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

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jan 11, 2020
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:: RCV001301867.7

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:: 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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001491051	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jan 11, 2020)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 29724903, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001491051

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jan 11, 2020)

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical 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. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001491051.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical 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. 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. 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"). This variant has been observed in individual(s) with myelodysplastic syndrome (PMID: 29724903). This variant is not present in population databases (ExAC no frequency).

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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