CNTNAP1 Mutations in an Adult with Charcot Marie Tooth Disease

Charcot-Marie-Tooth (CMT) disease comprises a heterogeneous group of diseases that are broadly classified into CMT1 (demyelinating) and CMT2 (axonal) neuropathy and are inherited in an autosomal dominant, autosomal recessive or X-linked pattern.¹ PMP22 gene duplication causes 70% of cases of CMT1.¹ Despite over 40 known CMT genes or loci, nearly 50% of cases have no known molecular diagnosis.² Mutations in CNTNAP1 have been reported to cause lethal congenital contracture syndrome (LCCS) or congenital hypomyelinating neuropathy (CHN) but have not been reported in CMT patients.^3,4,5 We describe a rare heterozygous missense variant of CNTNAP1 in trans with a pathogenic frameshift mutation in a young man with childhood-onset CMT and mild intellectual disability.

Case Report:

A 21-year-old man was born at term after an uncomplicated pregnancy. Hypotonia and global delay were noted in infancy. He sat at 15 months, walked and began speaking at 4 years old. He underwent surgery to correct cavovarus deformities of the feet. He graduated from high school with an individualized learning plan, and is attending community college.

His height was 50^th %tile, and skeletal exam showed cubitus valgus and cavovarus foot deformity without heel cord contractures. His neurological examination showed fluent, moderately dysarthric speech. Muscle bulk was reduced throughout with 4+ to full strength. Sensation was diminished to pinprick distal to the ankles but normal to light touch sensation and proprioception. Tendon reflexes were hypoactive or absent. Coordination testing was slow without dysmetria. His gait was narrow based with intoeing. He has one full sister and no affected family members.

Nerve conduction study (NCS) was abnormal, demonstrating multifocal slowing of conduction velocities (CVs) and prolonged distal motor latencies, as well as partial motor conduction block and temporal dispersion, more substantially in the lower extremities than upper extremities (Table 1). Needle EMG was not performed. A right vastus lateralis muscle biopsy including electron transport chain enzymology was normal. MRI of the brain was normal. Negative results of genetic testing included karyotype, Fragile X, chromosome 15q11 methylation, chromosomal microarray, PMP22 duplication and sequencing of GJB1 and MPZ. A nuclear mitochondrial gene panel (Courtagen, 1185 genes) revealed heterozygous coding variants in SCN4A and SPG7 interpreted as likely pathogenic and one variant of uncertain significance (VUS) in the OPA1 gene. Upon review, we considered them non-diagnostic because of inheritance from an unaffected parent, or absence of expected clinical findings.

Table 1.

Nerve Conduction Studies

	Motor Nerve Conduction Studies
	Left Median		Left Ulnar			Left Peroneal			Left Tibial
	Wrist	Elbow	Wrist	Below elbow	Above elbow	Ankle	Fibular head	Knee	Ankle	Popliteal fossa
DML (ms)	4.3*	-	6.2*	-	-	11.9*	-	-	8.4*	-
CMAP (mV)	5.5	5.3	6.0	4.5	4.3	1.8*	0.5	0.5	2.3*	1.5
MNCV (m/s)	-	47*	-	46*	40*	-	16*	32*	-	22*
F-wave latency (ms)	25.2*								105.5*
	Sensory Nerve Conduction Studies
	Left Median		Left ulnar			Left peroneal		Left sural
SNAP (μV)	53.5		38.6			10.7		6.4
SNCV (m/s)	50		47			33*		32*

Abbreviations: DML, distal motor latency; CMAP, compound motor action potential; MNCV, motor nerve conduction velocity; SNAP, sensory nerve action potential; SNCV, sensory nerve conduction velocity.

^*Abnormal value.

When the patient returned for reevaluation, we proceeded with clinical trio exome sequencing which revealed two variants in CNTNAP1 (Figure 1). The first is a deletion (c.2901_2902delCT) causing a frameshift resulting in a pathogenic premature termination (p.Cys968PhefsX11), and was proven to be paternally inherited. The second is a rare, maternally inherited, missense substitution, c.3047C>T resulting in p.Ala1016Val. The heterozygous frameshift variant is clearly pathogenic, and has been reported in the homozygous state to cause AMC with CVs <10 m/s.³ Our patient’s second variant results in a conservative amino acid substitution that has been reported in the heterozygous state in 1/65,000 European, non-Finnish individuals in the Exome Aggregation Consortium (ExAC) and in 1/38,000 individuals in the Genome Aggregation Database (GnomAD) and has not been reported in the homozygous state.⁶ In silico analysis is inconsistent in predicting the damaging effects on protein structure and function. Therefore, it was reported by the clinical laboratory as a VUS.

Figure 1.

Schematic of CNTNAP1 gene and its protein domains. This patient’s variants are noted: a frameshift mutation that leads to early termination of the protein at exon 18 and a missense mutation at exon 19.

Discussion:

We describe a patient with childhood CMT who was found to be compound heterozygous for one severe, premature terminating pathogenic variant, and one missense variant of uncertain significance in the CNTNAP1 gene.

CNTNAP1 encodes a neural immunoglobulin family cell adhesion molecule named contactin-associated protein 1 or CASPR, which forms a complex with contactin and is essential for normal myelin organization at the node of Ranvier in the peripheral nervous system.^7,8 In 2014, biallelic loss of function variants were identified in CNTNAP1 in infants with LCCS, a rare form of arthrogryposis multiplex congenital (AMC) characterized by decreased fetal movement, polyhydramnios, arthrogryposis, hypotonia, areflexia and respiratory distress and markedly slowed CVs.⁵ Nerve biopsies demonstrate peripheral hypomyelination.³ The phenotype associated with CNTNAP1 has expanded to include CHN without arthrogryposis and extremely slow CVs.^4,9 Survival beyond infancy is rare, with one 15- year-old reported with profound intellectual disability, central hypomyelination and demyelinating peripheral neuropathy with a homozygous p.Arg714Pro CNTNAP1 substitution.⁵ Our patient’s NCS results are consistent with a motor>sensory demyelinating polyneuropathy with additional limited axon loss.

He has one pathogenic CNTNAP1 allele and one VUS allele. We applied the American College of Medical Genetics (ACMG) guidelines for clinical laboratory interpretation of VUS.¹⁰ For our patient’s VUS, it is at extremely low frequency for a recessive condition in large population databases (PM2), and was proven to be in trans with a pathogenic variant by testing parents (PM3). A well-established functional study, particularly those used for clinical diagnosis, provides strong evidence (PS3). We consider the NCS abnormalities in our patient to provide strong, clinical evidence of a functional effect of the variant on nerve conduction. Unlike many forms of demyelinating CMT, especially CMT1A, which demonstrate uniform slowing of CV’s, the subject reported in this study showed evidence of patchy demyelination, including conduction block and abnormal dispersion, manifested in a more dramatic fashion in the lower extremities. This pattern of multifocal non-uniform slowing is also not uncommon in CMT and is seen especially in CMTX. The predominant involvement of the lower extremities is unusual, as CMT subtypes typically involve upper and lower extremities in a similar fashion. While it is not entirely clear how the specific mutation contributed to this phenotype, unlike many of the mutations which cause demyelinating CMT that affect the myelin sheath diffusely, the localization of CNTNAP1 to the paranodal regions might cause demyelination in a more stochastic fashion. The combination of ACMG criteria PS3 + PM2 + PM3 would reclassify the variant as Likely Pathogenic. We postulate that the combination of a milder variant with a loss of function variant expands the known range of clinical expression of CNTNAP1 to include childhood onset CMT with mild intellectual disability, compatible with ambulation, and survival to adulthood.

Abbreviations:

ACMG

American College of Medical Genetics

AMC

Arthrogryposis multiple congenital

CHN

Congenital Hypomyelinating Neuropathy

CV

Conduction Velocities

EMG/NCS

Electromyography/nerve conduction studies

ExAC

Exome Aggregation Consortium

GnomAD

Genome Aggregation Database

LCCS

Lethal congenital contracture syndrome

VUS

Variant of uncertain significance