IRX1

iroquois homeobox 1, the group of TALE class homeoboxes and pseudogenes

Basic information

Region (hg38): 5:3595831-3601403

Links

ENSG00000170549 ∙ NCBI:79192 ∙ OMIM:606197 ∙ HGNC:14358 ∙ Uniprot:P78414 ∙ 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 IRX1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IRX1 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				7	5	12
missense			36		1	37
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	36	7	6

Variants in IRX1

This is a list of pathogenic ClinVar variants found in the IRX1 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-3596145-G-C		not specified	Uncertain significance (Jan 04, 2024)
5-3596147-C-G			Likely benign (Jul 01, 2023)
5-3596149-C-T		not specified	Uncertain significance (Jun 19, 2024)
5-3596154-C-T		not specified	Uncertain significance (Dec 27, 2023)
5-3596197-C-T		not specified	Uncertain significance (Aug 12, 2021)
5-3596199-G-T		not specified	Uncertain significance (May 02, 2023)
5-3596201-T-G			Likely benign (Jun 01, 2023)
5-3596208-G-T		not specified	Uncertain significance (Apr 25, 2023)
5-3596294-G-A			Uncertain significance (Jul 01, 2023)
5-3596312-G-A			Likely benign (Apr 10, 2018)
5-3596316-G-C		not specified	Uncertain significance (Jul 20, 2022)
5-3596319-G-C		not specified	Uncertain significance (Jun 22, 2021)
5-3596323-C-T		not specified	Uncertain significance (Apr 08, 2023)
5-3596372-C-A		not specified	Uncertain significance (Oct 27, 2021)
5-3596380-T-C		not specified	Uncertain significance (Aug 16, 2022)
5-3599266-C-T		IRX1-related disorder	Benign (Mar 14, 2019)
5-3599304-C-T		not specified	Uncertain significance (May 16, 2023)
5-3599452-G-T		not specified	Uncertain significance (Jan 10, 2023)
5-3599532-C-T		not specified	Uncertain significance (May 30, 2023)
5-3599686-G-A		IRX1-related disorder	Likely benign (Mar 25, 2019)
5-3599703-C-T		not specified	Uncertain significance (Dec 15, 2023)
5-3599709-C-T		not specified	Uncertain significance (Dec 21, 2022)
5-3599712-C-T		not specified	Uncertain significance (Aug 17, 2022)
5-3599714-G-C		not specified	Uncertain significance (Dec 11, 2023)
5-3599718-C-A		not specified	Uncertain significance (Dec 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IRX1	protein_coding	protein_coding	ENST00000302006	4	5350

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000476	0.884	125728	0	13	125741	0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.593	266	240	1.11	0.0000122	3003
Missense in Polyphen		90	96.73	0.93043		1076
Synonymous	-3.62	161	112	1.43	0.00000620	1051
Loss of Function	1.40	7	12.3	0.569	5.31e-7	156

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000162	0.000149
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000447	0.0000440
Middle Eastern	0.000109	0.000109
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.122

Haploinsufficiency Scores

• pHI: 0.284
• hipred: Y
• hipred_score: 0.543
• ghis: 0.494

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.631

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Irx1
• Phenotype: growth/size/body region phenotype; homeostasis/metabolism phenotype; craniofacial 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); respiratory system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); skeleton phenotype

Zebrafish Information Network

• Gene name: irx1a
• Affected structure: retinal bipolar neuron
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

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