A Novel Splice-Site Variant in SLC12A6 Causes Andermann Syndrome without Agenesis of the Corpus Callosum

Abstract

Andermann syndrome, otherwise known as agenesis of the corpus callosum with peripheral neuropathy (ACCPN), is an autosomal recessive motor and sensory neuropathy known to be associated with ACC and mild-to-moderate intellectual disability. We present a 7-year-old girl with infantile-onset hypotonia, mild intellectual disability, and severe motor and sensory demyelinating peripheral neuropathy. Brain magnetic resonance imaging showed intact corpus callosum. Whole exome sequencing showed a novel splice-site pathogenic variant in the SLC12A6 gene. We confirm that ACC is not a mandatory feature and suggest that the term ACCPN may be misleading.

Introduction

Andermann syndrome, otherwise known as agenesis of the corpus callosum with peripheral neuropathy (ACCPN), was first described by Naiman and Fraser in 1955 who described two sisters with ACC associated with mental and physical disability. ¹ The same description was reported thereafter by Ziegler in 1958 who described two brothers with similar findings. ² In 1972, Andermann et al described two brothers with intellectual disability, areflexia, and paraparesis who were thought to have an anterior horn cell disease. ³ The clinical picture was the same as in the sisters reported by Naiman and Fraser in 1955, ¹ and the two families were French Canadian from the Charlevoix County in Quebec. In 1977, Andermann et al extended their observations to identify 45 patients in 24 families, descendants from a couple married in Quebec City, Charlevoix County, back in 1657. ⁴ Brain computed tomography imaging of those cases demonstrated ACC. ⁴ In 1993 Andermann syndrome was reported outside Quebec by Hauser et al who reported cases of ACC with neuronopathy in a brother and sister in Vienna. ⁵ In 2006, Uyanik et al reported three unrelated patients with Andermann syndrome: one was German and two were Turkish. ⁶ ACC was documented as a variable feature even in patients with identical variants. ⁷ We hereby describe a novel splice-site variant in SLC12A6 associated with Andermann syndrome without ACC and support that ACC is not a mandatory feature of the disease.

Case Report

We report a 7-year-old girl who was born to first-cousin parents and had three healthy elder siblings. She was born at term with no significant perinatal history. She was observed to be floppy and was very slow in gaining gross motor milestones early in infancy. She presented to our clinic with developmental delay and hypotonia at the age of 12 months. She had not achieved head control by then. She started to have head control at the age of 18 months, sat at 2 years, and never was able to walk. Currently, at the age of 7 years, she is able to sit independently, pull up to furniture, stand on her knees, and bottom shuffles. She developed the pincer grasp and can draw circles, triangles, squares, and faces but not letters and numbers. She can feed herself by spoon, although shaky, put food in her mouth, and drink by the cup. She is able to speak in clear sentences of four to five words that are appropriate. Socially, she enjoys family members, becomes withdrawn from strangers, and is still on diapers by day and night. She is able to recognize all the letters of the English alphabet, colors, and can count up to ten. There are no visual or hearing concerns. She has difficulty in chewing due to weak facial muscles but has no chocking or drooling. There was no history of abnormal movements. Physical examination at the age of 7 years was significant for a myopathic face but no dysmorphic features. Her growth parameters including head circumference were within the normal range for age and sex. She has central and peripheral hypotonia and cannot raise her upper limbs against resistance nor her legs against gravity with generalized areflexia. She had claw hands with wasting of thenar and hypothenar muscles, bilateral talipes valgus with pes cavus, and thoracolumbar scoliosis. There was no nystagmus or intention tremor. Intelligence quotient score was 60. Brain Magnetic resonance imaging (MRI) showed normally formed corpus callosum and bilateral patchy nonspecific subcortical, periventricular, and deep white matter hyper-intensities seen on the T2/fluid attenuation inversion recovery sequences. Repeat MRI after 2.3 years showed partial interval regression in the extent of these hyperintensities ( Fig. 1A–F ). Electroencephalography was normal. Nerve conduction studies showed severe demyelinating sensory and motor neuropathy pattern. Biochemical tests including lactate, ammonia, creatine kinase, transaminases, plasma amino acids, and urine organic acids were normal. Whole exome sequencing showed homozygosity for a splice-site variant in the SLC12A6 gene (NM_133647.1:c.1943 + 1G > T: P.?). This variant was not observed in the gnomAD database ( https://gnomad.broadinstitute.org ) neither in an in-house database of 484 exome nor Middle Eastern population specific database; Almena. ⁸ This canonical splice variant predicated to cause loss-of-function of the protein by multiple in silico pathogenic prediction tools (DANN, MutationTaster, FATHMM-MKL, and EIGEN). It was also predicted to affect splicing with high probability using the model dbscSNV, which was constructed on seven already developed splice-site altering SNV prediction tools. ⁹ Further confirmatory studies included segregation analysis which showed that both parents are heterozygous carries and siblings were either heterozygous carriers or homozygous for the wild type sequence supporting the pathogenicity of the variant. This was followed by messenger ribonucleic acid (mRNA) transcript analysis of the SLC12A6 , extracted from lymphocytes using PureLink RNA Mini Kit; complementary deoxyribonucleic acid (cDNA) was synthesized using iScript cDNA synthesis kit. Analysis of the cDNA using the following primers (SLC12A6-RT-F; 5-ACCGTTTCTGAGGGTTTTTG-3 and SLC12A6-RT-R; 5-TTTCTCAGCTCCTTGGTATTCA-3) confirmed that this splicing variant abolishes completely the SLC12A6 transcript in the patient sample, compared with control. This variant was classified as pathogenic (PVS1, PM2, PP3) according to ACMG/AMP 2015 guideline. ¹⁰

Fig. 1.

Axial ( A ) and coronal ( B ) T2-weighted images from magnetic resonance imaging (MRI) done at the age of 12 months show scattered abnormal hyperintense areas seen in both subcortical (arrow) and deep periventricular (arrowheads) white matter distribution. Axial fluid attenuation inversion recovery images from MRI done at the age of 3.3 years ( C and D ) show similar areas of abnormal hyperintense white matter areas. Sagittal T1-weighted images at the age of 12 months ( E ) and 3.3 years ( F ) show normal formation and development of the corpus callosum (arrows). Well-developed cingulate gyrus (arrowheads) is also noted.

Discussion

Andermann syndrome (OMIM 218000), also known as Charlevoix disease, was originally described in the French-Canadian population of the Saguenay-Lac-St.-Jean and Charlevoix regions of north-eastern Quebec. In this population, Andermann syndrome had a reported incidence of 1 in 2,117 newborns. ¹¹ Fewer individuals with this disorder have been identified in other regions of the world, and this is the first case report of the syndrome in Oman.

The association of ACC was thought to be a cardinal feature of the disease, and hence the ACC with peripheral neuropathy (ACCPN) acronym was given. However, subsequent cases proved that ACC is a variable feature since complete ACC was seen in 58%, partial ACC in 9%, and a normally structured corpus callosum in 33% of 64 French-Canadian patients reviewed by Mathieu et al. ¹² The discordance of the ACC phenotype was documented in patients with the same variant including a pair of siblings that was reported by Rudnik-Schöneborn et al where only the presence of ACC in the younger brother pointed to the diagnosis of Andermann syndrome. ⁷ The presence of intact CC in our patient is supportive to the previous finding that ACC is not a mandatory feature and hence the ACCPN acronym may not be representing the pathognomonic features of the disease and may be rather misleading.

The gene SLC12A6 (solute carrier family 12, member 6) encodes for a potassium/chloride co-transporter 3, a co-transporter of potassium and chloride ions. ¹³ Variants in the SLC12A6 gene were confirmed to be associated with the disease in 2002 by Howard et al, after they identified four distinct protein-truncating variants: two in the French-Canadian population and two in non-French-Canadian families. A 1-bp deletion (NM_133647.1:c.2436 + 1delG) was determined to be the founder variant in the French-Canadian population. ¹³ Subsequent reports identified both truncating and missense variants in Andermann syndrome in different ethnic backgrounds, majority being truncating. Salin-Cantegrel et al in 2007 identified two truncating variants in exon 22 of the SLC12A6 gene in five unrelated, non-French-Canadian families with ACCPN, including families from Turkey, South Africa, Sudan, and the Netherlands ¹⁴ and concluded that SLC12A6 variants in exon 22 constitute a recurrent variant site for hereditary motor and sensory neuropathy with agenesis of the corpus callosum (HMSN/ACC), regardless of ethnic origin.

Our patient has a truncating splice-site variant, NM_133647.1:c.1943 + 1G > T that was not reported previously in ClinVar. Pathogenicity of the variant was confirmed by the segregation analysis and the complete absence of the SLC12A6 mRNA transcript in the patient sample.

Conclusion

We hereby document the first Omani child with Andermann disease with a novel splice-site variant in the SLC12A6 gene. We also support the finding established before that ACC is a variable feature of the disease and suggest that the acronym ACCPN may be misleading.