REXO1

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

Basic information

Region (hg38): 19:1815247-1848483

Previous symbols: [ "TCEB3BP1" ]

Links

ENSG00000079313 ∙ NCBI:57455 ∙ OMIM:609614 ∙ HGNC:24616 ∙ Uniprot:Q8N1G1 ∙ 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 REXO1 gene.

• Inborn genetic diseases (82 variants)
• not provided (4 variants)
• not specified (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the REXO1 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	2
missense			77	6	2	85
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	78	7	3

Variants in REXO1

This is a list of pathogenic ClinVar variants found in the REXO1 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-1816091-C-T		not specified	Uncertain significance (Apr 19, 2023)
19-1816257-G-T		not specified	Uncertain significance (Aug 21, 2023)
19-1816270-G-A		not specified	Uncertain significance (Feb 09, 2022)
19-1816278-C-T		not specified	Uncertain significance (Nov 21, 2023)
19-1816531-C-A		not specified	Uncertain significance (Dec 20, 2023)
19-1816538-C-T		not specified	Uncertain significance (Dec 07, 2021)
19-1816722-T-C		not specified	Uncertain significance (Oct 16, 2023)
19-1816766-G-C		not specified	Uncertain significance (Apr 25, 2023)
19-1816776-G-A		not specified	Uncertain significance (Jul 19, 2023)
19-1816780-C-G		not specified	Uncertain significance (Feb 14, 2024)
19-1816801-A-C		not specified	Uncertain significance (Apr 22, 2022)
19-1817260-C-T		not specified	Uncertain significance (Nov 30, 2021)
19-1817736-C-T		not specified	Uncertain significance (Feb 03, 2022)
19-1817777-G-A		not specified	Uncertain significance (May 03, 2023)
19-1818490-C-T		not specified	Uncertain significance (Mar 31, 2023)
19-1818529-C-T		not specified	Uncertain significance (Jan 04, 2024)
19-1818538-C-T		not specified	Uncertain significance (Nov 21, 2023)
19-1818557-G-C		not specified	Uncertain significance (Sep 12, 2023)
19-1818768-G-A		not specified	Uncertain significance (Sep 12, 2023)
19-1819035-C-T		not specified	Uncertain significance (Aug 09, 2021)
19-1819051-G-A		not specified	Uncertain significance (May 03, 2023)
19-1819059-G-A		not specified	Uncertain significance (Sep 14, 2022)
19-1819089-C-T		not specified	Uncertain significance (May 16, 2023)
19-1819096-C-A		not specified	Uncertain significance (Feb 10, 2023)
19-1819113-A-G			Benign (Jun 29, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
REXO1	protein_coding	protein_coding	ENST00000170168	16	33205

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.986	0.0136	125524	0	22	125546	0.0000876

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.198	756	741	1.02	0.0000523	7682
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000459	0.000459
Ashkenazi Jewish	0.000100	0.0000994
East Asian	0.00	0.00
Finnish	0.000114	0.0000924
European (Non-Finnish)	0.0000637	0.0000617
Middle Eastern	0.00	0.00
South Asian	0.000137	0.000131
Other	0.000167	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Seems to have no detectable effect on transcription elongation in vitro. {ECO:0000269|PubMed:12943681}.
• Pathway: Ribosome biogenesis in eukaryotes - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.106

Intolerance Scores

• loftool: 0.297
• rvis_EVS: -1.36
• rvis_percentile_EVS: 4.54

Haploinsufficiency Scores

• pHI: 0.223
• hipred: N
• hipred_score: 0.373
• ghis: 0.613

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.875

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rexo1

Gene ontology

• Biological process: nucleic acid phosphodiester bond hydrolysis
• Cellular component: nucleoplasm;nuclear body
• Molecular function: nucleic acid binding;exonuclease activity