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NM_032638.5(GATA2):c.1274C>T (p.Ser425Leu) AND not specified

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Apr 12, 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:
RCV001821589.4

Allele description [Variation Report for NM_032638.5(GATA2):c.1274C>T (p.Ser425Leu)]

NM_032638.5(GATA2):c.1274C>T (p.Ser425Leu)

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.1274C>T (p.Ser425Leu)
HGVS:
  • NC_000003.12:g.128481188G>A
  • NG_029334.1:g.17000C>T
  • NM_001145661.2:c.1274C>T
  • NM_001145662.1:c.1232C>T
  • NM_032638.5:c.1274C>TMANE SELECT
  • NP_001139133.1:p.Ser425Leu
  • NP_001139134.1:p.Ser411Leu
  • NP_116027.2:p.Ser425Leu
  • NP_116027.2:p.Ser425Leu
  • LRG_295t1:c.1274C>T
  • LRG_295t2:c.1274C>T
  • LRG_295:g.17000C>T
  • LRG_295p2:p.Ser425Leu
  • NC_000003.11:g.128200031G>A
  • NM_001145661.1:c.1274C>T
  • NM_032638.4:c.1274C>T
Protein change:
S411L
Links:
dbSNP: rs146554939
NCBI 1000 Genomes Browser:
rs146554939
Molecular consequence:
  • NM_001145661.2:c.1274C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001145662.1:c.1232C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_032638.5:c.1274C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
AllHighlyPenetrant
Identifiers:
MedGen: CN169374

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002065176Genetic Services Laboratory, University of Chicago
criteria provided, single submitter

(ACMG Guidelines, 2015)		Uncertain significance
(Apr 12, 2021) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenonot providednot providednot providednot providednot providedclinical 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, SCV002065176.1

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

Description

DNA sequence analysis of the GATA2 gene demonstrated a sequence change, c.1274C>T, in exon 6 that results in an amino acid change, p.Ser425Leu. This sequence change has been described in gnomAD with a frequency of 0.0028% in the African sub-population (dbSNP rs146554939). The p.Ser425Leu change affects a moderately conserved amino acid residue located in a domain of the GATA2 protein that is known to be functional. The p.Ser425Leu substitution appears to be benign using several in-silico pathogenicity prediction tools (SIFT, PolyPhen2, Align GVGD, REVEL). This sequence change does not appear to have been previously described in patients with GATA2-related disorders. Due to the lack of sufficient evidences, the clinical significance of the p.Ser425Leu change remains unknown at this time.

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

Last Updated: Oct 13, 2024