ClinVar Genomic variation as it relates to human health

Same nucleotide change resulting in same amino acid change has been previously reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000021054, PS1_S). Functional studies provide supporting evidence of the variant having a damaging effect on the gene or gene product(PMID: 8829657, 7942842) (PS3_P). In silico tool predictions suggest damaging effect of the variant on gene or gene product (SPLICEAI: 0.9>=0.8, PP3_P). It is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: 0.000060, PM2_M). Therefore, this variant is classified as pathogenic according to the recommendation of ACMG/AMP guideline.

The observed missense c.192G>T (p.Gln64His) variant in FAH gene has been reported in homozygous state in individuals affected with Tyrosinemia (Ijaz S et al. 2016). Functional studies provide supporting evidence of the variant having a damaging effect on the gene or gene product (Rootwelt H et al. 1996). The p.Gln64His variant is present with an allele frequency of 0.006% in gnomAD Exomes. This variant has been reported to the ClinVar database as Pathogenic (multiple submitters). The amino acid change p.Gln64His in FAH is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. The amino acid Gln at position 64 is changed to a His changing protein sequence and it might alter its composition and physicochemical properties. Computational evidence (Polyphen - Benign, SIFT - Damaging and MutationTaster - Disease causing) predicts conflicting evidence on protein structure and function for this variant. For these reasons, this variant has been classified as Pathogenic.

The missense c.192G>T(p.Gln64His) variant, which lies in splice region of FAH gene has been reported previously in multiple individuals affected with tyrosinemia type I (Ijaz S, et. al., 2016; Angileri F, et. al., 2015; Demers SI, et. al., 2003). Functional studies show that this variant causes aberrant splicing and affects gene or gene product (Rootwelt H, et. al., 1994). The p.Gln64His variant has been reported with allele frequency of 0.006% in gnomAD Exomes. This variant has been submitted to the ClinVar database as Pathogenic (multiple submissions). The amino acid change p.Gln64His in FAH is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. The amino acid Gln at position 64 is changed to a His changing protein sequence and it might alter its composition and physico-chemical properties. For these reasons, this variant has been classified as Pathogenic.

Variant summary: The FAH c.192G>T (p.Gln64His) variant involves the alteration of a conserved nucleotide. This variant defies the donor-splice-site consensus sequence and it is considered a splice-site mutation (Ijaz_JPEM_2015). Human 2/3 in silico tools predict a damaging outcome for this variant (SNPsandGO not captured due to low reliability index). 5/5 splice prediction tools predict a significant impact on normal splicing. ESE finder predicts the loss of the SF2/ASF binding motif and the creation of a splice donor site. Functional studies showed decreased or absent FAH mRNA and protein levels in HT1 patients with this variant The variant of interest has been found in a large, broad control population, ExAC in 8/121410 control chromosomes at a frequency of 0.0000659, which does not exceed the estimated maximal expected allele frequency of a pathogenic FAH variant (0.0025). This variant has been reported in multiple HT1 patients, in both homozygotes and heterozygotes (with unknown secondary allele)( Rootwelt_AJHG_1994, Rootwelt_HM_1996, Ijaz_JPEM_2015). In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as pathogenic. Taken together, this variant is classified as pathogenic.

NM_000137.2(FAH):c.192G>T(Q64H) is classified as pathogenic in the context of tyrosinemia type I. Sources cited for classification include the following: PMID 22975760, 23430822, 23193487, 14691918, 9101289 and 7942842. Classification of NM_000137.2(FAH):c.192G>T(Q64H) is based on the following criteria: This is a well-established pathogenic variant in the literature that has been observed more frequently in patients with clinical diagnoses than in healthy populations. Please note: this variant was assessed in the context of healthy population screening.

This sequence change replaces glutamine, which is neutral and polar, with histidine, which is basic and polar, at codon 64 of the FAH protein (p.Gln64His). RNA analysis indicates that this missense change induces altered splicing and may result in an absent or disrupted protein product. This variant is present in population databases (rs80338894, gnomAD 0.05%). This missense change has been observed in individual(s) with tyrosinemia type I (PMID: 7942842; Invitae). ClinVar contains an entry for this variant (Variation ID: 21054). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be tolerated. Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Studies have shown that this missense change results in retention of 94 nucleotides of intron 2 and introduces a premature termination codon (PMID: 7942842). The resulting mRNA is expected to undergo nonsense-mediated decay. For these reasons, this variant has been classified as Pathogenic.

A heterozygous frameshift insertion variant c.1079_1080insA in REN gene (chr1:204124285; Depth:139x) was detected. The variant results from insertion of one nucleotide at nucleotide position 1079th, causing a translational frameshift with a predicted alternate stop codon (p.Leu361AlafsTer34). This variant is not observed in Clinvar, 1000 genomes, topmed and gnomAD database. Based on the aforementioned evidence, the variant is classified as a likely pathogenic based on the ACMG-AMP classification system.

Pakistani-specific pathogenic variant resulting from founder effect or genetic drift [Angileri et al 2015].