EXO5

exonuclease 5, the group of Exonucleases

Basic information

Region (hg38): 1:40508741-40516038

Previous symbols: [ "C1orf176", "DEM1" ]

Links

ENSG00000164002 ∙ NCBI:64789 ∙ OMIM:618601 ∙ HGNC:26115 ∙ Uniprot:Q9H790 ∙ 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 EXO5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EXO5 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					3	3
missense			37		5	42
nonsense						0
start loss						0
frameshift				1	2	3
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					3	3
Total	0	0	37	1	13

Variants in EXO5

This is a list of pathogenic ClinVar variants found in the EXO5 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-40514205-G-A			Benign (Jun 20, 2021)
1-40514272-T-A			Benign (Jun 19, 2021)
1-40514273-C-A			Benign (Jun 19, 2021)
1-40514594-T-C		not specified	Uncertain significance (Feb 05, 2024)
1-40514599-G-C		not specified	Uncertain significance (Feb 25, 2025)
1-40514609-A-G		not specified	Uncertain significance (Jan 24, 2024)
1-40514636-T-TA			Likely benign (Dec 11, 2023)
1-40514656-A-G		not specified	Uncertain significance (Dec 02, 2024)
1-40514706-T-A		not specified	Uncertain significance (Nov 20, 2023)
1-40514707-G-A		not specified	Uncertain significance (Mar 14, 2023)
1-40514770-T-C		not specified	Uncertain significance (Dec 31, 2023)
1-40514772-C-G		not specified	Uncertain significance (Jan 22, 2024)
1-40514857-T-G		not specified	Uncertain significance (Aug 05, 2024)
1-40514867-C-T		not specified	Uncertain significance (Oct 19, 2024)
1-40514876-C-G		not specified	Uncertain significance (Jan 22, 2024)
1-40514887-G-A			Benign (Jan 29, 2025)
1-40514905-C-G		not specified	Uncertain significance (Feb 23, 2025)
1-40514920-C-G		not specified	Uncertain significance (Jan 24, 2023)
1-40514926-C-T		not specified	Uncertain significance (Oct 22, 2024)
1-40514945-T-C		not specified	Uncertain significance (Aug 29, 2024)
1-40514947-C-T		not specified	Uncertain significance (Dec 08, 2021)
1-40514996-T-C			Benign (Jan 20, 2025)
1-40515023-A-G			Uncertain significance (Feb 03, 2022)
1-40515043-C-T			Benign (Jan 27, 2024)
1-40515058-G-A		not specified	Uncertain significance (Mar 03, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EXO5	protein_coding	protein_coding	ENST00000372703	1	7816

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000227	0.511	122990	206	2551	125747	0.0110

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.951	154	191	0.806	0.00000923	2409
Missense in Polyphen		43	65.531	0.65618		877
Synonymous	1.42	59	74.6	0.790	0.00000345	762
Loss of Function	0.592	8	10.0	0.798	5.11e-7	148

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00834	0.00836
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.147	0.146
Finnish	0.000185	0.000185
European (Non-Finnish)	0.000352	0.000352
Middle Eastern	0.147	0.146
South Asian	0.00160	0.00160
Other	0.00473	0.00473

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Single-stranded DNA (ssDNA) bidirectional exonuclease involved in DNA repair. Probably involved in DNA repair following ultraviolet (UV) irradiation and interstrand cross-links (ICLs) damage. Has both 5'-3' and 3'-5' exonuclease activities with a strong preference for 5'-ends. Acts as a sliding exonuclease that loads at ssDNA ends and then slides along the ssDNA prior to cutting; however the sliding and the 3'-5' exonuclease activities are abolished upon binding to the replication protein A (RPA) complex that enforces 5'-directionality activity. {ECO:0000269|PubMed:23095756}.

Intolerance Scores

• rvis_EVS: 0.46
• rvis_percentile_EVS: 78.59

Haploinsufficiency Scores

• pHI: 0.128
• hipred: N
• hipred_score: 0.170
• ghis: 0.513

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: 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: Exo5

Gene ontology

• Biological process: interstrand cross-link repair;nucleic acid phosphodiester bond hydrolysis
• Cellular component: nucleus;nucleoplasm;cytosol
• Molecular function: DNA binding;single-stranded DNA 3'-5' exodeoxyribonuclease activity;protein homodimerization activity;single-stranded DNA 5'-3' exodeoxyribonuclease activity;metal ion binding;4 iron, 4 sulfur cluster binding