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NM_032638.5(GATA2):c.1391G>T (p.Ser464Ile) AND GATA2 deficiency with susceptibility to MDS/AML

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Mar 10, 2023
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV003153574.8

Allele description [Variation Report for NM_032638.5(GATA2):c.1391G>T (p.Ser464Ile)]

NM_032638.5(GATA2):c.1391G>T (p.Ser464Ile)

Gene:
GATA2:GATA binding protein 2 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
3q21.3
Genomic location:
Preferred name:
NM_032638.5(GATA2):c.1391G>T (p.Ser464Ile)
HGVS:
  • NC_000003.12:g.128481071C>A
  • NG_029334.1:g.17117G>T
  • NM_001145661.2:c.1391G>T
  • NM_001145662.1:c.1349G>T
  • NM_032638.5:c.1391G>TMANE SELECT
  • NP_001139133.1:p.Ser464Ile
  • NP_001139134.1:p.Ser450Ile
  • NP_116027.2:p.Ser464Ile
  • NP_116027.2:p.Ser464Ile
  • LRG_295t2:c.1391G>T
  • LRG_295:g.17117G>T
  • LRG_295p2:p.Ser464Ile
  • NC_000003.11:g.128199914C>A
  • NM_001145661.1:c.1391G>T
  • NM_032638.4:c.1391G>T
  • NM_032638.5:c.1391G>T
Protein change:
S450I
Links:
dbSNP: rs770949428
NCBI 1000 Genomes Browser:
rs770949428
Molecular consequence:
  • NM_001145661.2:c.1391G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001145662.1:c.1349G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_032638.5:c.1391G>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
GATA2 deficiency with susceptibility to MDS/AML
Identifiers:
MONDO: MONDO:0042982; MedGen: CN300066

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV003843093St. Jude Molecular Pathology, St. Jude Children's Research Hospital
criteria provided, single submitter

(St. Jude Assertion Criteria 2020)		Uncertain significance
(Mar 10, 2023) 		germlineclinical testing

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From St. Jude Molecular Pathology, St. Jude Children's Research Hospital, SCV003843093.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The GATA2 c.1391G>T (p.Ser464Ile) missense change has a maximum subpopulation frequency of 0.014% in gnomAD v2.1.1 (https://gnomad.broadinstitute.org/). The in silico tool REVEL is inconclusive about a pathogenic or benign effect of this variant on protein function, and to our knowledge functional studies have not been performed. To our knowledge, this variant has not been reported in individuals presenting with GATA2-associated clinical phenotypes. In summary, the evidence currently available is insufficient to determine the clinical significance of this variant. It has therefore been classified as of uncertain significance.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Nov 3, 2024