IRX4

iroquois homeobox 4, the group of TALE class homeoboxes and pseudogenes

Basic information

Region (hg38): 5:1877413-1887236

Links

ENSG00000113430NCBI:50805OMIM:606199HGNC:6129Uniprot:P78413AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • ventricular septal defect 1 (Limited), mode of inheritance: AD
  • congenital heart disease (Limited), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the IRX4 gene.

  • not_specified (86 variants)
  • not_provided (8 variants)
  • Ventricular_septal_defect_1 (2 variants)
  • Tetralogy_of_Fallot (1 variants)
  • See_cases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IRX4 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000016358.3. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
1
clinvar
1
clinvar
2
clinvar
4
missense
2
clinvar
87
clinvar
1
clinvar
1
clinvar
91
nonsense
0
start loss
1
1
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 3 0 89 1 3

Highest pathogenic variant AF is 0.00000821795

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
IRX4protein_codingprotein_codingENST00000505790 59810
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.01150.9811256830171257000.0000676
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.2022952851.030.00001503201
Missense in Polyphen6185.1760.71616974
Synonymous-0.1081401381.010.000008031138
Loss of Function2.34616.10.3726.89e-7196

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0002340.000234
Ashkenazi Jewish0.000.00
East Asian0.0001090.000109
Finnish0.00004660.0000462
European (Non-Finnish)0.00002670.0000264
Middle Eastern0.0001090.000109
South Asian0.0001060.0000980
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Likely to be an important mediator of ventricular differentiation during cardiac development.;
Pathway
Heart Development;Cardiac Progenitor Differentiation (Consensus)

Recessive Scores

pRec
0.119

Haploinsufficiency Scores

pHI
0.686
hipred
Y
hipred_score
0.559
ghis
0.493

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.790

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Irx4
Phenotype
muscle phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan);

Zebrafish Information Network

Gene name
irx4a
Affected structure
presumptive cardiac ventricle heart tube
Phenotype tag
abnormal
Phenotype quality
decreased size

Gene ontology

Biological process
regulation of transcription by RNA polymerase II;heart development;establishment of animal organ orientation
Cellular component
nucleus
Molecular function
DNA-binding transcription factor activity, RNA polymerase II-specific;sequence-specific DNA binding