IFI30

IFI30 lysosomal thiol reductase

Basic information

Region (hg38): 19:18173162-18178117

Links

ENSG00000216490 ∙ NCBI:10437 ∙ OMIM:604664 ∙ HGNC:5398 ∙ Uniprot:P13284 ∙ 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 IFI30 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IFI30 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			11	1	1	13
nonsense						0
start loss						0
frameshift				1		1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	11	2	1

Variants in IFI30

This is a list of pathogenic ClinVar variants found in the IFI30 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-18173891-TG-T			Likely benign (Mar 01, 2023)
19-18173940-C-G		not specified	Uncertain significance (Jan 30, 2024)
19-18175041-C-A		not specified	Uncertain significance (Jan 10, 2023)
19-18175086-C-T			Benign (Jun 01, 2022)
19-18175192-T-G		not specified	Uncertain significance (Nov 10, 2024)
19-18175211-G-A		not specified	Uncertain significance (Mar 02, 2023)
19-18175320-G-A		not specified	Uncertain significance (Jul 16, 2024)
19-18175326-G-A		not specified	Uncertain significance (Aug 10, 2023)
19-18175375-A-G		not specified	Uncertain significance (Aug 16, 2021)
19-18175604-G-A			Uncertain significance (Sep 16, 2018)
19-18175639-C-G		not specified	Uncertain significance (Sep 04, 2024)
19-18175650-A-G		not specified	Uncertain significance (Jun 16, 2024)
19-18175651-T-C		not specified	Uncertain significance (Jul 15, 2024)
19-18175667-G-C		not specified	Uncertain significance (Mar 08, 2024)
19-18175677-A-T		not specified	Uncertain significance (Oct 29, 2021)
19-18177196-G-A		not specified	Uncertain significance (May 26, 2024)
19-18177206-G-A		not specified	Uncertain significance (Mar 07, 2023)
19-18177228-A-C		not specified	Uncertain significance (Apr 05, 2023)
19-18177236-C-T		not specified	Uncertain significance (May 26, 2024)
19-18177738-C-T		not specified	Uncertain significance (Jan 10, 2023)
19-18177849-G-A		not specified	Uncertain significance (Sep 24, 2024)
19-18177868-G-C		not specified	Uncertain significance (Aug 19, 2024)
19-18177882-A-T			Likely benign (Sep 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IFI30	protein_coding	protein_coding	ENST00000407280	7	4956

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.96e-8	0.175	124590	0	28	124618	0.000112

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.630	112	132	0.846	0.00000709	1566
Missense in Polyphen		41	48.9	0.83845		571
Synonymous	-0.276	61	58.3	1.05	0.00000362	485
Loss of Function	0.203	12	12.8	0.939	5.97e-7	139

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000264	0.000255
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000667	0.0000556
Finnish	0.0000941	0.0000928
European (Non-Finnish)	0.000140	0.000133
Middle Eastern	0.0000667	0.0000556
South Asian	0.0000656	0.0000654
Other	0.000173	0.000165

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Lysosomal thiol reductase that can reduce protein disulfide bonds. May facilitate the complete unfolding of proteins destined for lysosomal degradation. Plays an important role in antigen processing. Facilitates the generation of MHC class II- restricted epitodes from disulfide bond-containing antigen by the endocytic reduction of disulfide bonds (By similarity). Facilitates also MHC class I-restricted recognition of exogenous antigens containing disulfide bonds by CD8+ T-cells or crosspresentation (By similarity). {ECO:0000250}.
• Pathway: Antigen processing and presentation - Homo sapiens (human);Cytokine Signaling in Immune system;MHC class II antigen presentation;Immune System;Adaptive Immune System;Interferon gamma signaling;Interferon Signaling (Consensus)

Intolerance Scores

• loftool: 0.555
• rvis_EVS: -0.09
• rvis_percentile_EVS: 46.74

Haploinsufficiency Scores

• pHI: 0.376
• hipred: N
• hipred_score: 0.153
• ghis: 0.545

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.190

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ifi30
• Phenotype: immune system phenotype

Gene ontology

• Biological process: antigen processing and presentation of exogenous peptide antigen via MHC class II;antigen processing and presentation of exogenous peptide antigen via MHC class I;oxidation-reduction process;interferon-gamma-mediated signaling pathway
• Cellular component: extracellular region;lysosome;cytosol;cell junction;lysosomal lumen;intracellular membrane-bounded organelle
• Molecular function: protein binding;oxidoreductase activity, acting on a sulfur group of donors