NM_032638.5(GATA2):c.724A>G (p.Thr242Ala) AND multiple conditions

Clinical significance:Uncertain significance (Last evaluated: Apr 20, 2020)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV000822691.3

Allele description [Variation Report for NM_032638.5(GATA2):c.724A>G (p.Thr242Ala)]

NM_032638.5(GATA2):c.724A>G (p.Thr242Ala)

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.724A>G (p.Thr242Ala)
HGVS:
  • NC_000003.12:g.128485874T>C
  • NG_029334.1:g.12314A>G
  • NM_001145661.2:c.724A>G
  • NM_001145662.1:c.724A>G
  • NM_032638.5:c.724A>GMANE SELECT
  • NP_001139133.1:p.Thr242Ala
  • NP_001139134.1:p.Thr242Ala
  • NP_116027.2:p.Thr242Ala
  • NP_116027.2:p.Thr242Ala
  • LRG_295t2:c.724A>G
  • LRG_295:g.12314A>G
  • LRG_295p2:p.Thr242Ala
  • NC_000003.11:g.128204717T>C
  • NM_032638.4:c.724A>G
Protein change:
T242A
Links:
dbSNP: rs886057931
NCBI 1000 Genomes Browser:
rs886057931
Molecular consequence:
  • NM_001145661.2:c.724A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001145662.1:c.724A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_032638.5:c.724A>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
SCV000963502Invitaecriteria provided, single submitter
Uncertain significance
(Apr 20, 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, SCV000963502.3

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

Description

This sequence change replaces threonine with alanine at codon 242 of the GATA2 protein (p.Thr242Ala). The threonine residue is moderately conserved and there is a small physicochemical difference between threonine and alanine. 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 disease. ClinVar contains an entry for this variant (Variation ID: 343138). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: Tolerated; PolyPhen-2: Probably Damaging; Align-GVGD: Class C0). 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 4, 2021

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