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NM_032638.5(GATA2):c.1348G>A (p.Gly450Arg)

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Interpretation:
Uncertain significance​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
3 (Most recent: Nov 3, 2021)
Last evaluated:
Oct 3, 2020
Accession:
VCV000404088.5
Variation ID:
404088
Description:
single nucleotide variant
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NM_032638.5(GATA2):c.1348G>A (p.Gly450Arg)

Allele ID
393498
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
3q21.3
Genomic location
3: 128481114 (GRCh38) GRCh38 UCSC
3: 128199957 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000003.11:g.128199957C>T
NM_032638.4:c.1348G>A NP_116027.2:p.Gly450Arg missense
NC_000003.12:g.128481114C>T
... more HGVS
Protein change
G450R, G436R
Other names
-
Canonical SPDI
NC_000003.12:128481113:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.00020 (T)

Allele frequency
The Genome Aggregation Database (gnomAD) 0.00001
1000 Genomes Project 0.00020
The Genome Aggregation Database (gnomAD), exomes 0.00004
Exome Aggregation Consortium (ExAC) 0.00007
Trans-Omics for Precision Medicine (TOPMed) 0.00001
Trans-Omics for Precision Medicine (TOPMed) 0.00002
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00015
Links
ClinGen: CA2599793
dbSNP: rs370164300
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Uncertain significance 1 criteria provided, single submitter Oct 3, 2020 RCV000473249.6
Uncertain significance 1 criteria provided, single submitter Oct 31, 2018 RCV000765708.1
Uncertain significance 1 criteria provided, single submitter Apr 15, 2020 RCV001764367.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
GATA2 Sufficient evidence for dosage pathogenicity No evidence available GRCh38
GRCh37
823 849

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Oct 03, 2020)
criteria provided, single submitter
Method: clinical testing
Dendritic cell, monocyte, B lymphocyte, and natural killer lymphocyte deficiency
Lymphedema, primary, with myelodysplasia
Allele origin: germline
Invitae
Accession: SCV000541517.6
Submitted: (Jan 07, 2021)
Evidence details
Comment:
This sequence change replaces glycine with arginine at codon 450 of the GATA2 protein (p.Gly450Arg). The glycine residue is moderately conserved and there is a … (more)
Uncertain significance
(Oct 31, 2018)
criteria provided, single submitter
Method: clinical testing
Acute myeloid leukemia
Lymphedema, primary, with myelodysplasia
Dendritic cell, monocyte, B lymphocyte, and natural killer lymphocyte deficiency
Myelodysplastic syndrome
Allele origin: unknown
Fulgent Genetics,Fulgent Genetics
Accession: SCV000897069.1
Submitted: (Nov 14, 2018)
Evidence details
Publications
PubMed (1)
DOI: 10.1038/gim.2015.30
Uncertain significance
(Apr 15, 2020)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV002000770.1
Submitted: (Nov 03, 2021)
Evidence details
Comment:
In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to … (more)

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Richards S Genetics in medicine : official journal of the American College of Medical Genetics 2015 PMID: 25741868

Text-mined citations for rs370164300...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Nov 27, 2021