NM_032638.5(GATA2):c.1042_1092dup (p.Cys348_Ala364dup) AND multiple conditions

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Aug 22, 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:: RCV001316672.7

Allele description [Variation Report for NM_032638.5(GATA2):c.1042_1092dup (p.Cys348_Ala364dup)]

NM_032638.5(GATA2):c.1042_1092dup (p.Cys348_Ala364dup)

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.1042_1092dup (p.Cys348_Ala364dup)

HGVS:

NC_000003.12:g.128481872_128481922dup
NG_029334.1:g.16268_16318dup
NM_001145661.2:c.1042_1092dup
NM_001145662.1:c.1018-18_1050dup
NM_032638.5:c.1042_1092dupMANE SELECT
NP_001139133.1:p.Cys348_Ala364dup
NP_116027.2:p.Cys348_Ala364dup
LRG_295:g.16268_16318dup
NC_000003.11:g.128200712_128200713insGGCGTTTCGGCGCCATAAGGTGGTGGTTGTCGTCTGACAATTTGCACAACA
NC_000003.11:g.128200715_128200765dup

Links:

dbSNP: rs2068633920

NCBI 1000 Genomes Browser:

rs2068633920

Molecular consequence:

NM_001145661.2:c.1042_1092dup - inframe_insertion - [Sequence Ontology: SO:0001821]
NM_032638.5:c.1042_1092dup - inframe_insertion - [Sequence Ontology: SO:0001821]
NM_001145662.1:c.1018-18_1050dup - splice acceptor variant - [Sequence Ontology: SO:0001574]

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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Tpnr1 thermal pain response 1 [Mus musculus]
Tpnr1 thermal pain response 1 [Mus musculus]
Gene ID:112118

Gene
Tpnr1 AND (alive[prop]) (1)
Gene
Time
Time
The dimension of the physical universe which, at a given place, orders the sequence of events. (McGraw-Hill Dictionary of Scientific and Technical Terms, 6th ed)...<br/>

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001507303	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Aug 22, 2022)	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

SCV001507303

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Aug 22, 2022)

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, SCV001507303.4

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

Description

Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. 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. ClinVar contains an entry for this variant (Variation ID: 1017513). 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.1042_1092dup, results in the insertion of 17 amino acid(s) of the GATA2 protein (p.Cys348_Ala364dup), 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

ClinVar

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