NM_001002295.2(GATA3):c.1201_1202del (p.Met401fs) AND not provided

Germline classification:: Pathogenic/Likely pathogenic (2 submissions)
Last evaluated:: Apr 1, 2021
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000489658.3

Allele description [Variation Report for NM_001002295.2(GATA3):c.1201_1202del (p.Met401fs)]

NM_001002295.2(GATA3):c.1201_1202del (p.Met401fs)

Gene:

GATA3:GATA binding protein 3 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

10p14

Genomic location:

Preferred name:

NM_001002295.2(GATA3):c.1201_1202del (p.Met401fs)

HGVS:

NC_000010.11:g.8073889_8073890del
NG_015859.1:g.24186_24187del
NM_001002295.2:c.1201_1202delMANE SELECT
NM_002051.3:c.1198_1199del
NP_001002295.1:p.Met401fs
NP_002042.1:p.Met400fs
NC_000010.10:g.8115852_8115853del
NM_001002295.1:c.1201_1202delAT
NM_001002295.2:c.1201_1202delATMANE SELECT

Protein change:

M400fs

Links:

dbSNP: rs1085307641

NCBI 1000 Genomes Browser:

rs1085307641

Molecular consequence:

NM_001002295.2:c.1201_1202del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_002051.3:c.1198_1199del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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Squamous cell carcinoma antigen recognized by T cells 3 [Homo sapiens]
Squamous cell carcinoma antigen recognized by T cells 3 [Homo sapiens]
gi|62739971|gb|AAH93784.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000576922	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Likely pathogenic (Apr 14, 2017)	germline	clinical testing	Citation Link,
SCV001760727	Laboratoire Génétique Moléculaire, CHRU TOURS	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Apr 1, 2021)	de novo	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

SCV000576922

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Likely pathogenic
(Apr 14, 2017)

germline

clinical testing

Citation Link,

SCV001760727

Laboratoire Génétique Moléculaire, CHRU TOURS

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Apr 1, 2021)

de novo

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	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	de novo	yes	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 GeneDx, SCV000576922.4

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

Description

The c.1201_1202delAT variant in the GATA3 gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. This frameshift variant replaces the typical last 44 amino acid residues in the GATA3 protein with 105 different amino acid residues. This alteration may interfere with the proper formation and/or function of the GATA3 protein. The c.1201_1202delAT variant is not observed in large population cohorts (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). We interpret c.1201_1202delAT as a likely pathogenic variant.

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

From Laboratoire Génétique Moléculaire, CHRU TOURS, SCV001760727.1

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

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

Last Updated: Jun 23, 2024

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