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NM_032638.5(GATA2):c.1036G>A (p.Gly346Ser) AND multiple conditions

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jun 27, 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:
RCV000704865.8

Allele description [Variation Report for NM_032638.5(GATA2):c.1036G>A (p.Gly346Ser)]

NM_032638.5(GATA2):c.1036G>A (p.Gly346Ser)

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.1036G>A (p.Gly346Ser)
HGVS:
  • NC_000003.12:g.128481926C>T
  • NG_029334.1:g.16262G>A
  • NM_001145661.2:c.1036G>A
  • NM_001145662.1:c.1018-24G>A
  • NM_032638.5:c.1036G>AMANE SELECT
  • NP_001139133.1:p.Gly346Ser
  • NP_116027.2:p.Gly346Ser
  • NP_116027.2:p.Gly346Ser
  • LRG_295t2:c.1036G>A
  • LRG_295:g.16262G>A
  • LRG_295p2:p.Gly346Ser
  • NC_000003.11:g.128200769C>T
  • NM_032638.4:c.1036G>A
Protein change:
G346S
Links:
dbSNP: rs1559985135
NCBI 1000 Genomes Browser:
rs1559985135
Molecular consequence:
  • NM_001145662.1:c.1018-24G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001145661.2:c.1036G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_032638.5:c.1036G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Deafness-lymphedema-leukemia syndrome
Synonyms:
Lymphedema, primary, with myelodysplasia; Emberger syndrome
Identifiers:
MONDO: MONDO:0013540; MedGen: C3279664; Orphanet: 3226; OMIM: 614038
Name:
Monocytopenia with susceptibility to infections
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

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000833836Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Jun 27, 2023) 		germlineclinical testing

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

Help

Summary from all submissions

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

Citations

PubMed

MDS-associated mutations in germline GATA2 mutated patients with hematologic manifestations.

McReynolds LJ, Yang Y, Yuen Wong H, Tang J, Zhang Y, Mulé MP, Daub J, Palmer C, Foruraghi L, Liu Q, Zhu J, Wang W, West RR, Yohe ME, Hsu AP, Hickstein DD, Townsley DM, Holland SM, Calvo KR, Hourigan CS.

Leuk Res. 2019 Jan;76:70-75. doi: 10.1016/j.leukres.2018.11.013. Epub 2018 Dec 4.

PubMed [citation]
PMID:
30578959
PMCID:
PMC6340496

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. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000833836.4

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

Description

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. 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) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on GATA2 protein function. ClinVar contains an entry for this variant (Variation ID: 581129). This missense change has been observed in individual(s) with clinical features of GATA2 deficiency (PMID: 30578959). This variant is not present in population databases (gnomAD no frequency). This sequence change replaces glycine, which is neutral and non-polar, with serine, which is neutral and polar, at codon 346 of the GATA2 protein (p.Gly346Ser).

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

Last Updated: Sep 29, 2024