitz, S. “Reverse mosaicism in Fanconi anemia: natural gene therapy via molecular self-correction”. . vol. 98. 2002. pp. 126-35.. (Report of the molecular basis of somatic mosaicism in Fanconi anemia)

Shimamura, A, Alter, BP. “Pathophysiology and management of inherited bone marrow failure syndromes”. . vol. 24. 2010. pp. 101-122. (Physical findings in Fanconi anemia.)

(Provides information on genes, and how each one corresponds to a distinct complementation group/subtype.)