IRX6

iroquois homeobox 6, the group of TALE class homeoboxes and pseudogenes

Basic information

Region (hg38): 16:55324203-55330756

Previous symbols: [ "IRX7" ]

Links

ENSG00000159387 ∙ NCBI:79190 ∙ OMIM:606196 ∙ HGNC:14675 ∙ Uniprot:P78412 ∙ 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 IRX6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IRX6 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						0
missense			47	1		48
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	47	1	0

Variants in IRX6

This is a list of pathogenic ClinVar variants found in the IRX6 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-55325105-A-G		not specified	Uncertain significance (Nov 30, 2022)
16-55325114-A-G		not specified	Uncertain significance (Jun 03, 2022)
16-55325117-C-G		not specified	Uncertain significance (Oct 30, 2023)
16-55325132-C-G		not specified	Uncertain significance (Dec 28, 2023)
16-55326370-G-T		not specified	Uncertain significance (Aug 29, 2022)
16-55326384-C-T		not specified	Uncertain significance (Jun 24, 2022)
16-55326421-C-A		not specified	Uncertain significance (Feb 16, 2023)
16-55326438-G-A		not specified	Uncertain significance (Aug 26, 2022)
16-55326462-G-A		not specified	Uncertain significance (Sep 14, 2022)
16-55326467-T-A		not specified	Uncertain significance (Dec 19, 2023)
16-55326495-G-A		not specified	Uncertain significance (Feb 11, 2022)
16-55326496-G-A		not specified	Uncertain significance (Dec 13, 2023)
16-55326517-C-A		not specified	Uncertain significance (Aug 27, 2024)
16-55326563-C-G		not specified	Uncertain significance (Dec 07, 2021)
16-55326573-C-T		not specified	Uncertain significance (Dec 19, 2022)
16-55327359-G-A		not specified	Uncertain significance (Oct 05, 2023)
16-55327387-G-A		not specified	Uncertain significance (Jan 04, 2024)
16-55327397-A-T		not specified	Uncertain significance (Jul 27, 2022)
16-55327401-G-A		not specified	Uncertain significance (Jan 22, 2024)
16-55327597-T-C		not specified	Uncertain significance (Aug 20, 2024)
16-55327600-A-T		not specified	Uncertain significance (Oct 13, 2023)
16-55327611-G-T		not specified	Uncertain significance (Dec 28, 2023)
16-55327614-G-A		not specified	Uncertain significance (Dec 16, 2023)
16-55327621-G-C		not specified	Uncertain significance (May 23, 2023)
16-55327630-C-T		not specified	Uncertain significance (Oct 04, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IRX6	protein_coding	protein_coding	ENST00000290552	6	7001

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.50e-12	0.0717	125668	1	79	125748	0.000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.85	345	261	1.32	0.0000139	2806
Missense in Polyphen		101	79.57	1.2693		824
Synonymous	-1.91	138	112	1.23	0.00000627	971
Loss of Function	0.393	19	20.9	0.907	0.00000106	220

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000449	0.000448
Ashkenazi Jewish	0.00	0.00
East Asian	0.000328	0.000326
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000410	0.000404
Middle Eastern	0.000328	0.000326
South Asian	0.000463	0.000425
Other	0.000327	0.000326

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0959

Intolerance Scores

• loftool: 0.164
• rvis_EVS: -0.75
• rvis_percentile_EVS: 13.58

Haploinsufficiency Scores

• pHI: 0.173
• hipred: N
• hipred_score: 0.207
• ghis: 0.487

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.161

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Irx6
• Phenotype: nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); vision/eye phenotype

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II
• Cellular component: nucleus
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;sequence-specific DNA binding