NM_032638.5(GATA2):c.1399_1401del (p.Phe467del) AND multiple conditions

Clinical significance:Uncertain significance (Last evaluated: Sep 15, 2020)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV001300014.1

Allele description [Variation Report for NM_032638.5(GATA2):c.1399_1401del (p.Phe467del)]

NM_032638.5(GATA2):c.1399_1401del (p.Phe467del)

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.1399_1401del (p.Phe467del)
HGVS:
  • NC_000003.12:g.128481062_128481064del
  • NG_029334.1:g.17125_17127del
  • NM_001145661.2:c.1399_1401del
  • NM_001145662.1:c.1357_1359del
  • NM_032638.5:c.1399_1401delMANE SELECT
  • NP_001139133.1:p.Phe467del
  • NP_001139134.1:p.Phe453del
  • NP_116027.2:p.Phe467del
  • LRG_295:g.17125_17127del
  • NC_000003.11:g.128199904_128199906del
  • NC_000003.11:g.128199905_128199907del
Protein change:
F453del
Links:
dbSNP: rs2068620357
NCBI 1000 Genomes Browser:
rs2068620357
Molecular consequence:
  • NM_001145661.2:c.1399_1401del - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NM_001145662.1:c.1357_1359del - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NM_032638.5:c.1399_1401del - inframe_deletion - [Sequence Ontology: SO:0001822]

Condition(s)

Name:
Lymphedema, primary, with myelodysplasia
Synonyms:
Emberger syndrome
Identifiers:
MONDO: MONDO:0013540; MedGen: C3279664; Orphanet: 3226; OMIM: 614038
Name:
Dendritic cell, monocyte, B lymphocyte, and natural killer lymphocyte deficiency (IMD21)
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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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001489136Invitaecriteria provided, single submitter
Uncertain significance
(Sep 15, 2020)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical 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):240-242.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Invitae, SCV001489136.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

This variant, c.1399_1401del, results in the deletion of 1 amino acid(s) of the GATA2 protein (p.Phe467del), but otherwise preserves the integrity of the reading frame. This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals with GATA2-related conditions. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. 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.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Dec 9, 2021

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