ClinVar Genomic variation as it relates to human health

A Heterozygous Missense variant c.503G>T in Exon 8 of the GFI1B gene that results in the amino acid substitution p.Cys168Phe was identified. The observed variant has a minor allele frequency of 0.00049% in gnomAD exomes and genomes, respectively. The severity of the impact of this variant on the protein is high, based on the effect of the protein and REVEL score. Rare Exome Variant Ensemble Learner (REVEL) is an ensembl method for predicting the pathogenicity of missense variants based on a combination of scores from 13 individual tools: MutPred, FATHMM v2.3, VEST 3.0, PolyPhen-2, SIFT, PROVEAN, MutationAssessor, MutationTaster, LRT, GERP++, SiPhy, phyloP, and phastCons. The REVEL score for an individual missense variant can range from 0 to 1, with higher scores reflecting greater likelihood that the variant is disease-causing. The variant has been reported to ClinVar as Uncertain significance: Pathogenic (1); with a status of (1 star) criteria provided, single submitter (Variation ID 1695382 as of 2022-12-17). Mutations in the gene have been documented to cause Platelet-type bleeding disorder 17 (Monteferrario, Davide et al., 2014). Based on the above evidence this variant has been classified as Likely Pathogenic according to the ACMG guidelines.

The missense variant p.C168F in GFI1B (NM_004188.6) has been previously reported in individuals as homozygous as well as heterozygous forms (Cheng et al, 2019). However, individuals with homozygous C168F variant suffered from clinical bleeding symptoms with thrombocytopenia and platelet aggregation dysfunction whereas heterozygous C168F patients only displayed macrothrombocytopenia with platelet CD34 expression (partial effect on the phenotype) (van Oorschot, Rinske et al, 2019). Experimental studies suggest that this mutation causes de-repression of other genes through disruption of the protein’s usual transcriptional repressor activity (Rabbolini et al, 2017). This variant has a gnomAD allele frequency of 0.04899 % and 5/978 (0.5112%) alleles from individuals of South Asian background in 1000 Genomes. It has been observed in homozygous form in two control individuals in the Gnomad database. The p.C168F missense variant is predicted to be damaging by both SIFT and PolyPhen2. The cysteine residue at codon 168 of GFI1B is conserved in all mammalian species. The nucleotide c.503 in GFI1B is predicted conserved by GERP++ and PhyloP across 100 vertebrates. For these reasons, this variant has been classified as Pathogenic.

The GFI1B c.503G>T variant is classified as LIKELY PATHOGENIC (PM2_Supporting, PS4_Moderate, PP1_Strong, PS3_Moderate) The GFI1B c.503G>T variant is a single nucleotide change in exon 8/11 of the GFI1B gene, which is predicted to change the amino acid cysteine at position 168 in the protein to phenylalanine. This variant is located within the zinc-finger binding domain of the GFI1B protein and is predicted to affect the conformation of the domain. This variant is present in population databases (gnomAD3.1.2 allele frequency = 0.011%; 18 het and 0 hom in 152230 sequenced alleles) (PM2_Supporting). It has been reported in a heterozygous state in patients with thrombocytopenia (PMID:31207059, 28880435, internal database) (PS4_Moderate) and found to segregate in an autosomal dominant manner in three unrelated families with mild to moderate macrothrombocytopenia, but without significant bruising or bleeding symptoms (PP1_Strong). Moreover, two individuals homozygous for the p.(Cys168Phe) mutation have been reported to have marked thrombocytopenia and abnormal platelet function, suggesting that this variant is a loss-of-function or hypomorphic allele (PMID: 25258084 and 30573501). Functional studies show a deleterious effect of this variant. p.(Cys168Phe) is predicted to disrupt znf1 structure and thereby GFI1B function. This was confirmed in functional experiments showing that p.(Cys168Phe) disrupts the repressive function of GFI1B gene expression (PMID: 30573501) (PS3_moderate). This patient’s haematological picture of thrombocytopenia with increased mean platelet volume is consistent with the typical presentation of cases with GFI1B p.(Cys168Phe). The variant has been reported in dbSNP (rs527297896) and in the HGMD database: CM1724779. It has been reported with conflicting interpretations of pathogenicity by other diagnostic laboratories (ClinVar Variation ID: 1695382).

PP5, PM1_supporting, PS3