NM_032638.5(GATA2):c.129C>G (p.Asp43Glu) AND multiple conditions

Clinical significance:Uncertain significance (Last evaluated: Aug 18, 2020)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV001364457.1

Allele description [Variation Report for NM_032638.5(GATA2):c.129C>G (p.Asp43Glu)]

NM_032638.5(GATA2):c.129C>G (p.Asp43Glu)

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.129C>G (p.Asp43Glu)
HGVS:
  • NC_000003.12:g.128486903G>C
  • NG_029334.1:g.11285C>G
  • NM_001145661.2:c.129C>G
  • NM_001145662.1:c.129C>G
  • NM_032638.5:c.129C>GMANE SELECT
  • NP_001139133.1:p.Asp43Glu
  • NP_001139134.1:p.Asp43Glu
  • NP_116027.2:p.Asp43Glu
  • LRG_295:g.11285C>G
  • NC_000003.11:g.128205746G>C
Protein change:
D43E
Molecular consequence:
  • NM_001145661.2:c.129C>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001145662.1:c.129C>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_032638.5:c.129C>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Lymphedema, primary, with myelodysplasia
Synonyms:
Emberger syndrome
Identifiers:
MONDO: MONDO:0013540; MedGen: C3279664; Orphanet: 3226; OMIM: 614038
Name:
Dendritic cell, monocyte, B lymphocyte, and natural killer lymphocyte deficiency (IMD21)
Synonyms:
MONOCYTOPENIA AND MYCOBACTERIAL INFECTION SYNDROME; MONOCYTOPENIA WITH SUSCEPTIBILITY TO MYCOBACTERIAL, FUNGAL, AND PAPILLOMAVIRUS INFECTIONS AND MYELODYSPLASIA; COMBINED IMMUNODEFICIENCY WITH SUSCEPTIBILITY TO MYCOBACTERIAL, VIRAL, AND FUNGAL INFECTIONS; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0013607; MedGen: C3280030; Orphanet: 228423; OMIM: 614172

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001560606Invitaecriteria provided, single submitter
Uncertain significance
(Aug 18, 2020)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Summary from all submissions

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

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240-242.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Invitae, SCV001560606.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

This sequence change replaces aspartic acid with glutamic acid at codon 43 of the GATA2 protein (p.Asp43Glu). The aspartic acid residue is moderately conserved and there is a small physicochemical difference between aspartic acid and glutamic acid. This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals with GATA2-related conditions. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt GATA2 protein function. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

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

Last Updated: Dec 9, 2021

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