DXO

decapping exoribonuclease

Basic information

Region (hg38): 6:31969809-31972290

Previous symbols: [ "DOM3Z" ]

Links

ENSG00000204348 ∙ NCBI:1797 ∙ OMIM:605996 ∙ HGNC:2992 ∙ Uniprot:O77932 ∙ 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 DXO gene.

• Inborn genetic diseases (16 variants)
• not specified (2 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DXO 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
missense			15		1	16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1	1		2
Total	0	0	16	1	2

Variants in DXO

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

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

Position	Type	Phenotype	Significance	ClinVar
6-31969929-T-G		not specified	Uncertain significance (Dec 09, 2023)
6-31969987-C-G		not specified	Uncertain significance (Oct 12, 2022)
6-31970023-G-A		not specified	Uncertain significance (Nov 08, 2021)
6-31970196-C-T		not specified	Uncertain significance (May 08, 2023)
6-31970389-G-A		not specified	Uncertain significance (Feb 14, 2023)
6-31970635-G-T		not specified	Benign (Mar 29, 2016)
6-31970651-G-A		not specified	Uncertain significance (Feb 02, 2022)
6-31970674-T-C		not specified	Benign (Mar 29, 2016)
6-31970757-G-A		not specified	Uncertain significance (Nov 22, 2021)
6-31970950-A-G		not specified	Uncertain significance (Nov 03, 2023)
6-31970974-C-T		not specified	Uncertain significance (Jan 22, 2024)
6-31970975-G-A		not specified	Uncertain significance (Mar 31, 2022)
6-31971001-G-A		not specified	Uncertain significance (May 04, 2023)
6-31971004-G-A		not specified	Uncertain significance (Dec 07, 2023)
6-31971054-C-G		not specified	Uncertain significance (Feb 28, 2023)
6-31971070-C-T		not specified	Uncertain significance (Sep 12, 2023)
6-31971368-A-G		not specified	Uncertain significance (Jan 18, 2023)
6-31971440-C-T		not specified	Uncertain significance (Jan 24, 2023)
6-31971485-G-T		not specified	Uncertain significance (Apr 25, 2022)
6-31971511-A-C		not specified	Uncertain significance (Aug 12, 2022)
6-31971617-T-C		not specified	Uncertain significance (Aug 02, 2022)
6-31972108-G-A		not specified	Uncertain significance (Oct 26, 2022)
6-31972121-C-T			Likely benign (Feb 01, 2023)
6-31972162-T-G		not specified	Uncertain significance (Dec 26, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DXO	protein_coding	protein_coding	ENST00000375349	6	2483

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.64e-10	0.180	125659	0	89	125748	0.000354

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.911	205	245	0.836	0.0000151	2549
Missense in Polyphen		77	89.309	0.86217		961
Synonymous	1.46	78	96.2	0.811	0.00000572	832
Loss of Function	0.555	16	18.6	0.861	9.84e-7	187

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000980	0.000960
Ashkenazi Jewish	0.00	0.00
East Asian	0.00104	0.000979
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000269	0.000264
Middle Eastern	0.00104	0.000979
South Asian	0.000523	0.000490
Other	0.000328	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Ribonuclease that specifically degrades pre-mRNAs with a defective 5' end cap and is part of a pre-mRNA capping quality control. Has decapping, pyrophosphohydrolase and 5'-3' exonuclease activities. Has decapping activity toward incomplete 5' end cap mRNAs such as unmethylated 5' end-capped RNA to release GpppN and 5' end monophosphate RNA. The 5' end monophosphate RNA is then degraded by the 5'-3' exoribonuclease activity, enabling this enzyme to decap and degrade incompletely capped mRNAs. Also possesses RNA 5'-pyrophosphohydrolase activity by hydrolyzing the 5' end triphosphate to release pyrophosphates (By similarity). {ECO:0000250}.

Intolerance Scores

• rvis_EVS: 0.17
• rvis_percentile_EVS: 65.96

Haploinsufficiency Scores

• pHI: 0.365
• hipred: N
• hipred_score: 0.381
• ghis: 0.521

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dxo

Gene ontology

• Biological process: mRNA catabolic process;RNA destabilization;nuclear mRNA surveillance;nucleic acid phosphodiester bond hydrolysis
• Cellular component: nucleus;cytosol;plasma membrane
• Molecular function: nucleotide binding;magnesium ion binding;mRNA binding;5'-3' exonuclease activity;RNA pyrophosphohydrolase activity