ISG20L2

interferon stimulated exonuclease gene 20 like 2, the group of Exonucleases

Basic information

Region (hg38): 1:156720796-156728766

Links

ENSG00000143319 ∙ NCBI:81875 ∙ OMIM:611930 ∙ HGNC:25745 ∙ Uniprot:Q9H9L3 ∙ 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 ISG20L2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ISG20L2 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			20	2		22
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	3	0

Variants in ISG20L2

This is a list of pathogenic ClinVar variants found in the ISG20L2 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-156723368-C-T		not specified	Likely benign (May 18, 2023)
1-156724225-G-A		not specified	Uncertain significance (Aug 17, 2021)
1-156724233-G-C		not specified	Uncertain significance (Mar 18, 2024)
1-156724233-G-T		not specified	Uncertain significance (Nov 09, 2023)
1-156724234-G-C		not specified	Uncertain significance (Sep 13, 2023)
1-156724273-G-A		not specified	Uncertain significance (Jul 14, 2023)
1-156724323-A-G		not specified	Uncertain significance (Nov 10, 2022)
1-156726911-C-T		not specified	Likely benign (Jan 17, 2023)
1-156726929-G-A		not specified	Uncertain significance (Aug 17, 2022)
1-156726938-T-C		not specified	Uncertain significance (Jan 07, 2022)
1-156726955-C-T		not specified	Uncertain significance (Oct 06, 2022)
1-156726966-C-A		not specified	Uncertain significance (Sep 14, 2021)
1-156727082-G-A		not specified	Uncertain significance (Jun 18, 2024)
1-156727097-T-C		not specified	Uncertain significance (Nov 17, 2023)
1-156727242-C-G		not specified	Uncertain significance (Jun 02, 2023)
1-156727247-A-T		not specified	Uncertain significance (Mar 14, 2024)
1-156727250-G-A		not specified	Uncertain significance (Dec 03, 2021)
1-156727250-G-C		not specified	Uncertain significance (Dec 19, 2023)
1-156727265-T-G		not specified	Uncertain significance (May 24, 2023)
1-156727308-T-G		not specified	Uncertain significance (May 28, 2024)
1-156727355-A-C		not specified	Uncertain significance (Aug 08, 2023)
1-156727368-T-C			Likely benign (Nov 01, 2022)
1-156727391-A-T		not specified	Uncertain significance (Jan 30, 2024)
1-156727417-T-C		not specified	Uncertain significance (Feb 10, 2023)
1-156727469-C-G		not specified	Uncertain significance (Aug 10, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ISG20L2	protein_coding	protein_coding	ENST00000313146	3	6909

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0878	0.904	125736	0	12	125748	0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.809	167	199	0.839	0.0000112	2311
Missense in Polyphen		54	82.376	0.65553		989
Synonymous	-0.0932	79	78.0	1.01	0.00000425	712
Loss of Function	2.31	4	13.0	0.309	8.37e-7	149

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000177	0.000177
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000352	0.0000352
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: 3'-> 5'-exoribonuclease involved in ribosome biogenesis in the processing of the 12S pre-rRNA. Displays a strong specificity for a 3'-end containing a free hydroxyl group. {ECO:0000269|PubMed:18065403}.

Recessive Scores

• pRec: 0.0904

Intolerance Scores

• rvis_EVS: 0.35
• rvis_percentile_EVS: 74.18

Haploinsufficiency Scores

• pHI: 0.119
• hipred: N
• hipred_score: 0.273
• ghis: 0.476

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.937

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Isg20l2

Gene ontology

• Biological process: rRNA processing;RNA phosphodiester bond hydrolysis, exonucleolytic
• Cellular component: nucleoplasm;nucleolus
• Molecular function: 3'-5'-exoribonuclease activity;RNA binding;protein binding