REXO2

protein-coding

RNA exonuclease 2, the group of Exonucleases

Gene summary

This gene encodes a 3'-to-5' exonuclease specific for small (primarily 5 nucleotides or less in length) single-stranded RNA and DNA oligomers. This protein may have a role in DNA repair, replication, and recombination, and in RNA processing and degradation. It may also be involved in resistance of human cells to UV-C-induced cell death through its role in the DNA repair process. [provided by RefSeq, Nov 2011]

MANE transcript

NM_015523.4

Inheritance

ClinVar variants

U:25B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.37

Max pathogenic AF

—

Genomic locus

chr11:114,439,435-114,450,279

External References & Databases

Ensembl (ENSG00000076043)

Transcript & Mutation Effects

hg38 • Region Span ~10.8 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

sporadic pheochromocytomaLIMITED

Inheritance Pattern: AD

Disease ID:MONDO:0017191

Submitter: Ambry Genetics

type 1 interferonopathy of childhoodMODERATE

Inheritance Pattern: AD

Disease ID:MONDO:0957408

Submitter: PanelApp Australia

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to REXO2 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 21

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_015523.4. 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						0
missense			21 clinvar	1 clinvar		22
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	0	25	1	0	26

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 53 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_015523.4	RefSeq	NP_056338.2	7	MANE Select
ENST00000265881.10	Ensembl	ENSP00000265881.5	7	MANE Select
ENST00000538198.5	Ensembl	ENSP00000441639.1	3	Standard
ENST00000539119.5	Ensembl	ENSP00000444421.1	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Ribosome biogenesis in eukaryotes - Homo sapiens (human)

Biological Process

nucleobase-containing compound metabolic process
nucleotide metabolic process
RNA phosphodiester bond hydrolysis, exonucleolytic

Molecular Function

3'-5'-exoribonuclease activity
nucleic acid binding
3'-5' exonuclease activity

Cellular Component

nucleus
nucleolus
mitochondrion
mitochondrial intermembrane space
mitochondrial matrix

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000265881
Coding exons: 7
Length: 10894
Individuals with no LoFs: 125729
Homozygous LoFs: 0
Heterozygous LoFs: 17
Defined: 125746
p: 0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.01	93	125	0.746	0.00000585	1569
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00019	0.00018	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0.000047	0.000046	rare
European (Non-Finnish)	0.00011	0.00011	rare
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.177

Intolerance Scores

LoFtool: 0.477
RVIS EVS: -0.07
RVIS percentile EVS: 48.12

Essentials

Essential (CRISPR): E
Essential (CRISPR2): E
Essential (gene trap): H
Indispensability pred.: N
Indispensability score: 0.387

Gene Damage Prediction

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