8-11708323-G-A

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PP3_ModerateBS2

The NM_001308093.3(GATA4):​c.11G>A​(p.Ser4Asn) variant causes a missense change. The variant allele was found at a frequency of 0.00000419 in 1,432,202 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★).

Frequency

Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000042 ( 0 hom. )

Consequence

GATA4
NM_001308093.3 missense

Scores

7
7
4

Clinical Significance

Uncertain significance criteria provided, multiple submitters, no conflicts U:2

Conservation

PhyloP100: 4.77
Variant links:
Genes affected
GATA4 (HGNC:4173): (GATA binding protein 4) This gene encodes a member of the GATA family of zinc-finger transcription factors. Members of this family recognize the GATA motif which is present in the promoters of many genes. This protein is thought to regulate genes involved in embryogenesis and in myocardial differentiation and function, and is necessary for normal testicular development. Mutations in this gene have been associated with cardiac septal defects. Additionally, alterations in gene expression have been associated with several cancer types. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2015]

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PP3
MetaRNN computational evidence supports a deleterious effect, 0.856
BS2
High AC in GnomAdExome4 at 6 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
GATA4NM_001308093.3 linkc.11G>A p.Ser4Asn missense_variant 2/7 ENST00000532059.6 NP_001295022.1 P43694-2B3KUF4B6DU75

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
GATA4ENST00000532059.6 linkc.11G>A p.Ser4Asn missense_variant 2/71 NM_001308093.3 ENSP00000435712.1 P43694-2

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
AF:
0.00000419
AC:
6
AN:
1432202
Hom.:
0
Cov.:
31
AF XY:
0.00000562
AC XY:
4
AN XY:
711404
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000543
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
32
Alfa
AF:
0.0000712
Hom.:
0
Bravo
AF:
0.00000378

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

Atrioventricular septal defect 4 Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpSep 12, 2023In 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. An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. This variant has not been reported in the literature in individuals affected with GATA4-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces serine, which is neutral and polar, with asparagine, which is neutral and polar, at codon 4 of the GATA4 protein (p.Ser4Asn). -
Cardiovascular phenotype Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingAmbry GeneticsOct 21, 2024The p.S4N variant (also known as c.11G>A), located in coding exon 1 of the GATA4 gene, results from a G to A substitution at nucleotide position 11. The serine at codon 4 is replaced by asparagine, an amino acid with highly similar properties. This amino acid position is conserved. In addition, the in silico prediction for this alteration is inconclusive. Based on the available evidence, the clinical significance of this variant remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
0.56
BayesDel_addAF
Uncertain
0.064
T
BayesDel_noAF
Benign
-0.15
CADD
Pathogenic
26
DANN
Uncertain
1.0
DEOGEN2
Benign
0.42
T;.;D;.;.;T
Eigen
Uncertain
0.44
Eigen_PC
Uncertain
0.38
FATHMM_MKL
Pathogenic
0.98
D
M_CAP
Pathogenic
0.93
D
MetaRNN
Pathogenic
0.86
D;D;D;D;D;D
MetaSVM
Pathogenic
1.1
D
MutationAssessor
Uncertain
2.1
.;.;M;.;M;.
PrimateAI
Pathogenic
0.88
D
PROVEAN
Benign
-1.1
.;.;N;N;N;.
REVEL
Pathogenic
0.70
Sift
Uncertain
0.0070
.;.;D;D;D;.
Sift4G
Pathogenic
0.0
.;D;T;D;T;D
Polyphen
0.99
.;.;D;.;.;.
Vest4
0.41, 0.46, 0.40
MutPred
0.63
Loss of glycosylation at S4 (P = 0.0115);Loss of glycosylation at S4 (P = 0.0115);Loss of glycosylation at S4 (P = 0.0115);Loss of glycosylation at S4 (P = 0.0115);Loss of glycosylation at S4 (P = 0.0115);Loss of glycosylation at S4 (P = 0.0115);
MVP
0.84
MPC
0.041
ClinPred
0.89
D
GERP RS
3.4
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7
Varity_R
0.43
gMVP
0.36

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1421266458; hg19: chr8-11565832; API