NM_032638.5(GATA2):c.1205A>G (p.Asn402Ser) AND multiple conditions

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Aug 11, 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:: RCV001040634.8

Allele description [Variation Report for NM_032638.5(GATA2):c.1205A>G (p.Asn402Ser)]

NM_032638.5(GATA2):c.1205A>G (p.Asn402Ser)

Gene:

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

Variant type:

single nucleotide variant

Cytogenetic location:

3q21.3

Genomic location:

Preferred name:

NM_032638.5(GATA2):c.1205A>G (p.Asn402Ser)

HGVS:

NC_000003.12:g.128481257T>C
NG_029334.1:g.16931A>G
NM_001145661.2:c.1205A>G
NM_001145662.1:c.1163A>G
NM_032638.5:c.1205A>GMANE SELECT
NP_001139133.1:p.Asn402Ser
NP_001139134.1:p.Asn388Ser
NP_116027.2:p.Asn402Ser
LRG_295t2:c.1205A>G
LRG_295:g.16931A>G
NC_000003.11:g.128200100T>C
NM_032638.4:c.1205A>G

Protein change:

N388S

Links:

dbSNP: rs375927513

NCBI 1000 Genomes Browser:

rs375927513

Molecular consequence:

NM_001145661.2:c.1205A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001145662.1:c.1163A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_032638.5:c.1205A>G - 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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Gene Links for GEO Profiles (Select 102081688) (2)
Gene
PCDH18 protocadherin 18 [Homo sapiens]
PCDH18 protocadherin 18 [Homo sapiens]
Gene ID:54510

Gene
Gene Links for GEO Profiles (Select 105709562) (1)
Gene
ACSL1 acyl-CoA synthetase long chain family member 1 [Homo sapiens]
ACSL1 acyl-CoA synthetase long chain family member 1 [Homo sapiens]
Gene ID:2180

Gene
Gene Links for GEO Profiles (Select 102079265) (1)
Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001204219	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Aug 11, 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

SCV001204219

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Aug 11, 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, SCV001204219.5

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

Description

Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt GATA2 protein function. 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. ClinVar contains an entry for this variant (Variation ID: 838976). This sequence change replaces asparagine, which is neutral and polar, with serine, which is neutral and polar, at codon 402 of the GATA2 protein (p.Asn402Ser). This variant is present in population databases (rs375927513, gnomAD 0.003%). This variant has not been reported in the literature in individuals affected with GATA2-related conditions.

#	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: Nov 3, 2024

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