chr3-128481908-A-G
Variant summary
Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PM1PM2PM5PP3_StrongPP5_Very_Strong
The NM_032638.5(GATA2):c.1054T>C(p.Cys352Arg) 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. 12/21 in silico tools predict a damaging outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. C352F) has been classified as Likely pathogenic.
Frequency
Consequence
NM_032638.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 18 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GATA2 | NM_001145661.2 | c.1054T>C | p.Cys352Arg | missense_variant | 6/7 | ENST00000487848.6 | |
GATA2 | NM_032638.5 | c.1054T>C | p.Cys352Arg | missense_variant | 5/6 | ENST00000341105.7 | |
GATA2 | NM_001145662.1 | c.1018-6T>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GATA2 | ENST00000341105.7 | c.1054T>C | p.Cys352Arg | missense_variant | 5/6 | 1 | NM_032638.5 | P1 | |
GATA2 | ENST00000487848.6 | c.1054T>C | p.Cys352Arg | missense_variant | 6/7 | 1 | NM_001145661.2 | P1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome Cov.: 32
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
Leukemia, acute myeloid, susceptibility to Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | May 09, 2015 | - - |
Deafness-lymphedema-leukemia syndrome;CN300066:GATA2 deficiency with susceptibility to MDS/AML Pathogenic:1
Likely pathogenic, criteria provided, single submitter | curation | Molecular Pathology Research Laboratory, SA Pathology | Jul 06, 2021 | PS4_Supporting, PM1, PM2, PM5, PP3 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at