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NM_001145661.2(GATA2):c.1018-1G>T

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Interpretation:
Likely pathogenic​

Review status:
criteria provided, single submitter
Submissions:
2 (Most recent: Jul 12, 2021)
Last evaluated:
Jul 6, 2021
Accession:
VCV000029716.2
Variation ID:
29716
Description:
single nucleotide variant
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NM_001145661.2(GATA2):c.1018-1G>T

Allele ID
38671
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
3q21.3
Genomic location
3: 128481945 (GRCh38) GRCh38 UCSC
3: 128200788 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000003.11:g.128200788C>A
NC_000003.12:g.128481945C>A
NM_032638.5:c.1018-1G>T MANE Select
... more HGVS
Protein change
-
Other names
IVS4AS, G-T, -1
Canonical SPDI
NC_000003.12:128481944:C:A
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
-
Links
ClinGen: CA358817
OMIM: 137295.0008
dbSNP: rs869320668
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely pathogenic 1 criteria provided, single submitter Jul 6, 2021 RCV001542153.1
Pathogenic 1 no assertion criteria provided Sep 8, 2011 RCV000022568.28
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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
813 839

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
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)
Allele origin: unknown
Molecular Pathology Research Laboratory,SA Pathology
Accession: SCV001760821.1
Submitted: (Jul 12, 2021)
Evidence details
Publications
PubMed (3)
Comment:
PVS1_Strong, PS4_Supporting, PM2
Pathogenic
(Sep 08, 2011)
no assertion criteria provided
Method: literature only
IMMUNODEFICIENCY 21
Allele origin: germline
OMIM
Accession: SCV000043857.2
Submitted: (Nov 02, 2011)
Evidence details
Publications
PubMed (2)

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
The evolution of cellular deficiency in GATA2 mutation. Dickinson RE Blood 2014 PMID: 24345756
Dendritic cell, monocyte, B and NK lymphoid deficiency defines the lost lineages of a new GATA-2 dependent myelodysplastic syndrome. Bigley V Haematologica 2011 PMID: 21810969
Exome sequencing identifies GATA-2 mutation as the cause of dendritic cell, monocyte, B and NK lymphoid deficiency. Dickinson RE Blood 2011 PMID: 21765025
The human syndrome of dendritic cell, monocyte, B and NK lymphoid deficiency. Bigley V The Journal of experimental medicine 2011 PMID: 21242295

Text-mined citations for rs869320668...

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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 Jul 26, 2021