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NM_005257.6(GATA6):c.551G>A (p.Ser184Asn) AND Atrial septal defect 9

Germline classification:
Pathogenic/Likely pathogenic (2 submissions)
Last evaluated:
Jan 6, 2020
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
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:
RCV000023131.3

Allele description [Variation Report for NM_005257.6(GATA6):c.551G>A (p.Ser184Asn)]

NM_005257.6(GATA6):c.551G>A (p.Ser184Asn)

Gene:
GATA6:GATA binding protein 6 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
18q11.2
Genomic location:
Preferred name:
NM_005257.6(GATA6):c.551G>A (p.Ser184Asn)
HGVS:
  • NC_000018.10:g.22171695G>A
  • NG_032677.2:g.7259G>A
  • NM_005257.6:c.551G>AMANE SELECT
  • NP_005248.2:p.Ser184Asn
  • NP_005248.2:p.Ser184Asn
  • NC_000018.9:g.19751656G>A
  • NM_005257.4:c.551G>A
  • NM_005257.5:c.551G>A
  • Q92908:p.Ser184Asn
Protein change:
S184N; SER184ASN
Links:
UniProtKB: Q92908#VAR_067382; OMIM: 601656.0005; dbSNP: rs387906816
NCBI 1000 Genomes Browser:
rs387906816
Molecular consequence:
  • NM_005257.6:c.551G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Atrial septal defect 9 (ASD9)
Identifiers:
MONDO: MONDO:0013770; MedGen: C3280943; Orphanet: 1478; OMIM: 614475

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000044422OMIM
no assertion criteria provided
Pathogenic
(Oct 1, 2010)
germlineliterature only

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

SCV001142479Reproductive Health Research and Development, BGI Genomics
no assertion criteria provided
Likely pathogenic
(Jan 6, 2020)
germlinecuration

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only
not providedgermlineunknownnot providednot providednot providednot providednot providedcuration

Citations

PubMed

A novel GATA6 mutation in patients with tetralogy of Fallot or atrial septal defect.

Lin X, Huo Z, Liu X, Zhang Y, Li L, Zhao H, Yan B, Liu Y, Yang Y, Chen YH.

J Hum Genet. 2010 Oct;55(10):662-7. doi: 10.1038/jhg.2010.84. Epub 2010 Jul 15.

PubMed [citation]
PMID:
20631719

Details of each submission

From OMIM, SCV000044422.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (1)

Description

In 3 sporadic Chinese patients with congenital heart defects, 2 with atrial septal defect (ASD9; 614475) and 1 with tetralogy of Fallot (TOF; 187500), Lin et al. (2010) identified heterozygosity for a 551G-A transition in exon 2 of the GATA6 gene, resulting in a ser184-to-asn (S184N) substitution at a highly conserved residue in the transcriptional activation domain. Functional analysis in HEK293 cells, using a direct cardiac downstream target, ANF (108780), as a luciferase reporter, demonstrated significantly decreased transcriptional activity and loss of dosage sensitivity for the mutant compared to wildtype. Studies in H9c2 rat cardiomyoblast cells using RT-PCR also showed impaired transcriptional ability of S184N GATA6. One of the ASD patients was a 3-year-old girl with an ostium secundum ASD and mild pulmonary arterial hypertension, whereas the other was a 4-year-old boy with an ostium secundum ASD and mild tricuspid valve disease and pulmonary valve replacement. The third patient was a 7-month-old boy with an overriding aorta (50% override), pulmonary stenosis, ventricular septal defect, and right atrial and ventricular hypertrophy. None of the patients had any other abnormalities. The S184N mutation was detected in the unaffected fathers of the boy with TOF and the girl with ASD, and it was also detected in the clinically unaffected mother of the boy with ASD, who was found to have bicuspid aortic valve on echocardiography. The mutation was not found in 500 ethnically matched controls.

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

From Reproductive Health Research and Development, BGI Genomics, SCV001142479.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcurationnot provided

Description

NM_005257.4:c.551G>A in the GATA6 gene has an allele frequency of 0.009 in East Asia subpopulation in the gnomAD database. Functional studies demonstrate that this variant clearly decreased transcriptional activity of GATA6 Ser184Asn in vitro (PMID: 20631719). In addition, Wang et al. identified c.551G>A in a patient with Tetralogy of Fallot. His parents had normal cardiac morphology and there were no GATA6 sequence variants identified, indicating a de novo event (PMID: 24841381). Taken together, we interprete this variant as Pathogenic/Likely pathogenic. ACMG/AMP criteria applied: PS3; PM2; PM6;

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

Last Updated: May 16, 2025