IRX4
Basic information
Region (hg38): 5:1877413-1887236
Links
Phenotypes
GenCC
Source:
- 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
- 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.
Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
---|---|---|---|---|---|---|
synonymous | 4 | |||||
missense | 87 | 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
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
IRX4 | protein_coding | protein_coding | ENST00000505790 | 5 | 9810 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.0115 | 0.981 | 125683 | 0 | 17 | 125700 | 0.0000676 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | -0.202 | 295 | 285 | 1.03 | 0.0000150 | 3201 |
Missense in Polyphen | 61 | 85.176 | 0.71616 | 974 | ||
Synonymous | -0.108 | 140 | 138 | 1.01 | 0.00000803 | 1138 |
Loss of Function | 2.34 | 6 | 16.1 | 0.372 | 6.89e-7 | 196 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000234 | 0.000234 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.000109 | 0.000109 |
Finnish | 0.0000466 | 0.0000462 |
European (Non-Finnish) | 0.0000267 | 0.0000264 |
Middle Eastern | 0.000109 | 0.000109 |
South Asian | 0.000106 | 0.0000980 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- 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
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
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