Novel Homozygous FA2H Variant Causing the Full Spectrum of Fatty Acid Hydroxylase-Associated Neurodegeneration (SPG35)

Abstract

Fatty acid hydroxylase-associated neurodegeneration (FAHN/SPG35) is caused by pathogenic variants in FA2H and has been linked to a continuum of specific motor and non-motor neurological symptoms, leading to progressive disability. As an ultra-rare disease, its mutational spectrum has not been fully elucidated. Here, we present the prototypical workup of a novel FA2H variant, including clinical and in silico validation. An 18-year-old male patient presented with a history of childhood-onset progressive cognitive impairment, as well as progressive gait disturbance and lower extremity muscle cramps from the age of 15. Additional symptoms included exotropia, dystonia, and limb ataxia. Trio exome sequencing revealed a novel homozygous c.75C>G (p.Cys25Trp) missense variant in the FA2H gene, which was located in the cytochrome b5 heme-binding domain. Evolutionary conservation, prediction models, and structural protein modeling indicated a pathogenic loss of function. Brain imaging showed characteristic features, thus fulfilling the complete multisystem neurodegenerative phenotype of FAHN/SPG35. In summary, we here present a novel FA2H variant and provide prototypical clinical findings and structural analyses underpinning its pathogenicity.

Keywords: FA2H; FAHN; SPG35; genetic variant modeling; hereditary spastic paraplegia.

Figure 1

Pedigree of the index patient (arrow) according to [18].

Figure 2

MRI Findings. “WHAT” tetrad: spotty FLAIR-hyperintensities affecting the parietal white matter (“W”; cross symbol in (a,d)), hypointensity of the globus pallidus in T2w FLAIR/SWI (“H”; asterisk in (a–c)), pontocerebellar atrophy with decreased midbrain but not pons midsagittal area (“A”; open arrows in (e,f) (the pontomesencephalic junction is defined by the yellow dotted line between the superior pontine notch and the inferior border of the quadrigeminal plate; the pontomedullary junction is defined by a line parallel to this line at the level of the inferior pontine notch)) and thinning of the corpus callosum, predominantly affecting the body (“T”; double-asterisk in (f)).

Figure 3

PolyPhen-2 shows strong preservation of cysteine at position 25 in FA2H and predicts “probably damaging” for the exchange with tryptophan.

Figure 4

Structural modeling of the Cys25Trp variant. (a) Overview of the FA2H structural model (AlphaFold) in a model membrane. While the FA hydroxylase domain inserts into the membrane, the Cyt-b5 domain remains accessible at the cytoplasm. (b) Detailed depiction of cysteine 25 (Cys25) in the Cyt-b5 domain in proximity to the iron-binding heme domain (heme). (c) Structure of the Cyt-b5 domain with a tryptophan at position 25 (Trp25). (d) A 2D representation of the heme group with residues in <5 Å distance. The coordination between both variants (FA2H wild type and SPG35) differs, which might result in inferior enzymatic activity in SPG35 patients.

Figure 5

Scanning electron microscopy (SEM) analysis of scalp hair. Comparative SEM analysis of hairs from the patient (bottom) and his mother (top) revealed a comparable cuticle structure. Both showed groove structures (white arrows) to a comparable extent. Scale bars 50 µm.