ISG20

interferon stimulated exonuclease gene 20, the group of Exonucleases

Basic information

Region (hg38): 15:88635670-88656483

Links

ENSG00000172183 ∙ NCBI:3669 ∙ OMIM:604533 ∙ HGNC:6130 ∙ Uniprot:Q96AZ6 ∙ 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 ISG20 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ISG20 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	4	6
missense			19		1	20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	2	5

Variants in ISG20

This is a list of pathogenic ClinVar variants found in the ISG20 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-88639379-C-T		not specified	Uncertain significance (Dec 11, 2023)
15-88639394-A-G		not specified	Uncertain significance (Dec 07, 2023)
15-88639403-G-A		not specified	Uncertain significance (Mar 20, 2023)
15-88639427-C-T		not specified	Uncertain significance (May 26, 2023)
15-88639456-C-T			Likely benign (May 15, 2018)
15-88639457-G-A		not specified	Uncertain significance (Jul 19, 2022)
15-88639462-C-T			Benign (Aug 15, 2018)
15-88639470-G-T		not specified	Uncertain significance (Aug 04, 2024)
15-88639493-A-C		not specified	Uncertain significance (Oct 17, 2024)
15-88639495-C-T			Benign (Aug 05, 2018)
15-88639496-C-T		not specified	Uncertain significance (Jul 12, 2023)
15-88639520-T-C		not specified	Uncertain significance (Jun 05, 2023)
15-88639577-G-A		not specified	Uncertain significance (Oct 26, 2024)
15-88639579-C-T			Likely benign (Dec 31, 2019)
15-88639588-G-C		not specified	Uncertain significance (Sep 01, 2021)
15-88652156-A-C		not specified	Uncertain significance (Dec 28, 2022)
15-88652189-G-A		not specified	Uncertain significance (Jul 07, 2024)
15-88652260-C-T		not specified	Uncertain significance (Mar 01, 2023)
15-88652287-C-T		not specified	Uncertain significance (Jun 26, 2024)
15-88652307-C-A			Benign (Jun 20, 2018)
15-88655416-A-G		not specified	Uncertain significance (Oct 01, 2024)
15-88655432-C-T			Benign (Jun 26, 2018)
15-88655437-C-T		not specified	Uncertain significance (Jun 26, 2024)
15-88655491-G-A			Benign (Jun 13, 2018)
15-88655493-G-T		not specified	Uncertain significance (Jun 24, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ISG20	protein_coding	protein_coding	ENST00000306072	3	20331

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00290	0.597	125717	0	22	125739	0.0000875

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.212	119	126	0.947	0.00000848	1163
Missense in Polyphen		37	46.389	0.79761		413
Synonymous	-0.400	56	52.3	1.07	0.00000344	391
Loss of Function	0.394	4	4.95	0.809	2.10e-7	57

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000558	0.000558
Ashkenazi Jewish	0.000198	0.000198
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000896	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.000167	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Interferon-induced antiviral exoribonuclease that acts on single-stranded RNA and also has minor activity towards single- stranded DNA. Exhibits antiviral activity against RNA viruses including hepatitis C virus (HCV), hepatitis A virus (HAV) and yellow fever virus (YFV) in an exonuclease-dependent manner. May also play additional roles in the maturation of snRNAs and rRNAs, and in ribosome biogenesis. {ECO:0000269|PubMed:11401564, ECO:0000269|PubMed:12594219, ECO:0000269|PubMed:16033969, ECO:0000269|PubMed:21036379}.
• Pathway: Cytokine Signaling in Immune system;Immune System;Interferon alpha/beta signaling;Interferon Signaling (Consensus)

Intolerance Scores

• rvis_EVS: -0.23
• rvis_percentile_EVS: 36.86

Haploinsufficiency Scores

• pHI: 0.0820
• hipred: N
• hipred_score: 0.296
• ghis: 0.568

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.866

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Isg20
• Phenotype: hematopoietic system phenotype; immune system phenotype

Gene ontology

• Biological process: DNA catabolic process, exonucleolytic;rRNA processing;RNA catabolic process;cell population proliferation;response to virus;negative regulation of viral genome replication;defense response to virus;type I interferon signaling pathway;RNA phosphodiester bond hydrolysis, exonucleolytic
• Cellular component: nucleus;nucleoplasm;nucleolus;cytoplasm;Cajal body;PML body
• Molecular function: 3'-5'-exoribonuclease activity;exonuclease activity;single-stranded DNA 3'-5' exodeoxyribonuclease activity;exoribonuclease II activity;U1 snRNA binding;U2 snRNA binding;U3 snoRNA binding;metal ion binding