REXO4

REX4 homolog, 3'-5' exonuclease, the group of Exonucleases

Basic information

Region (hg38): 9:133406059-133418096

Previous symbols: [ "XPMC2H" ]

Links

ENSG00000148300 ∙ NCBI:57109 ∙ OMIM:602930 ∙ HGNC:12820 ∙ Uniprot:Q9GZR2 ∙ 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 REXO4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the REXO4 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			23	3		26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	23	3	0

Variants in REXO4

This is a list of pathogenic ClinVar variants found in the REXO4 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-133406999-C-A		not specified	Uncertain significance (Jul 27, 2022)
9-133407005-C-T		not specified	Uncertain significance (Feb 05, 2024)
9-133407008-G-A		not specified	Uncertain significance (Mar 19, 2024)
9-133407027-T-C		not specified	Uncertain significance (Jan 23, 2024)
9-133407039-C-T		not specified	Likely benign (Nov 21, 2022)
9-133407059-T-G		not specified	Uncertain significance (Jan 23, 2024)
9-133407066-C-T		not specified	Uncertain significance (May 23, 2023)
9-133407069-G-C		not specified	Uncertain significance (Jan 09, 2024)
9-133407871-G-A		not specified	Uncertain significance (Nov 28, 2024)
9-133408793-T-C		not specified	Uncertain significance (Feb 12, 2024)
9-133408829-T-C		not specified	Uncertain significance (Dec 04, 2024)
9-133411058-A-G		not specified	Uncertain significance (Oct 09, 2024)
9-133412319-C-T		not specified	Uncertain significance (Mar 21, 2023)
9-133412320-G-A		not specified	Uncertain significance (Nov 22, 2021)
9-133412334-G-A		not specified	Uncertain significance (Sep 20, 2023)
9-133412359-C-T		not specified	Uncertain significance (Nov 15, 2023)
9-133412383-A-G		not specified	Uncertain significance (Dec 19, 2023)
9-133412827-T-C		not specified	Uncertain significance (Sep 01, 2021)
9-133412830-G-A		Recurrent spontaneous abortion	Uncertain significance (-)
9-133412921-C-T		not specified	Likely benign (Jan 30, 2024)
9-133414666-C-T		not specified	Uncertain significance (Jan 31, 2023)
9-133414693-T-C		not specified	Likely benign (Jul 31, 2024)
9-133414714-C-T		not specified	Likely benign (May 30, 2023)
9-133414773-T-C		not specified	Likely benign (Oct 05, 2023)
9-133414782-G-A		not specified	Uncertain significance (Oct 12, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
REXO4	protein_coding	protein_coding	ENST00000371942	8	11979

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.79e-7	0.767	125589	1	158	125748	0.000632

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.107	246	251	0.981	0.0000145	2764
Missense in Polyphen		52	69.182	0.75164		758
Synonymous	1.11	87	101	0.860	0.00000682	813
Loss of Function	1.29	12	17.9	0.671	8.58e-7	222

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00672	0.00667
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000212	0.000211
Middle Eastern	0.00	0.00
South Asian	0.000525	0.000523
Other	0.000816	0.000815

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0998

Intolerance Scores

• loftool: 0.655
• rvis_EVS: 0.38
• rvis_percentile_EVS: 75.51

Haploinsufficiency Scores

• pHI: 0.0731
• hipred: N
• hipred_score: 0.123
• ghis: 0.482

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.633

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rexo4

Gene ontology

• Biological process: regulation of transcription, DNA-templated;rRNA processing;nucleic acid phosphodiester bond hydrolysis
• Cellular component: nucleus;nucleolus;nuclear speck
• Molecular function: DNA-binding transcription factor activity;RNA binding;3'-5' exonuclease activity