NM_032638.5(GATA2):c.751_752dup (p.Tyr252fs) AND multiple conditions

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jun 8, 2022
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:: RCV001941808.4

Allele description [Variation Report for NM_032638.5(GATA2):c.751_752dup (p.Tyr252fs)]

NM_032638.5(GATA2):c.751_752dup (p.Tyr252fs)

Gene:

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

Variant type:

Duplication

Cytogenetic location:

3q21.3

Genomic location:

Preferred name:

NM_032638.5(GATA2):c.751_752dup (p.Tyr252fs)

HGVS:

NC_000003.12:g.128485847_128485848dup
NG_029334.1:g.12341_12342dup
NM_001145661.2:c.751_752dup
NM_001145662.1:c.751_752dup
NM_032638.5:c.751_752dupMANE SELECT
NP_001139133.1:p.Tyr252fs
NP_001139134.1:p.Tyr252fs
NP_116027.2:p.Tyr252fs
LRG_295:g.12341_12342dup
NC_000003.11:g.128204688_128204689insGA
NC_000003.11:g.128204690_128204691dup

Protein change:

Y252fs

Links:

dbSNP: rs2107672019

NCBI 1000 Genomes Browser:

rs2107672019

Molecular consequence:

NM_001145661.2:c.751_752dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001145662.1:c.751_752dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_032638.5:c.751_752dup - frameshift variant - [Sequence Ontology: SO:0001589]

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

Recent activity

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Homo sapiens RAB40C, member RAS oncogene family (RAB40C), mRNA
Homo sapiens RAB40C, member RAS oncogene family (RAB40C), mRNA
gi|46195788|ref|NM_021168.2|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002230082	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jun 8, 2022)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 21670465, 23223431, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002230082

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jun 8, 2022)

germline

clinical testing

PubMed (3)
[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

Mutations in GATA2 are associated with the autosomal dominant and sporadic monocytopenia and mycobacterial infection (MonoMAC) syndrome.

Hsu AP, Sampaio EP, Khan J, Calvo KR, Lemieux JE, Patel SY, Frucht DM, Vinh DC, Auth RD, Freeman AF, Olivier KN, Uzel G, Zerbe CS, Spalding C, Pittaluga S, Raffeld M, Kuhns DB, Ding L, Paulson ML, Marciano BE, Gea-Banacloche JC, Orange JS, et al.

Blood. 2011 Sep 8;118(10):2653-5. doi: 10.1182/blood-2011-05-356352. Epub 2011 Jun 13.

PubMed [citation]

PMID:: 21670465
PMCID:: PMC3172785

High frequency of GATA2 mutations in patients with mild chronic neutropenia evolving to MonoMac syndrome, myelodysplasia, and acute myeloid leukemia.

Pasquet M, Bellanné-Chantelot C, Tavitian S, Prade N, Beaupain B, Larochelle O, Petit A, Rohrlich P, Ferrand C, Van Den Neste E, Poirel HA, Lamy T, Ouachée-Chardin M, Mansat-De Mas V, Corre J, Récher C, Plat G, Bachelerie F, Donadieu J, Delabesse E.

Blood. 2013 Jan 31;121(5):822-9. doi: 10.1182/blood-2012-08-447367. Epub 2012 Dec 6.

PubMed [citation]

PMID:: 23223431
PMCID:: PMC3714670

See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002230082.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

This variant has not been reported in the literature in individuals affected with GATA2-related conditions. For these reasons, this variant has been classified as Pathogenic. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Tyr252Profs*75) in the GATA2 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in GATA2 are known to be pathogenic (PMID: 21670465, 23223431).

#	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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