IRAG1

inositol 1,4,5-triphosphate receptor associated 1

Basic information

Region (hg38): 11:10573091-10693988

Previous symbols: [ "MRVI1" ]

Links

ENSG00000072952 ∙ NCBI:10335 ∙ OMIM:604673 ∙ HGNC:7237 ∙ Uniprot:Q9Y6F6 ∙ 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 IRAG1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IRAG1 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		1
missense			53	6	4	63
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	53	7	5

Variants in IRAG1

This is a list of pathogenic ClinVar variants found in the IRAG1 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-10576447-T-A		not specified	Uncertain significance (Mar 11, 2024)
11-10576471-A-G		not specified	Uncertain significance (Jul 31, 2023)
11-10576526-A-G		not specified	Uncertain significance (Apr 11, 2023)
11-10576532-T-G		not specified	Uncertain significance (Apr 08, 2024)
11-10580521-C-T		not specified	Uncertain significance (Jun 13, 2023)
11-10580578-C-T		not specified	Uncertain significance (Mar 04, 2024)
11-10581910-G-T		not specified	Uncertain significance (Mar 07, 2024)
11-10591596-C-T		not specified	Uncertain significance (Sep 27, 2021)
11-10591611-G-A		not specified	Uncertain significance (Nov 08, 2022)
11-10593593-G-A		not specified	Uncertain significance (Nov 30, 2021)
11-10594180-C-A		not specified	Uncertain significance (Oct 04, 2022)
11-10594180-C-T		not specified	Uncertain significance (Jul 13, 2021)
11-10600936-G-A		not specified	Uncertain significance (Apr 27, 2024)
11-10600951-T-G		not specified	Uncertain significance (Aug 12, 2021)
11-10600980-G-A		not specified	Uncertain significance (Dec 06, 2021)
11-10601052-C-A		not specified	Uncertain significance (Aug 14, 2023)
11-10603124-C-T		not specified	Uncertain significance (May 02, 2024)
11-10603161-G-A		not specified	Uncertain significance (Jun 06, 2023)
11-10603191-C-T		not specified	Uncertain significance (Dec 14, 2021)
11-10603217-C-T		not specified	Uncertain significance (Jan 04, 2024)
11-10604406-G-A		not specified	Uncertain significance (Oct 14, 2023)
11-10604452-C-T		not specified	Uncertain significance (Dec 26, 2023)
11-10606732-A-C			Benign (Jul 23, 2018)
11-10606759-T-C		not specified	Uncertain significance (Dec 07, 2021)
11-10609741-T-G		not specified	Uncertain significance (Dec 14, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IRAG1	protein_coding	protein_coding	ENST00000423302	21	120898

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.26e-7	1.00	125444	0	47	125491	0.000187

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.451	477	506	0.944	0.0000290	5833
Missense in Polyphen		182	197.16	0.92309		2284
Synonymous	1.34	179	203	0.880	0.0000121	1851
Loss of Function	3.53	19	44.4	0.428	0.00000220	551

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000873	0.000845
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000576	0.0000544
Finnish	0.000140	0.000139
European (Non-Finnish)	0.000157	0.000150
Middle Eastern	0.0000576	0.0000544
South Asian	0.000131	0.000131
Other	0.000336	0.000327

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role as NO/PRKG1-dependent regulator of IP3- induced calcium release; its phosphorylation by PRKG1 inhibits bradykinin and IP3-induced calcium release from intracellular stores. Recruits PRKG1 to the endoplasmic reticulum and may mediate the assembly of PRKG1 and ITPR1 in a macrocomplex. Involved in PRKG1 signaling cascade leading to inhibition of platelet activation and aggregation. Mediates also NO-dependent inhibition of calcium signaling in gastrointestinal smooth muscle contributing to NO-dependent relaxation. {ECO:0000269|PubMed:14729908}.
• Pathway: Vascular smooth muscle contraction - Homo sapiens (human);cGMP-PKG signaling pathway - Homo sapiens (human);Hemostasis;cGMP effects;Nitric oxide stimulates guanylate cyclase;Platelet homeostasis (Consensus)

Recessive Scores

• pRec: 0.110

Intolerance Scores

• rvis_EVS: 2.07
• rvis_percentile_EVS: 97.82

Haploinsufficiency Scores

• pHI: 0.265
• hipred: N
• hipred_score: 0.426
• ghis: 0.416

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.479

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mrvi1
• Phenotype: muscle phenotype; digestive/alimentary 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)

Gene ontology

• Cellular component: endoplasmic reticulum membrane;integral component of membrane;sarcoplasmic reticulum;platelet dense tubular network membrane;perinuclear region of cytoplasm
• Molecular function: protein binding