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

Clinical significance:Uncertain significance (Last evaluated: Jan 11, 2020)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV001301867.1

Allele description [Variation Report for NM_032638.5(GATA2):c.937C>T (p.His313Tyr)]

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

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.937C>T (p.His313Tyr)
HGVS:
  • NC_000003.12:g.128483940G>A
  • NG_029334.1:g.14248C>T
  • NM_001145661.2:c.937C>T
  • NM_001145662.1:c.937C>T
  • NM_032638.5:c.937C>TMANE SELECT
  • NP_001139133.1:p.His313Tyr
  • NP_001139134.1:p.His313Tyr
  • NP_116027.2:p.His313Tyr
  • LRG_295:g.14248C>T
  • NC_000003.11:g.128202783G>A
Protein change:
H313Y
Links:
dbSNP: rs2068661887
NCBI 1000 Genomes Browser:
rs2068661887
Molecular consequence:
  • NM_001145661.2:c.937C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001145662.1:c.937C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_032638.5:c.937C>T - 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
SCV001491051Invitaecriteria provided, single submitter
Uncertain significance
(Jan 11, 2020)
germlineclinical testing

PubMed (2)
[See all records that cite these PMIDs]

Summary from all submissions

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

Citations

PubMed

Natural history of GATA2 deficiency in a survey of 79 French and Belgian patients.

Donadieu J, Lamant M, Fieschi C, de Fontbrune FS, Caye A, Ouachee M, Beaupain B, Bustamante J, Poirel HA, Isidor B, Van Den Neste E, Neel A, Nimubona S, Toutain F, Barlogis V, Schleinitz N, Leblanc T, Rohrlich P, Suarez F, Ranta D, Chahla WA, Bruno B, et al.

Haematologica. 2018 Aug;103(8):1278-1287. doi: 10.3324/haematol.2017.181909. Epub 2018 May 3.

PubMed [citation]
PMID:
29724903
PMCID:
PMC6068047

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, SCV001491051.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)

Description

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 moderate physicochemical difference between histidine and tyrosine. This variant is not present in population databases (ExAC no frequency). This variant has been observed in individual(s) with myelodysplastic syndrome (PMID: 29724903). 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: Deleterious; 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 9, 2021

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