Basic Science Pathology

Neurocutaneous Syndromes (Phakomatoses)

Neurocutaneous Syndromes (Phakomatoses)

What Do You Need to Know?

  • NF1 (neurofibromin, 17q11.2) — most common phakomatosis; diagnostic criteria require ≥2 of 7 features (café-au-lait macules, neurofibromas, axillary freckling, optic glioma, Lisch nodules, osseous lesion, family history)
  • NF2 (merlin/schwannomin, 22q12.2) — hallmark is bilateral vestibular schwannomas; also meningiomas, ependymomas, posterior subcapsular cataracts
  • TSC (hamartin 9q34 / tuberin 16p13.3) — cortical tubers, subependymal nodules, SEGA; seizures most common neurologic feature; mTOR inhibitors (everolimus) for SEGA
  • VHL (VHL gene, 3p25.3) — hemangioblastomas (cerebellar > spinal > retinal), clear cell renal cell carcinoma, pheochromocytoma
  • Sturge-Weber — somatic mosaic GNAQ mutation (NOT inherited); port-wine stain (V1), leptomeningeal angiomatosis, “tram-track” calcifications, seizures, glaucoma
  • Ataxia-telangiectasia (AR, ATM gene, 11q22.3) — progressive cerebellar ataxia, oculocutaneous telangiectasias, immunodeficiency, elevated AFP, DNA repair defect
  • Distinguish inheritance patterns: NF1, NF2, TSC, VHL are autosomal dominant; ataxia-telangiectasia is autosomal recessive; Sturge-Weber is sporadic (somatic)
Overview — Phakomatoses at a Glance
Disease Inheritance Gene / Protein Chromosome Key Features
NF1 AD NF1 / neurofibromin 17q11.2 Café-au-lait macules, neurofibromas, optic gliomas, Lisch nodules
NF2 AD NF2 / merlin (schwannomin) 22q12.2 Bilateral vestibular schwannomas, meningiomas, ependymomas
TSC AD TSC1 / hamartin; TSC2 / tuberin 9q34; 16p13.3 Cortical tubers, SEGA, angiofibromas, cardiac rhabdomyomas
VHL AD VHL / pVHL 3p25.3 Hemangioblastomas, renal cell carcinoma, pheochromocytoma
Sturge-Weber Sporadic (somatic) GNAQ (somatic mosaic) 9q21.2 Port-wine stain (V1), leptomeningeal angiomatosis, seizures, glaucoma
Ataxia-Telangiectasia AR ATM 11q22.3 Cerebellar ataxia, telangiectasias, immunodeficiency, elevated AFP
Neurofibromatosis Type 1 (von Recklinghausen Disease)

Genetics & Epidemiology

  • Inheritance: Autosomal dominant; ~50% are de novo mutations
  • Gene: NF1 on chromosome 17q11.2
  • Protein: Neurofibromin — a tumor suppressor that functions as a RAS-GTPase-activating protein (GAP); loss of function → unregulated RAS signaling → cell proliferation
  • Prevalence: ~1 in 3,000 — most common phakomatosis
  • Penetrance: Nearly 100% by age 5, but variable expressivity

Diagnostic Criteria (NIH — ≥2 Required)

  • ≥6 café-au-lait macules (>5 mm prepubertal; >15 mm postpubertal)
  • ≥2 neurofibromas of any type OR 1 plexiform neurofibroma
  • Axillary or inguinal freckling (Crowe sign)
  • Optic pathway glioma (typically pilocytic astrocytoma)
  • ≥2 Lisch nodules (iris hamartomas — seen on slit-lamp exam)
  • Distinctive osseous lesion: sphenoid wing dysplasia, thinning of long bone cortex ± pseudoarthrosis
  • First-degree relative with NF1 by above criteria

Updated 2021 Criteria Additions

  • Pathogenic NF1 variant (heterozygous) identified on genetic testing
  • Choroidal abnormalities (≥2 identified by optical coherence tomography/near-infrared reflectance imaging)

Associated Tumors

Tumor Key Points
Optic pathway glioma Most common CNS tumor in NF1 (~15%); pilocytic astrocytoma (WHO grade I); often asymptomatic; screen with ophthalmologic exam (NOT routine MRI in asymptomatic)
Neurofibroma Benign peripheral nerve sheath tumor; cutaneous (most common), subcutaneous, or plexiform types
Plexiform neurofibroma Diffuse, infiltrative along nerve; pathognomonic for NF1; ~10% risk of malignant transformation to MPNST
MPNST Malignant peripheral nerve sheath tumor; lifetime risk 8–13% in NF1; suspect if rapid growth, pain, new neurological deficit
Brainstem glioma More common in NF1 than general population; often indolent
Pheochromocytoma ~1–5% of NF1 patients; cause of secondary hypertension

Neurological Complications

  • Learning disability / ADHD: most common neurological complication (~50–60%); intellectual disability in ~5%
  • Seizures: ~6–10% of patients
  • UBOs (unidentified bright objects): T2/FLAIR hyperintensities in basal ganglia, cerebellum, brainstem; non-progressive; typically resolve by adulthood; do NOT enhance and are NOT tumors
  • Cerebrovascular: moyamoya-like vasculopathy, cerebral aneurysms, arterial stenosis
  • Hypertension: renal artery stenosis or pheochromocytoma
  • Sphenoid wing dysplasia: pulsating exophthalmos
Board Pearl

NF1 = neurofibromin = chromosome 17 (17 letters in “neurofibromatosis”). Lisch nodules are pathognomonic iris hamartomas that help distinguish NF1 from NF2 (NF2 does NOT have Lisch nodules). Plexiform neurofibromas are pathognomonic for NF1 and carry a ~10% lifetime risk of malignant transformation to MPNST.

Board Pearl

UBOs (T2-bright foci) on MRI in an NF1 patient are NOT tumors — they represent areas of myelin vacuolization. They do NOT enhance, do NOT cause mass effect, and typically disappear by adulthood. Do not biopsy or treat.

Neurofibromatosis Type 2

Genetics & Epidemiology

  • Inheritance: Autosomal dominant; ~50% de novo
  • Gene: NF2 on chromosome 22q12.2
  • Protein: Merlin (schwannomin) — a cytoskeletal tumor suppressor linking cell membrane to actin cytoskeleton
  • Prevalence: ~1 in 25,000–33,000 (much rarer than NF1)
  • Presentation: Typically in late teens to early 20s with hearing loss or tinnitus

Clinical Features

  • Bilateral vestibular schwannomas: hallmark and pathognomonic finding; present in >95% of NF2 patients
  • Meningiomas: ~50% of NF2 patients; often multiple; may be intracranial or spinal
  • Ependymomas: spinal ependymomas most common; intramedullary
  • Schwannomas: other cranial nerves (especially CN V, VII), spinal nerve roots, peripheral nerves
  • Posterior subcapsular cataracts: juvenile cataracts in ~60–80%; may be earliest sign
  • NO café-au-lait macules, NO Lisch nodules (distinguish from NF1)

MISME Mnemonic

  • Multiple
  • Inherited
  • Schwannomas
  • Meningiomas
  • Ependymomas

Diagnostic Criteria (Manchester Criteria)

  • Definite NF2: Bilateral vestibular schwannomas (VS) on imaging, OR
  • First-degree relative with NF2 + unilateral VS at age <30, OR
  • First-degree relative with NF2 + any 2 of: meningioma, schwannoma, glioma, posterior subcapsular cataract

Presentation & Complications

  • Hearing loss: progressive unilateral then bilateral sensorineural hearing loss (most common presenting symptom)
  • Tinnitus: often precedes hearing loss
  • Facial weakness/numbness: tumor growth compressing CN V and VII
  • Imbalance: vestibular dysfunction from VS
  • Myelopathy: from spinal schwannomas, ependymomas, or meningiomas
Board Pearl

NF2 = chromosome 22 (NF “2” = 22). Bilateral vestibular schwannomas are pathognomonic. NF2 patients do NOT get café-au-lait macules or Lisch nodules. A young adult with bilateral hearing loss/tinnitus + family history of brain tumors → think NF2. Posterior subcapsular cataracts may be the earliest clinical finding.

Tuberous Sclerosis Complex (TSC)

Genetics

  • Inheritance: Autosomal dominant; ~2/3 are de novo mutations
  • TSC1: chromosome 9q34hamartin
  • TSC2: chromosome 16p13.3tuberin
  • TSC2 mutations tend to cause more severe disease than TSC1
  • Hamartin and tuberin form a complex that inhibits the mTOR pathway → loss of function → unregulated mTOR signaling → cell growth and proliferation
  • Prevalence: ~1 in 6,000

Classic Triad (Vogt Triad)

  • Seizures + intellectual disability + facial angiofibromas (“adenoma sebaceum”)
  • Full triad present in only ~30% of patients
  • Seizures are the most common neurological manifestation (~80–90%); often infantile spasms in the first year of life

Skin Manifestations

Finding Description Key Points
Hypomelanotic macules (ash-leaf spots) Hypopigmented, leaf-shaped macules Earliest sign — present at birth; best seen with Wood lamp (UV light); typically ≥3 needed for diagnostic significance
Facial angiofibromas Red-brown papules in malar distribution Appear age 2–5; formerly “adenoma sebaceum” (misnomer — NOT sebaceous in origin); present in ~75%
Shagreen patch Connective tissue nevus; thickened, “orange-peel” skin Usually lumbosacral; present in ~50%
Periungual fibromas (Koenen tumors) Flesh-colored nodules around nail beds Pathognomonic; appear in adolescence/adulthood
Confetti skin lesions Scattered small hypopigmented macules Usually on extremities

CNS Manifestations

Finding Description Clinical Significance
Cortical tubers Focal areas of dysplastic, disorganized cortex Main cause of seizures and intellectual disability; T2/FLAIR hyperintense; may calcify with age
Subependymal nodules (SENs) Hamartomatous nodules lining the lateral ventricles “Candle-dripping” or “candle-guttering” appearance on imaging; calcified; present in ~80%
Subependymal giant cell astrocytoma (SEGA) Low-grade tumor arising from SEN near foramen of Monro Risk of obstructive hydrocephalus; treat with mTOR inhibitors (everolimus) or surgical resection; ~5–15% of TSC patients
White matter radial migration lines Radial bands of abnormal white matter Represent disrupted neuronal migration; visible on MRI

Systemic Manifestations

  • Cardiac rhabdomyomas: most common cardiac tumor in children; often multiple; may cause arrhythmias; tend to regress spontaneously; may be first prenatal finding
  • Renal angiomyolipomas (AML): ~80% of TSC patients; fat-containing benign tumors; risk of hemorrhage if >4 cm; treat with mTOR inhibitors or embolization
  • Renal cysts: when TSC2 is contiguously deleted with PKD1 gene → TSC + polycystic kidney disease
  • Lymphangioleiomyomatosis (LAM): cystic lung disease predominantly in women; progressive dyspnea; can cause pneumothorax
  • Retinal hamartomas: “mulberry lesion” or flat, translucent lesion; usually asymptomatic
Board Pearl

Infantile spasms + hypopigmented (ash-leaf) spots on exam → think TSC. Wood lamp examination is essential in any infant presenting with infantile spasms to look for ash-leaf spots. Subependymal nodules (“candle-dripping”) near the foramen of Monro that enlarge → suspect SEGA → treat with everolimus (mTOR inhibitor) or surgery.

Clinical Pearl — mTOR Pathway in TSC

TSC1/TSC2 normally inhibit mTOR signaling. Loss of hamartin-tuberin complex → constitutive mTOR activation → uncontrolled cell growth. Everolimus (mTOR inhibitor) is FDA-approved for SEGA and renal AML in TSC. It can shrink tumors without surgery but requires chronic administration — tumors may regrow upon discontinuation.

Von Hippel-Lindau (VHL) Disease

Genetics

  • Inheritance: Autosomal dominant
  • Gene: VHL on chromosome 3p25.3
  • Protein: pVHL — tumor suppressor that targets HIF (hypoxia-inducible factor) for degradation
  • Loss of pVHL → constitutive HIF activation → overproduction of VEGF, PDGF, EPO → vascular tumor proliferation and angiogenesis
  • Prevalence: ~1 in 36,000

Major Manifestations

Manifestation Frequency Key Points
Cerebellar hemangioblastoma 60–80% Most common CNS lesion in VHL; cystic with enhancing mural nodule; may cause obstructive hydrocephalus
Retinal hemangioblastoma (angioma) 50–70% Often earliest manifestation; may cause retinal detachment, vitreous hemorrhage; screen ophthalmologically from childhood
Spinal hemangioblastoma ~40–50% Intramedullary; may cause myelopathy; often multiple
Renal cell carcinoma (clear cell) 25–60% Leading cause of death in VHL; often bilateral and multifocal; mean age of diagnosis ~40 years
Pheochromocytoma 10–20% May be bilateral; paragangliomas also occur
Pancreatic cysts / neuroendocrine tumors 35–70% Cysts usually benign; neuroendocrine tumors may be malignant
Endolymphatic sac tumors 10–15% Papillary cystadenoma of temporal bone → sensorineural hearing loss, vertigo, tinnitus
Epididymal cystadenomas 25–60% Bilateral in VHL; usually asymptomatic

VHL Classification

Type Pheochromocytoma RCC Risk Hemangioblastoma
Type 1 Absent (low risk) High Yes
Type 2A Present Low Yes
Type 2B Present High Yes
Type 2C Present Low Absent

Hemangioblastoma Specifics

  • WHO grade I, benign, highly vascular
  • Classic imaging: cystic mass with enhancing mural nodule
  • Location in VHL: cerebellar (most common) > spinal cord > brainstem > retina
  • Secondary polycythemia: hemangioblastomas can secrete erythropoietin (EPO) → elevated hematocrit
  • VHL-associated hemangioblastomas: typically multiple and recurrent (vs. sporadic hemangioblastoma: single)
  • Sporadic hemangioblastomas are the most common primary intra-axial posterior fossa tumor in adults
Board Pearl

Hemangioblastoma with polycythemia = VHL until proven otherwise. Hemangioblastomas produce EPO → secondary polycythemia. A young patient with a posterior fossa cystic mass with mural nodule + family history of renal cell carcinoma → screen for VHL. Renal cell carcinoma (clear cell type) is the leading cause of death in VHL patients.

Sturge-Weber Syndrome (Encephalotrigeminal Angiomatosis)

Genetics & Pathogenesis

  • NOT inherited — caused by a somatic mosaic activating mutation in GNAQ gene (9q21.2)
  • GNAQ encodes Gαq protein involved in endothelin signaling → constitutive activation of downstream pathways → vascular malformation
  • Mutation occurs during embryonic development → affects structures derived from the cephalic neural crest
  • Sporadic — recurrence risk for siblings is negligible

Clinical Features

  • Port-wine stain (nevus flammeus):
    • Facial capillary malformation in V1 (ophthalmic) distribution — forehead and upper eyelid involvement is key
    • May extend to V2 and V3 distribution
    • Present at birth; does NOT blanch with pressure
    • NOT all port-wine stains indicate Sturge-Weber (only ~5–10% of V1 port-wine stains are associated with leptomeningeal angiomatosis)
  • Leptomeningeal angiomatosis:
    • Ipsilateral to the facial port-wine stain
    • Pial vascular malformation → venous stasis and chronic ischemia of underlying cortex
    • “Tram-track” calcifications: gyriform cortical calcifications on CT, ipsilateral to the port-wine stain (represent calcified cortex beneath the angioma)
  • Seizures:
    • Most common neurologic manifestation (~75–90%)
    • Typically focal, contralateral to the angioma; onset usually in the first year of life
    • May become refractory; hemispherectomy considered in severe cases
  • Contralateral hemiparesis: progressive; due to chronic cortical ischemia
  • Intellectual disability: ~50–60%; correlates with seizure severity and extent of angioma
  • Glaucoma: ipsilateral; due to elevated episcleral venous pressure from conjunctival/episcleral vascular malformation; present in 30–70%
  • Stroke-like episodes: may occur, resembling migrainous infarcts

Imaging

  • CT: “Tram-track” gyriform cortical calcifications (classic finding); cortical atrophy
  • MRI with contrast: leptomeningeal enhancement ipsilateral to the port-wine stain; cortical atrophy; enlarged choroid plexus (ipsilateral)
  • SWI/GRE: demonstrates calcification and venous abnormalities
Board Pearl

Sturge-Weber is the only major phakomatosis that is NOT inherited — it is caused by a somatic mosaic mutation in GNAQ. Port-wine stain involving the forehead/upper eyelid (V1) is the key risk marker for leptomeningeal involvement. “Tram-track” calcifications on CT are pathognomonic. Seizures are the most common neurologic feature and often present in infancy.

Ataxia-Telangiectasia (Louis-Bar Syndrome)

Genetics

  • Inheritance: Autosomal recessive (the only AR phakomatosis)
  • Gene: ATM (ataxia telangiectasia mutated) on chromosome 11q22.3
  • Protein: ATM kinase — critical for DNA double-strand break repair and cell-cycle checkpoint regulation
  • Prevalence: ~1 in 40,000–100,000

Clinical Features

  • Progressive cerebellar ataxia:
    • Earliest neurological sign; onset age 1–4 years (initially gait ataxia, then limb ataxia)
    • Progressive — most patients wheelchair-bound by age 10–12
    • Due to progressive cerebellar Purkinje cell degeneration
  • Oculocutaneous telangiectasias:
    • Appear by age 3–6 years (later than ataxia)
    • Bulbar conjunctivae (most prominent), ears, flexor surfaces of arms, face
  • Oculomotor apraxia: inability to generate voluntary saccades; compensatory head thrusting
  • Immunodeficiency:
    • IgA deficiency (most common), IgG2 subclass deficiency, low IgE
    • T-cell dysfunction (thymic hypoplasia)
    • → Recurrent sinopulmonary infections (leading cause of morbidity)
  • Cancer predisposition:
    • Defective DNA repair → increased sensitivity to ionizing radiation
    • ~25–30% lifetime cancer risk; lymphoma and leukemia most common
    • Carriers (heterozygotes) have increased breast cancer risk
  • Other: choreoathetosis, peripheral neuropathy (later), endocrine dysfunction (growth failure, insulin resistance)

Laboratory Findings

  • Elevated alpha-fetoprotein (AFP): found in >95% of patients; important diagnostic clue
  • Low immunoglobulins: IgA, IgG2, IgE
  • Elevated CEA (less specific)
  • Chromosomal instability: spontaneous chromosomal breaks, translocations (especially involving chromosomes 7 and 14 at TCR and Ig gene loci)
  • Radiation sensitivity: in vitro lymphocyte testing shows increased sensitivity to ionizing radiation
Board Pearl

Child with progressive cerebellar ataxia + telangiectasias + elevated AFP + recurrent infections → ataxia-telangiectasia. It is the only major phakomatosis with AR inheritance. ATM gene defect → impaired DNA repair → avoid ionizing radiation (increased chromosomal breakage and cancer risk). Elevated AFP is a key diagnostic marker.

Clinical Pearl — DNA Repair Disorders with Neurological Features

Ataxia-telangiectasia is the most board-tested DNA repair disorder with neurological involvement. Other DNA repair disorders to recognize: xeroderma pigmentosum (nucleotide excision repair defect; photosensitivity + neurodegeneration), Cockayne syndrome (dwarfism, microcephaly, retinal degeneration, cataracts), and ataxia with oculomotor apraxia types 1 and 2 (AOA1/AOA2; clinically similar to A-T but without telangiectasias or immunodeficiency).

Other Neurocutaneous Syndromes
Syndrome Inheritance / Genetics Key Features
Klippel-Trénaunay-Weber Sporadic; somatic PIK3CA mutations Port-wine stain + limb hypertrophy + varicose veins; usually affects one lower extremity; may have associated cerebral vascular malformations
Incontinentia pigmenti X-linked dominant; IKBKG (NEMO), Xq28; lethal in males Skin lesions evolving in 4 stages (vesicular → verrucous → hyperpigmented → atrophic) following Blaschko lines; seizures, intellectual disability, retinal vascular anomalies
Hypomelanosis of Ito Sporadic; genetic mosaicism Hypopigmented whorls and streaks following Blaschko lines; seizures (~50%), intellectual disability, musculoskeletal anomalies
PHACE syndrome Sporadic Posterior fossa malformations, Hemangiomas (large facial), Arterial anomalies, Cardiac defects/coarctation of aorta, Eye abnormalities; predominantly female
Epidermal nevus syndrome Sporadic; mosaic mutations (HRAS, KRAS, FGFR3) Linear epidermal nevi + CNS malformations (hemimegalencephaly, cortical dysplasia) + skeletal/ocular anomalies; seizures common
Neurocutaneous melanosis Sporadic; somatic NRAS mutations Large/multiple congenital melanocytic nevi + leptomeningeal melanosis/melanoma; seizures, hydrocephalus, elevated ICP
Clinical Pearl — Blaschko Lines

Blaschko lines represent pathways of epidermal cell migration during embryonic development. They are NOT dermatomes and do NOT follow vascular or neural distributions. Skin lesions following Blaschko lines (whorls on trunk, linear on extremities) suggest genetic mosaicism. Key conditions: incontinentia pigmenti, hypomelanosis of Ito, epidermal nevi, and linear morphea.

Quick Reference — High-Yield Board Comparisons

NF1 vs. NF2

Feature NF1 NF2
Chromosome 17q11.2 22q12.2
Protein Neurofibromin Merlin (schwannomin)
Prevalence 1 in 3,000 1 in 25,000
Hallmark tumor Neurofibromas, optic gliomas Bilateral vestibular schwannomas
Skin findings Café-au-lait macules, axillary freckling Minimal or absent
Eye findings Lisch nodules (iris hamartomas) Posterior subcapsular cataracts
Meningiomas Rare Common (often multiple)
Malignancy risk MPNST (~10% from plexiform neurofibromas) Low (tumors are benign but cause compression)

Phakomatosis Tumor Associations

Tumor Associated Phakomatosis
Optic pathway glioma NF1
Bilateral vestibular schwannomas NF2
Subependymal giant cell astrocytoma (SEGA) TSC
Hemangioblastoma VHL
Clear cell renal cell carcinoma VHL
Cardiac rhabdomyoma TSC
Multiple meningiomas NF2
MPNST NF1

References

  • Ropper AH, Samuels MA, Klein JP, Prasad S. Adams and Victor’s Principles of Neurology. 12th ed. McGraw Hill; 2023.
  • Blumenfeld H. Neuroanatomy Through Clinical Cases. 3rd ed. Sinauer Associates; 2021.
  • Korf BR. Neurofibromatosis type 1 (NF1): pathogenesis, clinical features, and diagnosis. UpToDate. 2024.
  • Northrup H, Krueger DA; International Tuberous Sclerosis Complex Consensus Group. Tuberous sclerosis complex diagnostic criteria update: recommendations of the 2012 International TSC Consensus Conference. Pediatr Neurol. 2013;49(4):243–254.
  • Legius E, Messiaen L, Wolkenstein P, et al. Revised diagnostic criteria for neurofibromatosis type 1 and Legius syndrome: an international consensus recommendation. Genet Med. 2021;23(8):1506–1513.
  • Shirley MD, Tang H, Gallione CJ, et al. Sturge-Weber syndrome and port-wine stains caused by somatic mutation in GNAQ. N Engl J Med. 2013;368(21):1971–1979.
  • Lonser RR, Glenn GM, Walther M, et al. Von Hippel-Lindau disease. Lancet. 2003;361(9374):2059–2067.
  • Lavin MF, Shiloh Y. The genetic defect in ataxia-telangiectasia. Annu Rev Immunol. 1997;15:177–202.
  • Evans DGR, Baser ME, O’Reilly B, et al. Management of the patient and family with neurofibromatosis 2: a consensus conference statement. Br J Neurosurg. 2005;19(1):5–12.
  • Franz DN, Belousova E, Sparagana S, et al. Everolimus for subependymal giant cell astrocytoma in patients with tuberous sclerosis complex: 2-year open-label extension of the randomised EXIST-1 study. Lancet Oncol. 2014;15(13):1513–1520.