ClinVar Genomic variation as it relates to human health

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease.

For these reasons, this variant has been classified as Pathogenic. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt FA2H protein function. ClinVar contains an entry for this variant (Variation ID: 320501). This missense change has been observed in individual(s) with FA2H related conditions (PMID: 31135052, 31429931). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. It has also been observed to segregate with disease in related individuals. This variant is present in population databases (rs527421775, gnomAD 0.06%). This sequence change replaces glutamic acid, which is acidic and polar, with lysine, which is basic and polar, at codon 78 of the FA2H protein (p.Glu78Lys).

Variant summary: FA2H c.232G>A (p.Glu78Lys) results in a conservative amino acid change located in the Cytochrome b5-like heme/steroid binding domain (IPR001199) of the encoded protein sequence. Four of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 0.00031 in 170850 control chromosomes. The observed variant frequency is approximately 1.6 fold of the estimated maximal expected allele frequency for a pathogenic variant in FA2H causing Neurodegeneration With Brain Iron Accumulation phenotype (0.00019), suggesting that the variant may be benign. c.232G>A has been reported in the literature as a compound heterozygous genotype in settings of whole exome (WES) analysis among individuals presenting with early onset cerebellar ataxia (example, Shakya_2019), phenotypes from the neurodegeneration with brain iron accumulation (fatty acid hydroxylase- associated neurodegeneration, FAHN), hereditary spastic paraplegia (HSP type SPG35) and leukodystrophy (leukodystrophy with spasticity and dystonia) spectrum (example, Rattay_2019), and in an undiagnosed disease exome sequencing cohort (example, Klee_2021). These data indicate that the variant may be associated with disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Six clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as uncertain significance. Based on the evidence outlined above, the variant was classified as uncertain significance.

Reported previously with another FA2H variant in two unrelated patients in the published literature with complicated HSP, but it is not known whether the variants occurred on the same (in cis) or on different (in trans) chromosomes in both cases (Rattay et al., 2019); Reported previously with a variant on the opposite allele (in trans) in two patients in the published literature; one with early onset cerebellar ataxia (Shakya et al., 2019) and one with an immune phenotype (Klee et al., 2021); In silico analysis supports that this missense variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 31135052, 31429931, 33144682)

The c.232G>A (p.E78K) alteration is located in exon 1 (coding exon 1) of the FA2H gene. This alteration results from a G to A substitution at nucleotide position 232, causing the glutamic acid (E) at amino acid position 78 to be replaced by a lysine (K). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.