REXO1

protein-coding

RNA exonuclease 1 homolog, the group of MicroRNA protein coding host genes|Exonucleases

Gene summary

Predicted to enable exonuclease activity. Predicted to be involved in rRNA 3'-end processing. Located in nuclear body. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

TCEB3BP1

MANE transcript

NM_020695.4

Inheritance

—

ClinVar variants

U:288B:20

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.15

Max pathogenic AF

—

Genomic locus

chr19:1,815,248-1,848,483

External References & Databases

Ensembl (ENSG00000079313)

Transcript & Mutation Effects

hg38 • Region Span ~33.2 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 REXO1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 292

not providedTotal: 6

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_020695.4. 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			2 clinvar	1 clinvar	1 clinvar	4
missense			281 clinvar	16 clinvar	2 clinvar	299
nonsense			1 clinvar			1
start loss						0
frameshift			2 clinvar			2
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	288	17	3	308

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 21 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_020695.4	RefSeq	NP_065746.3	16	MANE Select
ENST00000170168.9	Ensembl	ENSP00000170168.3	16	MANE Select
ENST00000586343.2	Ensembl	ENSP00000481515.1	3	Standard
ENST00000590936.5	Ensembl	ENSP00000468713.1	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

nucleic acid phosphodiester bond hydrolysis

Molecular Function

nucleic acid binding
exonuclease activity

Cellular Component

nucleoplasm
nuclear body

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000170168
Coding exons: 16
Length: 33205
Individuals with no LoFs: 125524
Homozygous LoFs: 0
Heterozygous LoFs: 22
Defined: 125546
p: 0.0000876

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.198	756	741	1.02	0.0000523	7682
Missense (PolyPhen)		178	227.89	0.78108		2521
Synonymous	-4.22	438	339	1.29	0.0000265	2604
Loss of Function	4.94	6	39.5	0.152	0.00000191	520

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.00046	0.00020	rare
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0	0.0	absent
Finnish	0.00011	0.000092	rare
European (Non-Finnish)	0.000064	0.000062	rare
South Asian	0.00014	0.00013	rare
Other	0.00017	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Seems to have no detectable effect on transcription elongation in vitro. {ECO:0000269|PubMed:12943681}.;

Recessive Scores

pRec: 0.106

Intolerance Scores

LoFtool: 0.297
RVIS EVS: -1.36
RVIS percentile EVS: 4.54

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.875

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High