NM_032638.5(GATA2):c.1166_1181delinsCATG (p.Lys389_Gln394delinsThrTrp) AND multiple conditions

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Oct 23, 2019
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:: RCV001241681.2

Allele description [Variation Report for NM_032638.5(GATA2):c.1166_1181delinsCATG (p.Lys389_Gln394delinsThrTrp)]

NM_032638.5(GATA2):c.1166_1181delinsCATG (p.Lys389_Gln394delinsThrTrp)

Gene:

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

Variant type:

Indel

Cytogenetic location:

3q21.3

Genomic location:

Preferred name:

NM_032638.5(GATA2):c.1166_1181delinsCATG (p.Lys389_Gln394delinsThrTrp)

HGVS:

NC_000003.12:g.128481281_128481296delinsCATG
NG_029334.1:g.16892_16907delinsCATG
NM_001145661.2:c.1166_1181delinsCATG
NM_001145662.1:c.1124_1139delinsCATG
NM_032638.5:c.1166_1181delinsCATGMANE SELECT
NP_001139133.1:p.Lys389_Gln394delinsThrTrp
NP_001139134.1:p.Lys375_Gln380delinsThrTrp
NP_116027.2:p.Lys389_Gln394delinsThrTrp
LRG_295t2:c.1166_1181delinsCATG
LRG_295:g.16892_16907delinsCATG
NC_000003.11:g.128200124_128200139delinsCATG
NM_032638.4:c.1166_1181delinsCATG

Links:

dbSNP: rs2068625186

NCBI 1000 Genomes Browser:

rs2068625186

Molecular consequence:

NM_001145661.2:c.1166_1181delinsCATG - inframe_indel - [Sequence Ontology: SO:0001820]
NM_001145662.1:c.1124_1139delinsCATG - inframe_indel - [Sequence Ontology: SO:0001820]
NM_032638.5:c.1166_1181delinsCATG - inframe_indel - [Sequence Ontology: SO:0001820]

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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PODANS_5_1200 [Podospora anserina S mat+]
PODANS_5_1200 [Podospora anserina S mat+]
Gene ID:6188456

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001414715	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Oct 23, 2019)	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

SCV001414715

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Oct 23, 2019)

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, SCV001414715.1

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

Description

This variant, c.1166_1181delinsCATG, is a complex sequence change that results in the deletion of 6 and insertion of 2 amino acid(s) in the GATA2 protein (p.Lys389_Gln394delinsThrTrp). This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals with GATA2-related conditions. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. 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.

#	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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