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NM_032638.5(GATA2):c.937C>T (p.His313Tyr)

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely pathogenic(1);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
2 (Most recent: Jul 12, 2021)
Last evaluated:
Jul 6, 2021
Accession:
VCV001005061.2
Variation ID:
1005061
Description:
single nucleotide variant
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NM_032638.5(GATA2):c.937C>T (p.His313Tyr)

Allele ID
989235
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
3q21.3
Genomic location
3: 128483940 (GRCh38) GRCh38 UCSC
3: 128202783 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000003.11:g.128202783G>A
NC_000003.12:g.128483940G>A
NG_029334.1:g.14248C>T
... more HGVS
Protein change
H313Y
Other names
-
Canonical SPDI
NC_000003.12:128483939:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
The Genome Aggregation Database (gnomAD) 0.00001
Links
dbSNP: rs2068661887
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 Jan 11, 2020 RCV001301867.1
Likely pathogenic 1 criteria provided, single submitter Jul 6, 2021 RCV001542223.1
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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 More information
Uncertain significance
(Jan 11, 2020)
criteria provided, single submitter
Method: clinical testing
Dendritic cell, monocyte, B lymphocyte, and natural killer lymphocyte deficiency
Lymphedema, primary, with myelodysplasia
Affected status: unknown
Allele origin: germline
Invitae
Accession: SCV001491051.1
Submitted: (Jan 07, 2021)
Publications:
PubMed (1)
PubMed: 29724903
Comment:
This sequence change replaces histidine with tyrosine at codon 313 of the GATA2 protein (p.His313Tyr). The histidine residue is moderately conserved and there is a … (more)
Likely pathogenic
(Jul 06, 2021)
criteria provided, single submitter
Method: curation
GATA2 deficiency with susceptibility to MDS/AML
Lymphedema, primary, with myelodysplasia
(Autosomal dominant inheritance)
Affected status: yes
Allele origin: germline
Molecular Pathology Research Laboratory,SA Pathology
Accession: SCV001760891.1
Submitted: (Jul 12, 2021)
Publications:
PubMed (1)
PubMed: 29724903
Comment:
PS4_Supporting, PM1, PM2, PP3
Number of individuals with the variant: 1
Clinical Features:
Myelodysplasia (yes) , Acute Myeloid Leukemia (yes) , Immunodeficiency (yes)

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
Natural history of GATA2 deficiency in a survey of 79 French and Belgian patients. Donadieu J Haematologica 2018 PMID: 29724903

Text-mined citations for rs2068661887...

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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 Dec 09, 2021