NM_032638.5(GATA2):c.416_417del (p.Ser139fs) AND multiple conditions

Germline classification:: 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:: RCV001542179.1

Allele description [Variation Report for NM_032638.5(GATA2):c.416_417del (p.Ser139fs)]

NM_032638.5(GATA2):c.416_417del (p.Ser139fs)

Gene:

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

Variant type:

Microsatellite

Cytogenetic location:

3q21.3

Genomic location:

Preferred name:

NM_032638.5(GATA2):c.416_417del (p.Ser139fs)

HGVS:

NC_000003.12:g.128486181AG[2]
NG_029334.1:g.12002CT[2]
NM_001145661.2:c.416_417del
NM_001145662.1:c.416_417del
NM_032638.5:c.416_417delMANE SELECT
NP_001139133.1:p.Ser139fs
NP_001139134.1:p.Ser139fs
NP_116027.2:p.Ser139fs
LRG_295:g.12002CT[2]
NC_000003.11:g.128205024AG[2]

Protein change:

S139fs

Links:

dbSNP: rs2107672708

NCBI 1000 Genomes Browser:

rs2107672708

Molecular consequence:

NM_001145661.2:c.416_417del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001145662.1:c.416_417del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_032638.5:c.416_417del - frameshift variant - [Sequence Ontology: SO:0001589]

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

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001760847	Molecular Pathology Research Laboratory, SA Pathology	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Jul 6, 2021)	unknown	curation	PubMed (2) [See all records that cite these PMIDs] 26702063, 25741868

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001760847

Molecular Pathology Research Laboratory, SA Pathology

criteria provided, single submitter

(ACMG Guidelines, 2015)

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

Prevalence, clinical characteristics, and prognosis of GATA2-related myelodysplastic syndromes in children and adolescents.

Wlodarski MW, Hirabayashi S, Pastor V, Starý J, Hasle H, Masetti R, Dworzak M, Schmugge M, van den Heuvel-Eibrink M, Ussowicz M, De Moerloose B, Catala A, Smith OP, Sedlacek P, Lankester AC, Zecca M, Bordon V, Matthes-Martin S, Abrahamsson J, Kühl JS, Sykora KW, Albert MH, et al.

Blood. 2016 Mar 17;127(11):1387-97; quiz 1518. doi: 10.1182/blood-2015-09-669937. Epub 2015 Dec 23.

PubMed [citation]

PMID:: 26702063

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, SCV001760847.1

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

Description

PVS1, PS4_Supporting, PM2

#	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: Dec 24, 2023

ClinVar

Relating variation to medicine