IRX2

iroquois homeobox 2, the group of TALE class homeoboxes and pseudogenes

Basic information

Region (hg38): 5:2745844-2751677

Links

ENSG00000170561 ∙ NCBI:153572 ∙ OMIM:606198 ∙ HGNC:14359 ∙ Uniprot:Q9BZI1 ∙ 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 IRX2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IRX2 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				1	2	3
missense			33	3		36
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	33	4	2

Variants in IRX2

This is a list of pathogenic ClinVar variants found in the IRX2 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-2748372-G-T		not specified	Uncertain significance (Feb 27, 2023)
5-2748377-C-G		not specified	Uncertain significance (Dec 06, 2022)
5-2748395-G-A		not specified	Uncertain significance (May 17, 2023)
5-2748485-A-G		not specified	Uncertain significance (Nov 03, 2023)
5-2748497-C-T		not specified	Uncertain significance (Dec 15, 2022)
5-2748572-C-T		not specified	Uncertain significance (Sep 15, 2021)
5-2748591-G-T		not specified	Uncertain significance (May 15, 2023)
5-2748611-G-A		not specified	Uncertain significance (Mar 31, 2023)
5-2748618-C-G		not specified	Uncertain significance (Oct 06, 2023)
5-2748626-G-T		not specified	Uncertain significance (Jan 19, 2022)
5-2748651-C-A		not specified	Uncertain significance (Aug 08, 2023)
5-2748659-C-G		not specified	Uncertain significance (Apr 07, 2023)
5-2748733-G-C		not specified	Uncertain significance (Nov 20, 2023)
5-2748743-G-T		not specified	Uncertain significance (Apr 07, 2023)
5-2748770-C-T		not specified	Uncertain significance (Oct 06, 2023)
5-2748773-T-A		not specified	Likely benign (Apr 07, 2023)
5-2748792-C-G		not specified	Uncertain significance (Jan 26, 2022)
5-2748837-A-C		not specified	Likely benign (Apr 07, 2023)
5-2748872-G-A		not specified	Uncertain significance (Jun 05, 2024)
5-2748873-G-A		not specified	Uncertain significance (Apr 17, 2024)
5-2748881-C-T		not specified	Likely benign (Apr 07, 2023)
5-2748888-C-T		not specified	Uncertain significance (Sep 16, 2021)
5-2748895-C-G		not specified	Uncertain significance (Apr 07, 2023)
5-2748915-C-T		not specified	Uncertain significance (Apr 26, 2023)
5-2748966-G-A		not specified	Uncertain significance (May 09, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IRX2	protein_coding	protein_coding	ENST00000382611	4	7011

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0218	0.964	125697	0	8	125705	0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.557	221	246	0.900	0.0000163	2927
Missense in Polyphen		74	101.14	0.73164		1195
Synonymous	-1.18	154	136	1.13	0.0000116	1011
Loss of Function	2.14	5	13.5	0.371	5.80e-7	195

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000116	0.000116
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000391	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.152

Haploinsufficiency Scores

• pHI: 0.534
• hipred: Y
• hipred_score: 0.641
• ghis: 0.535

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.370

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Irx2
• Phenotype: normal phenotype

Zebrafish Information Network

• Gene name: irx2a
• Affected structure: whole organism
• Phenotype tag: abnormal
• Phenotype quality: lacks all parts of type

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;specification of loop of Henle identity;proximal/distal pattern formation involved in metanephric nephron development
• Cellular component: nucleus
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription repressor activity, RNA polymerase II-specific;sequence-specific DNA binding