NM_032638.5(GATA2):c.346_351del (p.Trp116_Thr117del) AND not specified

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Sep 28, 2020
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:: RCV001817978.4

Allele description [Variation Report for NM_032638.5(GATA2):c.346_351del (p.Trp116_Thr117del)]

NM_032638.5(GATA2):c.346_351del (p.Trp116_Thr117del)

Gene:

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

Variant type:

Deletion

Cytogenetic location:

3q21.3

Genomic location:

Preferred name:

NM_032638.5(GATA2):c.346_351del (p.Trp116_Thr117del)

HGVS:

NC_000003.12:g.128486249_128486254del
NG_029334.1:g.11936_11941del
NM_001145661.2:c.346_351del
NM_001145662.1:c.346_351del
NM_032638.5:c.346_351delMANE SELECT
NP_001139133.1:p.Trp116_Thr117del
NP_001139134.1:p.Trp116_Thr117del
NP_116027.2:p.Trp116_Thr117del
LRG_295t2:c.346_351del
LRG_295:g.11936_11941del
NC_000003.11:g.128205092_128205097del
NM_032638.4:c.346_351del

Links:

dbSNP: rs2107672791

NCBI 1000 Genomes Browser:

rs2107672791

Molecular consequence:

NM_001145661.2:c.346_351del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001145662.1:c.346_351del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_032638.5:c.346_351del - inframe_deletion - [Sequence Ontology: SO:0001822]

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002067537	Genetic Services Laboratory, University of Chicago	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Sep 28, 2020)	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

SCV002067537

Genetic Services Laboratory, University of Chicago

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Sep 28, 2020)

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	no	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

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 Genetic Services Laboratory, University of Chicago, SCV002067537.1

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

Description

DNA sequence analysis of the GATA2 gene demonstrated a 6 base pair deletion in exon 3, c.346_351del. This in-frame deletion is predicted to result in the deletion of two amino acid residues, p.Trp116_Thr117del. This sequence change does not appear to have been previously described in patients with GATA2-related disorders and has also not been described in population databases (gnomAD, ExAC). The p.Trp116_Thr117del change is located in a domain of the GATA2 protein that is known to be functional. Due to the availability of limited information, the functional significance of this sequence change is not known at present and its contribution to a disease phenotype cannot definitively be determined.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	no	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Dec 24, 2023

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