rs587776454
Variant summary
Our verdict is Likely pathogenic. Variant got 9 ACMG points: 9P and 0B. PM1PM2PM5PP3_ModeratePP5
The NM_002049.4(GATA1):c.622G>A(p.Gly208Arg) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another nucleotide change resulting in same amino acid change has been previously reported as Uncertain significancein ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G208S) has been classified as Pathogenic.
Frequency
Consequence
NM_002049.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_pathogenic. Variant got 9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GATA1 | NM_002049.4 | c.622G>A | p.Gly208Arg | missense_variant | 4/6 | ENST00000376670.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GATA1 | ENST00000376670.9 | c.622G>A | p.Gly208Arg | missense_variant | 4/6 | 1 | NM_002049.4 | P4 |
Frequencies
GnomAD3 genomes ? Cov.: 23
GnomAD4 exome Cov.: 33
GnomAD4 genome ? Cov.: 23
ClinVar
Submissions by phenotype
not provided Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | GeneDx | May 04, 2018 | The G208R pathogenic variant in the GATA1 gene has been reported previously in several males with anemia and thrombocytopenia (Del Vecchio et al., 2005; Kratz et al., 2008; Duhrsen et al., 2011; Doshi et al., 2014). The G208R variant was not observed in approximately 6,500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. This substitution occurs at a position that is conserved across species at a region in the N-terminal zinc finger domain important for binding FOG1, a cofactor necessary for erythroid and megakaryocyte development (Campbell et al., 2013). Functional studies have shown that G208R is associated with decreased FOG1 binding, reduced transcriptional activation and repression, and reduced megakaryocyte maturation (Campbell et al., 2013). We interpret G208R as a pathogenic variant. - |
Diamond-Blackfan anemia;C1845837:GATA binding protein 1 related thrombocytopenia with dyserythropoiesis Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Nov 17, 2023 | This sequence change replaces glycine, which is neutral and non-polar, with arginine, which is basic and polar, at codon 208 of the GATA1 protein (p.Gly208Arg). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with GATA1-related conditions (PMID: 16103636, 17713552, 20922527, 25232504). ClinVar contains an entry for this variant (Variation ID: 372762). 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 expected to disrupt GATA1 protein function with a positive predictive value of 80%. Experimental studies have shown that this missense change affects GATA1 function (PMID: 23704091). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at