An ABCA7 partial deletion and a GRN variant in a semantic variant of primary progressive aphasia patient

Abstract Background ABCA7 gene (ATP‐binding cassette transporter A7) loss‐of‐function mutations are related to increased risk of suffering Alzheimer’s disease (AD). On the other hand, mutations in GRN (Progranulin) gene are causative of frontotemporal dementia (FTD). Methods The proband was a patient diagnosed from semantic variant of primary progressive aphasia. Age at onset was at 50 years‐old, presenting progressive cognitive decline with an important language loss. The MRI showed a left temporal atrophy. AD CSF biomarkers were normal and no familial history of dementia was reported. Next generation sequencing was performed with Illumina NextSeq500. Single nucleotide variants were detected using GATK and copy number variants using ExomeDepth algorithm. Sanger sequencing was performed for GRN variant confirmation and MLPA technique for ABCA7 deletion validation. C9orf72 repeat expansion was studied with a repeat primed PCR and fragment analysis. Biological samples from his mother and a brother were obtained. Commercial ELISA kit was used to measure serum PGRN levels (Adipogen). Results Patient showed an ABCA7 partial deletion (exons 17‐47) plus 4 contiguous genes, of a total of 105 kb in size (hg19 chr19:g.1048865_1154298). Deletion was confirmed in the proband and discarded in the proband’s mother and brother by MLPA. Patient and his mother (asymptomatic at 81 yo) were also carriers of a reported GRN variant, p.(Asp33Glu; rs63750742). Progranulin serum levels were normal in the patient and his family members. C9orf72 screening was negative. Conclusions The patient harbored two genetic alterations in genes related to dementia risk, although it is unlikely that any of them alone could be responsible of the FTD phenotype. ABCA7 deletion should be de novo or father inherited. ABCA7 protein truncating variant at exon 14 (p.Arg578fs), which has a similar protein consequence, is relatively frequent in control population, although has showed a 1.8‐fold enrichment in AD patients. Moreover, GRN variant does not seem to be pathogenic or low penetrance because proband’s mother is unaffected and serum progranulin levels are normal. In conclusion, these variants per se are likely not sufficient to cause the disease, but rather risk variants of intermediate to high penetrance along with other factors.