IRAG2

inositol 1,4,5-triphosphate receptor associated 2

Basic information

Region (hg38): 12:25004341-25108335

Previous symbols: [ "LRMP" ]

Links

ENSG00000118308 ∙ NCBI:4033 ∙ OMIM:602003 ∙ HGNC:6690 ∙ Uniprot:Q12912 ∙ 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 IRAG2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IRAG2 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			20	1		21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	20	1	0

Variants in IRAG2

This is a list of pathogenic ClinVar variants found in the IRAG2 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-25069423-A-C		not specified	Uncertain significance (Feb 16, 2023)
12-25079245-A-G		not specified	Uncertain significance (Apr 04, 2023)
12-25079450-A-G		not specified	Likely benign (Apr 08, 2024)
12-25079674-T-A		not specified	Uncertain significance (Oct 29, 2021)
12-25079707-C-T		not specified	Uncertain significance (Jun 11, 2021)
12-25079751-A-T		not specified	Uncertain significance (Feb 06, 2024)
12-25083434-G-C		not specified	Uncertain significance (Sep 22, 2023)
12-25083471-A-C		not specified	Uncertain significance (May 21, 2024)
12-25083482-A-G		not specified	Uncertain significance (Aug 17, 2022)
12-25097018-G-A		not specified	Uncertain significance (Apr 08, 2024)
12-25097039-A-G		not specified	Uncertain significance (Mar 28, 2024)
12-25101182-G-A		not specified	Uncertain significance (Jul 13, 2022)
12-25101185-G-A		not specified	Uncertain significance (Dec 28, 2022)
12-25101230-T-C		not specified	Uncertain significance (Jun 06, 2023)
12-25101233-A-G		not specified	Uncertain significance (Jan 16, 2024)
12-25101311-C-T		not specified	Uncertain significance (Jun 21, 2023)
12-25103843-T-C		not specified	Uncertain significance (Dec 19, 2022)
12-25103850-G-A		not specified	Uncertain significance (May 23, 2024)
12-25104031-A-G		not specified	Uncertain significance (May 03, 2023)
12-25104363-G-A		not specified	Uncertain significance (Jan 30, 2024)
12-25107893-A-G		not specified	Likely benign (Feb 22, 2023)
12-25107954-A-G		not specified	Uncertain significance (Feb 16, 2023)
12-25107968-G-A		not specified	Uncertain significance (Aug 21, 2023)
12-25107981-A-G		not specified	Uncertain significance (Sep 26, 2022)
12-25108050-C-T		not specified	Uncertain significance (Jan 25, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IRAG2	protein_coding	protein_coding	ENST00000354454	17	87333

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.43e-10	0.955	125693	0	54	125747	0.000215

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.782	228	264	0.865	0.0000135	3267
Missense in Polyphen		85	97.835	0.86881		1264
Synonymous	-0.823	105	94.8	1.11	0.00000502	920
Loss of Function	2.07	20	32.8	0.609	0.00000172	403

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000544	0.000543
Ashkenazi Jewish	0.00	0.00
East Asian	0.000711	0.000707
Finnish	0.0000934	0.0000924
European (Non-Finnish)	0.000141	0.000141
Middle Eastern	0.000711	0.000707
South Asian	0.000237	0.000229
Other	0.000181	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in the delivery of peptides to major histocompatibility complex (MHC) class I molecules; this occurs in a transporter associated with antigen processing (TAP)-independent manner. May play a role in taste signal transduction via ITPR3. May play a role during fertilization in pronucleus congression and fusion.
• Pathway: Neutrophil degranulation;Innate Immune System;Immune System (Consensus)

Recessive Scores

• pRec: 0.0971

Intolerance Scores

• loftool: 0.713
• rvis_EVS: 0.26
• rvis_percentile_EVS: 70.52

Haploinsufficiency Scores

• pHI: 0.375
• hipred: N
• hipred_score: 0.280
• ghis: 0.477

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.486

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lrmp

Zebrafish Information Network

• Gene name: lrmp
• Affected structure: blastomere
• Phenotype tag: abnormal
• Phenotype quality: detached from

Gene ontology

• Biological process: vesicle targeting;vesicle fusion;single fertilization;neutrophil degranulation
• Cellular component: spindle pole;nuclear envelope;chromosome;endoplasmic reticulum membrane;microtubule organizing center;plasma membrane;integral component of plasma membrane;membrane;integral component of membrane;azurophil granule membrane