IRX3

iroquois homeobox 3, the group of TALE class homeoboxes and pseudogenes

Basic information

Region (hg38): 16:54283304-54286787

Links

ENSG00000177508 ∙ NCBI:79191 ∙ OMIM:612985 ∙ HGNC:14360 ∙ Uniprot:P78415 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the IRX3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IRX3 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				2	2	4
missense			25			25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	25	2	2

Variants in IRX3

This is a list of pathogenic ClinVar variants found in the IRX3 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-54284303-C-G		not specified	Uncertain significance (Feb 27, 2024)
16-54284546-C-T			Likely benign (May 18, 2018)
16-54284559-G-A		not specified	Uncertain significance (Jun 28, 2022)
16-54284587-G-A		not specified	Uncertain significance (Mar 18, 2024)
16-54284634-G-A		not specified	Uncertain significance (Jul 06, 2021)
16-54284681-C-T			Likely benign (Jun 01, 2018)
16-54284692-G-C		not specified	Uncertain significance (Oct 05, 2022)
16-54284745-G-A		not specified	Uncertain significance (Jun 18, 2021)
16-54284760-G-A		not specified	Uncertain significance (Jun 07, 2023)
16-54284769-C-A		not specified	Uncertain significance (Sep 27, 2021)
16-54284798-G-C		not specified	Uncertain significance (Nov 23, 2021)
16-54284805-G-C		not specified	Uncertain significance (Nov 22, 2024)
16-54284851-G-T		not specified	Uncertain significance (Aug 09, 2021)
16-54284865-G-T		not specified	Uncertain significance (Feb 28, 2024)
16-54284878-C-A		not specified	Uncertain significance (Jun 28, 2022)
16-54284898-G-T		not specified	Uncertain significance (Jun 28, 2023)
16-54284926-C-T		not specified	Uncertain significance (Jul 06, 2021)
16-54285072-A-T		not specified	Uncertain significance (May 30, 2023)
16-54285096-G-A		not specified	Uncertain significance (Oct 03, 2022)
16-54285185-C-G		not specified	Uncertain significance (Dec 02, 2024)
16-54285217-C-G		not specified	Uncertain significance (Jan 25, 2023)
16-54285292-T-A		not specified	Uncertain significance (Mar 21, 2024)
16-54285408-C-G		not specified	Uncertain significance (Nov 10, 2024)
16-54285409-C-T		not specified	Uncertain significance (Jan 04, 2024)
16-54285422-G-T			Benign (Dec 31, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IRX3	protein_coding	protein_coding	ENST00000329734	4	3460

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.892	0.108	125700	0	3	125703	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.581	191	215	0.889	0.00000987	3033
Missense in Polyphen		50	60.242	0.82999		738
Synonymous	-1.06	115	101	1.13	0.00000504	1089
Loss of Function	2.88	1	11.6	0.0862	4.95e-7	170

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000886	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.0000665	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcription factor. Involved in SHH-dependent neural patterning. Together with NKX2-2 and NKX6-1 acts to restrict the generation of motor neurons to the appropriate region of the neural tube. Belongs to the class I proteins of neuronal progenitor factors, which are repressed by SHH signals. Involved in the transcriptional repression of MNX1 in non-motor neuron cells (By similarity). {ECO:0000250}.
• Pathway: FTO Obesity Variant Mechanism (Consensus)

Recessive Scores

• pRec: 0.144

Haploinsufficiency Scores

• pHI: 0.782
• ghis: 0.457

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.467

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Irx3
• Phenotype: growth/size/body region phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); homeostasis/metabolism phenotype; liver/biliary system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); 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: irx3a
• Affected structure: pancreatic bud
• Phenotype tag: abnormal
• Phenotype quality: has fewer parts of type

Gene ontology

• Biological process: metanephros development;regulation of transcription by RNA polymerase II;mesoderm development;negative regulation of neuron differentiation;positive regulation of neuron differentiation;specification of loop of Henle identity;energy homeostasis
• Cellular component: nucleus;cytoplasm;axon
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;sequence-specific DNA binding