GeneBe

GATA5

protein-coding

GATA binding protein 5, the group of GATA zinc finger domain containing

Gene summary

The protein encoded by this gene is a transcription factor that contains two GATA-type zinc fingers. The encoded protein is known to bind to hepatocyte nuclear factor-1alpha (HNF-1alpha), and this interaction is essential for cooperative activation of the intestinal lactase-phlorizin hydrolase promoter. In other organisms, similar proteins may be involved in the establishment of cardiac smooth muscle cell diversity. [provided by RefSeq, Jul 2008]

MANE transcript

NM_080473.5

Inheritance

AD, AR

ClinVar variants

P:6U:329B:181

Top phenotype

Congenital heart defects, multiple types, 5

gnomAD constraint

pLI —, LoF o/e 0.24

Max pathogenic AF

—

Genomic locus

chr20:62,463,497-62,475,995

External References & Databases

Ensembl (ENSG00000130700)NCBI Gene (140628)OMIM (611496)HGNC:15802GenCCUniProt (Q9BWX5)AlphaFoldClinVar (GATA5)gnomADPubMedJAXSFARI

Transcript & Mutation Effects

hg38 • Region Span ~12.5 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

congenital heart defects, multiple types, 5LIMITED

Inheritance Pattern: Unknown

Disease ID:MONDO:0060663

Submitter: Labcorp Genetics (formerly Invitae)

congenital heart defects, multiple types, 5LIMITED

Inheritance Pattern: AD

Disease ID:MONDO:0060663

Submitter: Ambry Genetics

tetralogy of fallotSUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0008542

Submitter: Orphanet

familial bicuspid aortic valveSUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0007194

Submitter: Orphanet

congenital heart defects, multiple types, 5MODERATE

Inheritance Pattern: AD

Disease ID:MONDO:0060663

Submitter: PanelApp Australia

familial atrial fibrillationSUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0018054

Submitter: Orphanet

congenital heart defects, multiple types, 5MODERATE

Inheritance Pattern: AR

Disease ID:MONDO:0060663

Submitter: PanelApp Australia

Clinical Genomic Database (CGD)

Congenital heart defects, multiple types, 5AD

Manifestation: Cardiovascular

Intervention: Cardiovascular

Rationale: Individuals have been described with findins including arrhythmias (atrial fibrillation), and awareness may allow prompt diagnosis and management

Comments: Bi-allelic variants have also been described

Refs: 22483626; 22961344; 23031282; 23175127; 23295592; 25543888; 27066509; 28180938Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to GATA5 variants in ClinVar

8 Conditions Cataloged
not providedTotal: 577
not specifiedTotal: 114
GATA5-related disorderTotal: 30
Congenital heart defects, multiple types, 5Total: 25
Congenital heart defects, multiple typesTotal: 3
Inborn genetic diseasesTotal: 2
Congenital heart diseaseTotal: 1
Congenital anomaly of kidney and urinary tractTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_080473.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
3
clinvar
156
clinvar
 159
missense
4
clinvar
1
clinvar
310
clinvar
25
clinvar
 340
nonsense
4
clinvar
 4
start loss
1
clinvar
 1
frameshift
9
clinvar
 9
splice donor/acceptor (+/-2bp)
1
clinvar
2
clinvar
 3
Total423291810516

Highest pathogenic variant AF is 0.000037457205

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 14 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_080473.5RefSeqNP_536721.16MANE Select
ENST00000252997.3EnsemblENSP00000252997.26MANE Select
ENST00000861188.1EnsemblENSP00000531247.16Standard
ENST00000861189.1EnsemblENSP00000531248.16Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / ModelOrganismObserved Phenotype
gata5Danio rerio

Structure: anatomical system

Quality: quality

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

  • Factors involved in megakaryocyte development and platelet production
  • Hemostasis

Biological Process

  • aortic valve morphogenesis
  • endocardial cushion fusion
  • blood coagulation
  • negative regulation of cardiac muscle hypertrophy
  • positive regulation of gene expression

Molecular Function

  • RNA polymerase II proximal promoter sequence-specific DNA binding
  • DNA-binding transcription factor activity, RNA polymerase II-specific
  • DNA-binding transcription factor activity
  • zinc ion binding
  • transcription regulatory region DNA binding

Cellular Component

  • nuclear chromatin
  • nucleus
  • nucleoplasm

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000252997
Coding exons
6
Length
12474
Individuals with no LoFs
125365
Homozygous LoFs
0
Heterozygous LoFs
10
Defined
125375
p
0.0000399
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense1.071461870.7800.00001232433
Missense (PolyPhen)5986.8210.67956955
Synonymous-0.02698584.71.000.00000600844
Loss of Function2.46312.30.2436.15e-7154

Population LoF Frequency

PopulationCAFp-valueStatus
African00.0absent
Latino/Admixed American0.0000310.000029rare
Ashkenazi Jewish00.0absent
East Asian0.000120.00011rare
Finnish00.0absent
European (Non-Finnish)0.0000480.000044rare
South Asian0.0000700.000065rare
Other00.0absent

dbNSFP Gene Annotations

Source: dbNSFP

Function
FUNCTION: Transcription factor required during cardiovascular development (PubMed:23289003). Plays an important role in the transcriptional program(s) that underlies smooth muscle cell diversity (By similarity). Binds to the functionally important CEF-1 nuclear protein binding site in the cardiac-specific slow/cardiac troponin C transcriptional enhancer (PubMed:25543888). {ECO:0000250|UniProtKB:P97489, ECO:0000269|PubMed:23289003, ECO:0000269|PubMed:25543888}.;
Disease
DISEASE: Congenital heart defects, multiple types, 5 (CHTD5) [MIM:617912]: A disorder characterized by congenital developmental abnormalities involving structures of the heart. Common defects include transposition of the great arteries, aortic stenosis, atrial septal defect, ventricular septal defect, pulmonic stenosis, patent ductus arteriosus, and tetralogy of Fallot. Some patients also have cardiac arrhythmias, which may be due to the anatomic defect itself or to surgical interventions. CHTD5 inheritance can be autosomal dominant or recessive. {ECO:0000269|PubMed:22483626, ECO:0000269|PubMed:22641149, ECO:0000269|PubMed:22961344, ECO:0000269|PubMed:23031282, ECO:0000269|PubMed:23175127, ECO:0000269|PubMed:23289003, ECO:0000269|PubMed:23295592, ECO:0000269|PubMed:24573614, ECO:0000269|PubMed:24638895, ECO:0000269|PubMed:25543888}. Note=The disease is caused by mutations affecting the gene represented in this entry.;

Recessive Scores

pRec
0.303

Essentials

Essential (CRISPR)
N
Essential (CRISPR2)
N
Essential (gene trap)
N
Indispensability pred.
E
Indispensability score
0.625

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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