NM_032638.5(GATA2):c.1027_1041del (p.Arg343_Thr347del) AND multiple conditions

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jan 14, 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:: RCV003800291.2

Allele description [Variation Report for NM_032638.5(GATA2):c.1027_1041del (p.Arg343_Thr347del)]

NM_032638.5(GATA2):c.1027_1041del (p.Arg343_Thr347del)

Gene:

GATA2:GATA binding protein 2 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

3q21.3

Genomic location:

Preferred name:

NM_032638.5(GATA2):c.1027_1041del (p.Arg343_Thr347del)

HGVS:

NC_000003.12:g.128481923_128481937del
NG_029334.1:g.16253_16267del
NM_001145661.2:c.1027_1041del
NM_001145662.1:c.1018-33_1018-19del
NM_032638.5:c.1027_1041delMANE SELECT
NP_001139133.1:p.Arg343_Thr347del
NP_001139133.1:p.Arg343_Thr347del
NP_116027.2:p.Arg343_Thr347del
NP_116027.2:p.Arg343_Thr347del
LRG_295t1:c.1025_1039del
LRG_295t2:c.1025_1039del
LRG_295:g.16253_16267del
LRG_295p1:p.Arg343_Thr347del
LRG_295p2:p.Arg343_Thr347del
NC_000003.11:g.128200764_128200778del
NC_000003.11:g.128200766_128200780del
NM_001145661.1:c.1025_1039delCCAGAAGAGCCGGCA
NM_032638.4:c.1025_1039delCCAGAAGAGCCGGCA

Molecular consequence:

NM_001145661.2:c.1027_1041del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_032638.5:c.1027_1041del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001145662.1:c.1018-33_1018-19del - intron variant - [Sequence Ontology: SO:0001627]

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
SCV004593289	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jan 14, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004593289

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jan 14, 2023)

germline

clinical testing

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

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

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, SCV004593289.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

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. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. This variant has not been reported in the literature in individuals affected with GATA2-related conditions. This variant is not present in population databases (gnomAD no frequency). This variant, c.1027_1041del, results in the deletion of 5 amino acid(s) of the GATA2 protein (p.Arg343_Thr347del), but otherwise preserves the integrity of the reading frame.

#	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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