ISG20L2

protein-coding

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

Gene summary

This gene encodes a 3'-5' exoribonuclease that may be involved in the processing of the 12S pre-rRNA. Pseudogenes have been identified on chromosomes 6 and 11. [provided by RefSeq, Dec 2014]

MANE transcript

NM_001370150.2

Inheritance

—

ClinVar variants

U:34B:5

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.31

Max pathogenic AF

—

Genomic locus

chr1:156,720,796-156,728,766

External References & Databases

Ensembl (ENSG00000143319)

Transcript & Mutation Effects

hg38 • Region Span ~8.0 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ISG20L2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 36

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001370150.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	1 clinvar		2
missense			33 clinvar	4 clinvar		37
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	34	5	0	39

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 34 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001370150.2	RefSeq	NP_001357079.1	3	MANE Select
ENST00000368219.2	Ensembl	ENSP00000357202.2	3	MANE Select
NM_001303095.1	RefSeq	NP_001290024.1	3	Standard
NM_001370151.1	RefSeq	NP_001357080.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

rRNA processing
RNA phosphodiester bond hydrolysis, exonucleolytic

Molecular Function

3'-5'-exoribonuclease activity
RNA binding
protein binding

Cellular Component

nucleoplasm
nucleolus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000313146
Coding exons: 3
Length: 6909
Individuals with no LoFs: 125736
Homozygous LoFs: 0
Heterozygous LoFs: 12
Defined: 125748
p: 0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.809	167	199	0.839	0.0000112	2311
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.00012	0.00012	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000054	0.000054	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.000035	0.000035	rare
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): E
Essential (CRISPR2): E
Essential (gene trap): E
Indispensability pred.: E
Indispensability score: 0.937

Gene Damage Prediction

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