SPATA5 mutations

Inspired by a patient

Puusepp S, Kovacs-Nagy R, Alhaddad B, Braunisch M, Hoffmann GF, Kotzaeridou U, Lichvarova L, Liiv M, Makowski C, Mandel M, Meitinger T, Pajusalu S, Rodenburg RJ, Safiulina D, Strom TM, Talvik I, Vaarmann A, Wilson C, Kaasik A, Haack TB, Õunap K. Compound heterozygous SPATA5 variants in four families and functional studies of SPATA5 deficiency. Eur J Hum Genet. 2018 Mar;26(3):407-419.

Abstract

Variants in the SPATA5 gene were recently described in a cohort of patients with global developmental delay, sensorineural hearing loss, seizures, cortical visual impairment and microcephaly. SPATA5 protein localizes predominantly in the mitochondria and is proposed to be involved in mitochondrial function and brain developmental processes. However no functional studies have been performed. This study describes five patients with psychomotor developmental delay, microcephaly, epilepsy and hearing impairment, who were thought clinically to have a mitochondrial disease with subsequent whole-exome sequencing analysis detecting compound heterozygous variants in the SPATA5 gene. A summary of clinical data of all the SPATA5 patients reported in the literature confirms the characteristic phenotype. To assess SPATA5's role in mitochondrial dynamics, functional studies were performed on rat cortical neurons. SPATA5-deficient neurons had a significant imbalance in the mitochondrial fusion-fission rate, impaired energy production and short axons. In conclusion, SPATA5 protein has an important role in mitochondrial dynamics and axonal growth. Biallelic variants in the SPATA5 gene can affect mitochondria in cortical neurons and should be considered in patients with a neurodegenerative disorder and/or with clinical presentation resembling a mitochondrial disorder.

Puusepp S, Reinson K, Pajusalu S, Murumets Ü, Õiglane-Shlik E, Rein R, Talvik I, Rodenburg RJ, Õunap K. Effectiveness of whole exome sequencing in unsolved patients with a clinical suspicion of a mitochondrial disorder in Estonia. Mol Genet Metab Rep. 2018 Mar 15;15:80-89.

Abstract

OBJECTIVE:

Reaching a genetic diagnosis of mitochondrial disorders (MDs) is challenging due to their broad phenotypic and genotypic heterogeneity. However, there is growing evidence that the use of whole exome sequencing (WES) for diagnosing patients with a clinical suspicion of an MD is effective (39-60%). We aimed to study the effectiveness of WES in clinical practice in Estonia, in patients with an unsolved, but suspected MD. We also show our first results of mtDNA analysis obtained from standard WES reads.

METHODS:

Retrospective cases were selected from a database of 181 patients whose fibroblast cell cultures had been stored from 2003 to 2013. Prospective cases were selected during the period of 2014-2016 from patients referred to a clinical geneticist in whom an MD was suspected. We scored each patient according to the mitochondrial disease criteria (MDC) (Morava et al., 2006) after re-evaluation of their clinical data, and then performed WES analysis.

RESULTS:

A total of 28 patients were selected to the study group. A disease-causing variant was found in 16 patients (57%) using WES. An MD was diagnosed in four patients (14%), with variants in the SLC25A4, POLG, SPATA5, and NDUFB11 genes. Other variants found were associated with a neuromuscular disease (SMN1, MYH2, and LMNA genes), neurodegenerative disorder (TSPOAP1, CACNA1A, ALS2, and SCN2A genes), multisystemic disease (EPG5, NKX1-2, ATRX, and ABCC6 genes), and one in an isolated cardiomyopathy causing gene (MYBPC3). The mtDNA point mutation was found in the MT-ATP6 gene of one patient upon mtDNA analysis.

CONCLUSIONS:

The diagnostic yield of WES in our cohort was 57%, proving to be a very good effectiveness. However, MDs were found in only 14% of the patients. We suggest WES analysis as a first-tier method in clinical genetic practice for children with any multisystem, neurological, and/or neuromuscular problem, as nuclear DNA variants are more common in children with MDs; a large number of patients harbor disease-causing variants in genes other than the mitochondria-related ones, and the clinical presentation might not always point towards an MD. We have also successfully conducted analysis of mtDNA from standard WES reads, providing further evidence that this method could be routinely used in the future.

Kurata H, Terashima H, Nakashima M, Okazaki T, Matsumura W, Ohno K, Saito Y, Maegaki Y, Kubota M, Nanba E, Saitsu H, Matsumoto N, Kato M. Characterization of SPATA5-related encephalopathy in early childhood. Clin Genet. 2016 Nov;90(5):437-444.

Abstract

Mutations in SPATA5 have recently been shown to result in a phenotype of microcephaly, intellectual disability, seizures, and hearing loss in childhood. Our aim in this report is to delineate the SPATA5 syndrome as a clinical entity, including the facial appearance, neurophysiological, and neuroimaging findings. Using whole-exome sequencing and Sanger sequencing, we identified three children with SPATA5 mutations from two families. Two siblings carried compound heterozygous mutations, c.989_991del (p.Thr330del) and c.2130_2133del (p.Glu711Profs*21), and the third child had c.967T>A (p.Phe323Ile) and c.2146G>C (p.Ala716Pro) mutations. The three patients manifested microcephaly, psychomotor retardation, hypotonus or hypertonus, and bilateral hearing loss from early infancy. Common facies were a depressed nasal bridge/ridge, broad eyebrows, and retrognathia. Epileptic spasms or tonic seizures emerged at 6-12 months of age. Interictal electroencephalography showed multifocal spikes and bursts of asynchronous diffuse spike-wave complexes. Augmented amplitudes of visually evoked potentials were detected in two patients. Magnetic resonance imaging revealed hypomyelination, thin corpus callosum, and progressive cerebral atrophy. Blood copper levels were also elevated or close to the upper normal levels in these children. Clinical delineation of the SPATA5-related encephalopathy should improve diagnosis, facilitating further clinical and molecular investigation.

Szczałuba K, Szymańska K, Kosińska J, Pollak A, Murcia V, Kędra A, Stawiński P, Rydzanicz M, Demkow U, Płoski R. Isolated Hearing Impairment Caused by SPATA5 Mutations in a Family with Variable Phenotypic Expression. Adv Exp Med Biol. 2017;980:59-66.

Abstract

Biallelic mutations in the SPATA5 gene, encoding ATPase family protein, are an important cause of newly recognized epileptic encephalopathy classified as epilepsy, hearing loss, and mental retardation syndrome (EHLMRS, OMIM: 616577). Herein we describe a family in which two SPATA5 mutations with established pathogenicity (p.Thr330del and c.1714+1G>A) were found in the proband and her younger sister. The proband had a similar clinical picture to the previous descriptions of EHLMRS. In the sister, the only manifestation was an isolated sensorineural hearing loss. Our findings extend the phenotypic spectrum of SPATA5-associated diseases and indicate that SPATA5 defects may account for a fraction of isolated sensorineural hearing impairment cases.