Novel detection of mutation in the TECPR2 gene in a Chinese hereditary spastic paraplegia 49 patient: a case report

Novel TECPR2 variant in two cases of hereditary sensory and autonomic neuropathy type 9: insights from genetic characterization and comprehensive literature review

BACKGROUND

Hereditary sensory and autonomic neuropathy type 9 (HSAN9) is a rare genetic disorder caused by genetic alterations in the TECPR2 locus and is characterized by developmental and intellectual disability, respiratory dysfunction, gastroesophageal reflux disease (GERD), and sensory and autonomic dysfunction, which are shared among the HSAN family.

METHODS

Whole-exome sequencing (WES) was performed on samples from both probands, and the relevant genetic variants were confirmed in their families using Sanger sequencing. Additionally, a comprehensive literature review was conducted on previously reported cases of HSAN9, and the clinical and genetic data were assessed to provide insight into the genetic and clinical characteristics of the disease.

RESULTS

We identified two new cases of HSAN9 with a shared novel variant of TECPR2 (NM_014844.5), c.1568del: p.Ser523PhefsTer12, classified as pathogenic according to ACMG guidelines. The probands showed characteristics of GERD, respiratory dysfunction, gait abnormalities, and developmental and speech delay, and both cases were deceased as a result of severe respiratory infection. The results of the literature review included 34 cases from 9 studies, revealing a wide range of genetic and clinical characteristics.

CONCLUSIONS

Our study identified two new cases of HSAN9 with a novel variant in TECPR2, confirmed by WES. The clinical characteristics of the patients as well as the conduction of a comprehensive literature review are crucial in the early diagnosis and management of the disease and establishment of genotype-phenotype correlations.

TECPR2-related hereditary sensory and autonomic neuropathy in two siblings from Palestine

Due to the majority of currently available genome data deriving from individuals of European ancestry, the clinical interpretation of genomic variants in individuals from diverse ethnic backgrounds remains a major diagnostic challenge. Here, we investigated the genetic cause of a complex neurodevelopmental phenotype in two Palestinian siblings. Whole exome sequencing identified a homozygous missense TECPR2 variant (Chr14(GRCh38):g.102425085G>A; NM_014844.5:c.745G>A, p.(Gly249Arg)) absent in gnomAD, segregating appropriately with the inheritance pattern in the family. Variant assessment with in silico pathogenicity prediction and protein modeling tools alongside population database frequencies led to classification as a variant of uncertain significance. As pathogenic TECPR2 variants are associated with hereditary sensory and autonomic neuropathy with intellectual disability, we reviewed previously published candidate TECPR2 missense variants to clarify clinical outcomes and variant classification using current approved guidelines, classifying a number of published variants as of uncertain significance. This work highlights genomic healthcare inequalities and the challenges in interpreting rare genetic variants in populations underrepresented in genomic databases. It also improves understanding of the clinical and genetic spectrum of TECPR2-related neuropathy and contributes to addressing genomic data disparity and inequalities of the genomic architecture in Palestinian populations.