NM_032638.5(GATA2):c.1117T>C (p.Cys373Arg) AND multiple conditions

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Jul 6, 2021
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:: RCV001542161.1

Allele description [Variation Report for NM_032638.5(GATA2):c.1117T>C (p.Cys373Arg)]

NM_032638.5(GATA2):c.1117T>C (p.Cys373Arg)

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.1117T>C (p.Cys373Arg)

HGVS:

NC_000003.12:g.128481845A>G
NG_029334.1:g.16343T>C
NM_001145661.2:c.1117T>C
NM_001145662.1:c.1075T>C
NM_032638.5:c.1117T>CMANE SELECT
NP_001139133.1:p.Cys373Arg
NP_001139134.1:p.Cys359Arg
NP_116027.2:p.Cys373Arg
NP_116027.2:p.Cys373Arg
LRG_295t2:c.1117T>C
LRG_295:g.16343T>C
LRG_295p2:p.Cys373Arg
NC_000003.11:g.128200688A>G
NM_032638.4:c.1117T>C
P23769:p.Cys373Arg

Protein change:

C359R; CYS373ARG

Links:

UniProtKB: P23769#VAR_066645; OMIM: 137295.0012; dbSNP: rs387906633

NCBI 1000 Genomes Browser:

rs387906633

Molecular consequence:

NM_001145661.2:c.1117T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001145662.1:c.1075T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_032638.5:c.1117T>C - 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:: GATA2 deficiency with susceptibility to MDS/AML
Identifiers:: MONDO: MONDO:0042982; MedGen: CN300066

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001760829	Molecular Pathology Research Laboratory, SA Pathology	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Jul 6, 2021)	unknown	curation	PubMed (2) [See all records that cite these PMIDs] 21892158, 25741868

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001760829

Molecular Pathology Research Laboratory, SA Pathology

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Jul 6, 2021)

unknown

curation

PubMed (2)
[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	unknown	yes	1	1	not provided	not provided	not provided	curation

Citations

PubMed

Mutations in GATA2 cause primary lymphedema associated with a predisposition to acute myeloid leukemia (Emberger syndrome).

Ostergaard P, Simpson MA, Connell FC, Steward CG, Brice G, Woollard WJ, Dafou D, Kilo T, Smithson S, Lunt P, Murday VA, Hodgson S, Keenan R, Pilz DT, Martinez-Corral I, Makinen T, Mortimer PS, Jeffery S, Trembath RC, Mansour S.

Nat Genet. 2011 Sep 4;43(10):929-31. doi: 10.1038/ng.923.

PubMed [citation]

PMID:: 21892158

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Molecular Pathology Research Laboratory, SA Pathology, SCV001760829.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	1	not provided	not provided	curation	PubMed (2)

Description

PS3_Supporting, PS4_Supporting, PM1, PM2, PM5, PP3

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	yes	not provided	not provided	not provided		1	not provided	1	not provided

Last Updated: Apr 23, 2022

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