NM_001308093.3(GATA4):c.286G>A (p.Gly96Arg) AND Atrioventricular septal defect 4

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Nov 27, 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:: RCV001898632.4

Allele description [Variation Report for NM_001308093.3(GATA4):c.286G>A (p.Gly96Arg)]

NM_001308093.3(GATA4):c.286G>A (p.Gly96Arg)

Gene:

GATA4:GATA binding protein 4 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

8p23.1

Genomic location:

Preferred name:

NM_001308093.3(GATA4):c.286G>A (p.Gly96Arg)

HGVS:

NC_000008.11:g.11708598G>A
NG_008177.2:g.36680G>A
NM_001308093.3:c.286G>AMANE SELECT
NM_001308094.2:c.-6+7820G>A
NM_001374273.1:c.-3+4294G>A
NM_001374274.1:c.-3+584G>A
NM_002052.5:c.286G>A
NP_001295022.1:p.Gly96Arg
NP_002043.2:p.Gly96Arg
NC_000008.10:g.11566107G>A

Protein change:

G96R

Links:

dbSNP: rs2130069132

NCBI 1000 Genomes Browser:

rs2130069132

Molecular consequence:

NM_001308094.2:c.-6+7820G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001374273.1:c.-3+4294G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001374274.1:c.-3+584G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001308093.3:c.286G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_002052.5:c.286G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Atrioventricular septal defect 4 (AVSD4)
Identifiers:: MONDO: MONDO:0013747; MedGen: C3280781; OMIM: 614430

Recent activity

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uncharacterized protein Dmel_CG31522, isoform I [Drosophila melanogaster]
uncharacterized protein Dmel_CG31522, isoform I [Drosophila melanogaster]
gi|440217055|gnl|FlyBase|CG31522-PI GB95637.1|

Protein
ATPase subunit 8, partial (mitochondrion) [Icterus northropi]
ATPase subunit 8, partial (mitochondrion) [Icterus northropi]
gi|408669166|gb|AFU75905.1|

Protein
histone 4, partial [Euphaedusa steetzneri]
histone 4, partial [Euphaedusa steetzneri]
gi|2324144142|gb|UYX56975.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002160316	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Nov 27, 2021)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 22648249, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002160316

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Nov 27, 2021)

germline

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Novel GATA4 mutations in patients with congenital ventricular septal defects.

Yang YQ, Wang J, Liu XY, Chen XZ, Zhang W, Wang XZ, Liu X, Fang WY.

Med Sci Monit. 2012 Jun;18(6):CR344-50.

PubMed [citation]

PMID:: 22648249
PMCID:: PMC3560722

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. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002160316.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

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. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. This missense change has been observed in individual(s) with ventricular septal defects (PMID: 22648249). It has also been observed to segregate with disease in related individuals. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces glycine, which is neutral and non-polar, with arginine, which is basic and polar, at codon 96 of the GATA4 protein (p.Gly96Arg).

#	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

Last Updated: Sep 29, 2024

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