NM_001002295.2(GATA3):c.708dup (p.Ser237fs) AND not provided

Germline classification:: Pathogenic (2 submissions)
Last evaluated:: Aug 4, 2023
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:: RCV002570570.4

Allele description [Variation Report for NM_001002295.2(GATA3):c.708dup (p.Ser237fs)]

NM_001002295.2(GATA3):c.708dup (p.Ser237fs)

Gene:

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

Variant type:

Duplication

Cytogenetic location:

10p14

Genomic location:

Preferred name:

NM_001002295.2(GATA3):c.708dup (p.Ser237fs)

HGVS:

NC_000010.11:g.8058771dup
NG_015859.1:g.9068dup
NM_001002295.2:c.708dupMANE SELECT
NM_002051.3:c.708dup
NP_001002295.1:p.Ser237fs
NP_002042.1:p.Ser237fs
NC_000010.10:g.8100727_8100728insC
NC_000010.10:g.8100734dup

Protein change:

S237fs

Links:

dbSNP: rs771019738

NCBI 1000 Genomes Browser:

rs771019738

Molecular consequence:

NM_001002295.2:c.708dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_002051.3:c.708dup - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003441477	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (May 1, 2022)	germline	clinical testing	PubMed (5) [See all records that cite these PMIDs] 14985365, 21242646, 30396722, 33120464, 28492532
SCV005198011	Clinical Genetics Laboratory, Skane University Hospital Lund	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Aug 4, 2023)	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

SCV003441477

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(May 1, 2022)

germline

clinical testing

PubMed (5)
[See all records that cite these PMIDs]

SCV005198011

Clinical Genetics Laboratory, Skane University Hospital Lund

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Aug 4, 2023)

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	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Characterization of GATA3 mutations in the hypoparathyroidism, deafness, and renal dysplasia (HDR) syndrome.

Nesbit MA, Bowl MR, Harding B, Ali A, Ayala A, Crowe C, Dobbie A, Hampson G, Holdaway I, Levine MA, McWilliams R, Rigden S, Sampson J, Williams AJ, Thakker RV.

J Biol Chem. 2004 May 21;279(21):22624-34. Epub 2004 Feb 24.

PubMed [citation]

PMID:: 14985365

GATA3 abnormalities in six patients with HDR syndrome.

Fukami M, Muroya K, Miyake T, Iso M, Kato F, Yokoi H, Suzuki Y, Tsubouchi K, Nakagomi Y, Kikuchi N, Horikawa R, Ogata T.

Endocr J. 2011;58(2):117-21. Epub 2011 Jan 13.

PubMed [citation]

PMID:: 21242646

See all PubMed Citations (6)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003441477.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (5)

Description

This sequence change creates a premature translational stop signal (p.Ser237Glnfs*67) in the GATA3 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in GATA3 are known to be pathogenic (PMID: 14985365, 21242646). The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This premature translational stop signal has been observed in individual(s) with GATA3-related conditions (PMID: 30396722, 33120464). ClinVar contains an entry for this variant (Variation ID: 977148). For these reasons, this variant has been classified as Pathogenic.

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

From Clinical Genetics Laboratory, Skane University Hospital Lund, SCV005198011.1

#	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	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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