NM_032638.5(GATA2):c.1410_1411delinsAA (p.His471Asn) AND multiple conditions

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jul 17, 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:: RCV002592426.3

Allele description [Variation Report for NM_032638.5(GATA2):c.1410_1411delinsAA (p.His471Asn)]

NM_032638.5(GATA2):c.1410_1411delinsAA (p.His471Asn)

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.1410_1411delinsAA (p.His471Asn)

HGVS:

NC_000003.12:g.128481051_128481052delinsTT
NG_029334.1:g.17136_17137delinsAA
NM_001145661.2:c.1410_1411delinsAA
NM_001145662.1:c.1368_1369delinsAA
NM_032638.5:c.1410_1411delinsAAMANE SELECT
NP_001139133.1:p.His471Asn
NP_001139133.1:p.His471Asn
NP_001139134.1:p.His457Asn
NP_116027.2:p.His471Asn
NP_116027.2:p.His471Asn
LRG_295t1:c.1410_1411delCCinsAA
LRG_295t2:c.1410_1411delCCinsAA
LRG_295:g.17136_17137delinsAA
LRG_295p1:p.His471Asn
LRG_295p2:p.His471Asn
NC_000003.11:g.128199894_128199895delinsTT
NM_001145661.1:c.1410_1411delCCinsAA
NM_032638.4:c.1410_1411delCCinsAA

Protein change:

H457N

Molecular consequence:

NM_001145661.2:c.1410_1411delinsAA - missense variant - [Sequence Ontology: SO:0001583]
NM_001145662.1:c.1368_1369delinsAA - missense variant - [Sequence Ontology: SO:0001583]
NM_032638.5:c.1410_1411delinsAA - 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
SCV003500335	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jul 17, 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

SCV003500335

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jul 17, 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, SCV003500335.2

#	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. Information on the frequency of this variant in the gnomAD database is not available, as this variant may be reported differently in the database. This variant, c.1410_1411delinsAA, is a complex sequence change that results in the deletion of 1 and insertion of 1 amino acid(s) in the GATA2 protein (p.His471Asn).

#	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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