IRGC

immunity related GTPase cinema

Basic information

Region (hg38): 19:43716076-43720021

Previous symbols: [ "IRGC1" ]

Links

ENSG00000124449 ∙ NCBI:56269 ∙ ∙ HGNC:28835 ∙ Uniprot:Q6NXR0 ∙ 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 IRGC gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IRGC 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				2	2	4
missense			45	2		47
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	45	4	2

Variants in IRGC

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

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

Position	Type	Phenotype	Significance	ClinVar
19-43718577-C-T		not specified	Uncertain significance (Jun 08, 2022)
19-43718580-G-A		not specified	Uncertain significance (Jan 04, 2024)
19-43718607-A-G		not specified	Uncertain significance (Mar 23, 2023)
19-43718683-A-T		not specified	Uncertain significance (Oct 24, 2024)
19-43718707-C-G		not specified	Uncertain significance (Nov 21, 2024)
19-43718737-C-T		not specified	Uncertain significance (Feb 16, 2023)
19-43718742-G-A		not specified	Uncertain significance (Jul 14, 2024)
19-43718745-T-C		not specified	Uncertain significance (Sep 01, 2021)
19-43718806-G-C		not specified	Uncertain significance (Jul 05, 2023)
19-43718871-C-T		not specified	Uncertain significance (Dec 26, 2024)
19-43718877-G-T		not specified	Uncertain significance (Mar 07, 2024)
19-43718915-C-T			Likely benign (Sep 01, 2022)
19-43718934-C-G		not specified	Uncertain significance (Mar 15, 2024)
19-43718955-C-T		not specified	Uncertain significance (Jan 04, 2024)
19-43718959-A-G		not specified	Uncertain significance (Jun 30, 2024)
19-43718979-T-G		not specified	Uncertain significance (Jan 26, 2022)
19-43718985-C-T		not specified	Uncertain significance (Oct 18, 2021)
19-43718989-G-A		not specified	Uncertain significance (Feb 17, 2023)
19-43719000-G-A		not specified	Uncertain significance (Nov 09, 2021)
19-43719007-C-T		not specified	Uncertain significance (Apr 18, 2024)
19-43719010-G-A		not specified	Uncertain significance (Sep 27, 2024)
19-43719013-T-C		not specified	Uncertain significance (Nov 10, 2024)
19-43719082-C-T		not specified	Uncertain significance (Dec 04, 2024)
19-43719100-G-A		not specified	Uncertain significance (Mar 11, 2022)
19-43719119-G-A			Benign (Mar 30, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IRGC	protein_coding	protein_coding	ENST00000244314	1	4012

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0473	0.931	125597	0	12	125609	0.0000478

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.14	268	326	0.822	0.0000234	2928
Missense in Polyphen		117	149.44	0.78291		1309
Synonymous	-1.22	179	159	1.12	0.0000127	1036
Loss of Function	2.00	4	11.2	0.357	5.65e-7	120

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000551	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000628	0.0000616
Middle Eastern	0.0000551	0.0000544
South Asian	0.0000988	0.0000980
Other	0.000167	0.000163

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.472
• rvis_EVS: -0.11
• rvis_percentile_EVS: 45.49

Haploinsufficiency Scores

• pHI: 0.156
• hipred: N
• hipred_score: 0.272
• ghis: 0.404

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.303

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Irgc1

Gene ontology

• Cellular component: membrane
• Molecular function: GTPase activity;GTP binding