IRX4

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

Basic information

Region (hg38): 5:1877412-1887236

Links

ENSG00000113430 ∙ NCBI:50805 ∙ OMIM:606199 ∙ HGNC:6129 ∙ Uniprot:P78413 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

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 provided (29 variants)
• Inborn genetic diseases (20 variants)
• Tetralogy of Fallot (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.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					5	5
missense			23		2	25
nonsense						0
start loss			1			1
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding				1	17	18
Total	0	0	24	1	24

Variants in IRX4

This is a list of pathogenic ClinVar variants found in the IRX4 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
5-1877907-G-A			Benign (Nov 12, 2018)
5-1878098-G-A			Benign (Aug 16, 2019)
5-1878123-G-A			Uncertain significance (Aug 16, 2019)
5-1878139-G-A		not specified	Uncertain significance (Jun 10, 2022)
5-1878147-T-C		not specified	Uncertain significance (Jan 26, 2022)
5-1878237-G-A		not specified	Uncertain significance (Jul 13, 2021)
5-1878251-C-A		not specified	Uncertain significance (Oct 03, 2022)
5-1878279-G-T		not specified	Uncertain significance (Sep 26, 2023)
5-1878326-C-T		See cases	Benign (Oct 17, 2018)
5-1878357-G-A		Tetralogy of Fallot	Uncertain significance (Jan 01, 2017)
5-1878385-C-A			Benign (Apr 10, 2018)
5-1878407-T-C			Benign (Jan 19, 2018)
5-1878429-C-A		not specified	Uncertain significance (Oct 16, 2023)
5-1878430-G-A		not specified	Uncertain significance (Mar 20, 2023)
5-1878438-G-A		not specified	Uncertain significance (Dec 13, 2021)
5-1878451-C-T		not specified	Uncertain significance (Nov 29, 2021)
5-1878460-C-A		not specified	Uncertain significance (Jan 23, 2024)
5-1878508-C-T		not specified	Uncertain significance (Sep 26, 2023)
5-1878537-G-A			Uncertain significance (Jan 30, 2020)
5-1878571-G-T		not specified	Uncertain significance (Jan 24, 2024)
5-1878609-G-C		not specified	Uncertain significance (Dec 27, 2022)
5-1878995-A-AT			Benign (Jun 19, 2021)
5-1878995-A-ATT			Benign (Jun 19, 2021)
5-1879114-C-T			Benign (Nov 12, 2018)
5-1879271-G-C			Benign (Nov 12, 2018)

GnomAD

Source: gnomAD

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: 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

	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