REXO2

RNA exonuclease 2, the group of Exonucleases

Basic information

Region (hg38): 11:114439435-114450279

Links

ENSG00000076043 ∙ NCBI:25996 ∙ OMIM:607149 ∙ HGNC:17851 ∙ Uniprot:Q9Y3B8 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• sporadic pheochromocytoma (Limited), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the REXO2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the REXO2 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			10	1		11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	1	0

Variants in REXO2

This is a list of pathogenic ClinVar variants found in the REXO2 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-114439539-G-A		not specified	Uncertain significance (Mar 24, 2023)
11-114439542-C-T		not specified	Uncertain significance (Dec 22, 2023)
11-114439578-G-A		not specified	Uncertain significance (Dec 13, 2022)
11-114439632-C-A		not specified	Uncertain significance (Jan 23, 2023)
11-114439657-G-A		not specified	Uncertain significance (Mar 02, 2023)
11-114440669-A-G		not specified	Uncertain significance (Dec 01, 2022)
11-114443919-G-A		not specified	Uncertain significance (Mar 27, 2023)
11-114444644-C-T		not specified	Uncertain significance (Oct 27, 2022)
11-114446062-G-A		not specified	Uncertain significance (Jan 19, 2024)
11-114446084-G-A		not specified	Uncertain significance (Jul 11, 2023)
11-114449917-T-C		not specified	Likely benign (Aug 26, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
REXO2	protein_coding	protein_coding	ENST00000265881	7	10894

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0232	0.964	125729	0	17	125746	0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.01	93	125	0.746	0.00000585	1569
Missense in Polyphen		25	42.409	0.5895		542
Synonymous	0.174	42	43.5	0.966	0.00000207	424
Loss of Function	2.17	5	13.6	0.367	7.60e-7	158

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000189	0.000185
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000466	0.0000462
European (Non-Finnish)	0.000108	0.000105
Middle Eastern	0.00	0.00
South Asian	0.0000333	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: 3'-to-5' exoribonuclease specific for small oligoribonucleotides. Active on small (primarily </=5 nucleotides in length) single-stranded RNA and DNA oligomers. May have a role in cellular nucleotide recycling. {ECO:0000269|PubMed:23741365}.
• Pathway: Ribosome biogenesis in eukaryotes - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.177

Intolerance Scores

• loftool: 0.477
• rvis_EVS: -0.07
• rvis_percentile_EVS: 48.12

Haploinsufficiency Scores

• pHI: 0.363
• hipred: Y
• hipred_score: 0.699
• ghis: 0.559

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: H
• gene_indispensability_pred: N
• gene_indispensability_score: 0.387

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rexo2
• Phenotype: homeostasis/metabolism phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Gene ontology

• Biological process: nucleobase-containing compound metabolic process;nucleotide metabolic process;RNA phosphodiester bond hydrolysis, exonucleolytic
• Cellular component: nucleus;nucleolus;mitochondrion;mitochondrial intermembrane space;mitochondrial matrix;focal adhesion
• Molecular function: 3'-5'-exoribonuclease activity;nucleic acid binding;3'-5' exonuclease activity