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Letter
Whole-exome sequencing identified novel KIF5A mutations in Chinese patients with amyotrophic lateral sclerosis and Charcot-Marie-Tooth type 2
  1. Jing He1,
  2. Xiaoxuan Liu1,
  3. Lu Tang1,
  4. Chen Zhao1,
  5. Ji He1,
  6. Dongsheng Fan1,2
  1. 1Neurology, Peking University Third Hospital, Beijing, China
  2. 2Key Laboratory for Neuroscience, National Health Commission/Ministry of Education, Peking University, Bejing, China
  1. Correspondence to Professor Dongsheng Fan, Neurology, Peking University Third Hospital, Beijing 100191, China; dsfan2010{at}aliyun.com

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Introduction

The kinesin heavy chain isoform 5A (KIF5A) gene on chromosome 12q13.3 encodes a neuron-specific kinesin heavy chain (KHC), which consists of an N-terminal motor domain, a stalk domain and a C-terminal cargo-binding domain. KIF5A is an ATPase-active molecular motor protein and is involved in the microtubule-dependent axonal transport of cytoplasmic cargo. KIF5A gene has been identified as a causative gene of hereditary spastic paraplegia (HSP), Charcot-Marie-Tooth (CMT) type 2 (CMT2) and amyotrophic lateral sclerosis (ALS).1 2 As HSP, CMT and ALS affect central and peripheral nervous systems differently, what play a key role for the patients with KIF5A mutation to manifest different phenotype is little known.

In previous reports, the use of different genetic testing methods and ranges may yield inconsistent findings. Hence, we conducted a study using whole-exome sequencing (WES) with the aim of screening the KIF5A gene and other CMT or ALS-causative genes in Chinese CMT2 and ALS patients.

Methods

A total of 154 unrelated CMT2 probands, 581 sporadic ALS (sALS) patients and 1015 controls without history of neurological diseases were enrolled from the Department of Neurology of Peking University Third Hospital from 2007 to 2018. All ALS cases were diagnosed as possible, probable or definite ALS according to the revised El Escorial criteria. The diagnosis of CMT2 was based on clinical manifestations and neurophysiology. All subjects signed informed consent forms.

Fragment-length and repeat-primed PCR was performed to detect duplications or deletions of PMP22 gene in CMT2 patients, as well as ATXN2 and C9orf72 (hexanucleotide repeat expansion) in ALS patients first. Then we used WES to screen the full-length of KIF5A and other genes causing HSP, CMT and ALS. All suspected variants were validated using Sanger sequencing and interpreted according to the American College of Medical Genetics and Genomics (ACMG) standards and guidelines. Detailed information are listed in the supplementary file (online supplementary methods and online supplementary table 1).

Results

A total of nine rare variants were found in our ALS/CMT2 patients. None of these mutations were present in the controls or other databases, except p.R297Q, which had a very low allele frequency in gnomAD (http://gnomad.broadinstitute.org/). All of 154 CMT2 patients were pre-screened for the absence of the PMP22 duplication/deletion and the CMT patients with KIF5A mutations were negative for other CMT-causative gene mutations, including those in MPZ, MFN2, GJB1, and MME. Consistent with low frequency of C9orf72 mutation as previous reported,in Chinese population, no C9orf72 mutation were found in ALS patients.3 The ALS patients with KIF5A mutations were negative for other ALS-causative genes, including SOD1, TARDBP, FUS, TBK1, ATXN2, ANXA11, NEK1, PFN1, UBLN2, TUBA4A, OPTN, DCTN1, and SQSTM1.

Two KIF5A mutations identified in our study were concluded to be pathogenic. First, p.R204W (c.610C>T, patient C-2), a missense mutation located in exon eight encoding the KIF5A N-terminal, was found in a CMT2 patient. p.R204W was a mutational hot-spot reported previously. Second, we identified one homozygous deletion (c.2999delC, p.T1001Qfs, patient A-6) in an ALS patient. This mutation was predicted to be pathogenic as it may result in the loss of the stop codon. Other seven mutations were concluded to be uncertain significance according to ACMG Standards and Guidelines (detailed information was listed in figure 1, online supplementary table 2, supplementary figures 1 and 2).

Figure 1

Distribution of mutations in the kinesin heavy chain isoform 5A (KIF5A) gene in different diseases. This figure shows all of the reported KIF5A mutations and their distribution in each disease. Mutations reported in the current or previous studies are marked in red or black, respectively. (A) KIF5A mutations found in hereditary spastic paraplegia (HSP)/Charcot-Marie-Tooth type 2 (CMT2) patients. p.V12A and p.S189P are two novel mutations found in our CMT2 patients. The third mutation, p.R204W, identified in our study was previously reported. Most of the mutations found in HSP/CMT2 patients are in the motor domain. (B) KIF5A mutations identified in amyotrophic lateral sclerosis patients. Most previously reported mutations (marked in black) are in the C-terminal cargo-binding domain.

Discussion

In our study, the KIF5A mutation frequency was 1.95% (3/154) among patients with CMT2, which was similar to the frequency reported in a Korean study (1.95%)4 but lower than that reported in a European population (2.78%).1 Furthermore, KIF5A loss-of-function (LOF) mutations were found in 0.34% (2/581) of our sALS patients compared with 0.47%–0.53% of Caucasian fALS patients2 and 0.16%–0.41% of Chinese sALS patients.5

Most of previously reported ALS-associated KIF5A variants are splice site mutations that cause exon skipping. The mutation c.2999delC (p.T1001Qfs, patient A-6) described herein is novel and is the first deletion reported in Chinese ALS population. It results in the loss of the stop codon and a prolonged protein. This patient was a male from a Han family with disease onset at 45 years, and the onset site was the upper limb. He was diagnosed with definite ALS and survived for 30 months.

The CMT2 patient (p.R204W, patient C-2) was with pyramidal signs, deafness and cognitive impairment. R204 is a mutational hot-spot and a target of mutation, such as p.R204Q and p.R204W. It locates in the switch I motif (residues 199–204), which is crucial for formation of the γ-phosphate-sensing regions of KIF5A and is involved in a conformational change in KIF5A during nucleotide hydrolysis.

In addition, we also identified a CMT2 case (patient C-1) caused by compound heterozygous KIF5A mutations (p.V12A and p.S189P). This patient was a 30-year-old woman with a 13-year history of progressive walking difficulties and distal paraesthesias. Neurological examination revealed lower limb weakness, no Babinski reflex, marked sensory reduction and pes cavus. Nerve conduction studies revealed axonal sensory and motor peripheral neuropathy. Direct sequencing showed that p.V12A (c.35T>C) was inherited from her father, who manifested a mild scissor gait beginning in childhood that did not affect daily life. p.S189P (c.565T>C) was inherited from her mother, who was asymptomatic. Notably, another variant, p.S189L (c.566C>T) which causes substitution of serine with leucine, was reported to be associated with autosomal dominant HSP by the Illumina Clinical Services Laboratory (https://www.ncbi.nlm.nih.gov/clinvar/variation/309935/).

Interestingly, as previous reported, HSP/CMT2-associated KIF5A mutations are almost missense mutations in N-terminal motor domain, while ALS-associated KIF5A mutations are primarily LOF mutations in C-terminal cargo-binding domain. While parts of our identifications (p.T1001Qfs, p.R204W) are consistent with previous reports, we detected three unreported missense mutations in the motor domain in ALS cases (p.K29R, p.P46S and p.R297Q). Although the significance of these mutations is uncertain (ACMG guideline), it prompts to some extent that the phenotype-mutation distribution theory is not absolute and remains to be confirmed in future.

In conclusion, we reported KIF5A mutations in Chinese patients with ALS or CMT2. And our findings further expanded the genotypic spectrum of KIF5A and supplemented the previous conclusions.

Acknowledgments

The authors thank to the patients and controls for their participation in this study.

References

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Footnotes

  • JH and XL contributed equally.

  • JH and DF contributed equally.

  • Contributors DF and XL conceived and designed the study. JinH, JiH, LT and CZ performed the experiments. JinH and JiH analysed the data and wrote the paper. DF reviewed and edited the manuscript. All authors read and approved the manuscript.

  • Funding This work was supported by grants from the National Science Foundation of China (81601105, 81873784).

  • Competing interests None declared.

  • Patient consent for publication Not required.

  • Ethics approval This study was approved by the Ethics Committee of Peking University Third Hospital (IRB 00006761).

  • Provenance and peer review Not commissioned; externally peer reviewed.

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