GeneBe

EXO1

exonuclease 1, the group of Exonucleases

Basic information

Region (hg38): 1:241847967-241895148

Links

ENSG00000174371 ∙ NCBI:9156 ∙ OMIM:606063 ∙ HGNC:3511 ∙ Uniprot:Q9UQ84 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

  • Lynch syndrome (Refuted Evidence), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the EXO1 gene.

  • not_specified (77 variants)
  • EXO1-related_disorder (28 variants)
  • not_provided (16 variants)
  • Hereditary_breast_ovarian_cancer_syndrome (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EXO1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000130398.4. Only rare variants are included in the table.

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.

EffectPLPVUSLBBSum
synonymous
11
clinvar
1
clinvar
 12
missense
74
clinvar
11
clinvar
7
clinvar
 92
nonsense
0
start loss
0
frameshift
1
clinvar
 1
splice donor/acceptor (+/-2bp)
1
clinvar
 1
Total 0 1 74 23 8

Highest pathogenic variant AF is 0.0000043374057

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
EXO1protein_codingprotein_codingENST00000366548 1347182
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
8.12e-130.86312527924671257480.00187
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-1.035004391.140.00002285542
Missense in Polyphen130132.840.978591684
Synonymous-0.8591821681.080.000009501617
Loss of Function1.922537.70.6620.00000205485

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.003250.00325
Ashkenazi Jewish0.0004980.000496
East Asian0.0001630.000163
Finnish0.0008320.000832
European (Non-Finnish)0.002850.00283
Middle Eastern0.0001630.000163
South Asian0.0005890.000588
Other0.002130.00212

dbNSFP

Source: dbNSFP

Function
FUNCTION: 5'->3' double-stranded DNA exonuclease which may also possess a cryptic 3'->5' double-stranded DNA exonuclease activity. Functions in DNA mismatch repair (MMR) to excise mismatch- containing DNA tracts directed by strand breaks located either 5' or 3' to the mismatch. Also exhibits endonuclease activity against 5'-overhanging flap structures similar to those generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. Required for somatic hypermutation (SHM) and class switch recombination (CSR) of immunoglobulin genes. Essential for male and female meiosis. {ECO:0000269|PubMed:10364235, ECO:0000269|PubMed:10608837, ECO:0000269|PubMed:11809771, ECO:0000269|PubMed:11842105, ECO:0000269|PubMed:12414623, ECO:0000269|PubMed:12704184, ECO:0000269|PubMed:14636568, ECO:0000269|PubMed:14676842, ECO:0000269|PubMed:15225546, ECO:0000269|PubMed:15886194, ECO:0000269|PubMed:16143102, ECO:0000269|PubMed:9685493}.;
Pathway
Mismatch repair - Homo sapiens (human);Mismatch repair;Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta);Mismatch Repair;HDR through Single Strand Annealing (SSA);HDR through Homologous Recombination (HR) or Single Strand Annealing (SSA);DNA Repair;Gene expression (Transcription);DNA Double-Strand Break Repair;Generic Transcription Pathway;Homology Directed Repair;RNA Polymerase II Transcription;G2/M DNA damage checkpoint;G2/M Checkpoints;Cell Cycle Checkpoints;Regulation of TP53 Activity through Phosphorylation;Regulation of TP53 Activity;Transcriptional Regulation by TP53;Cell Cycle;Processing of DNA double-strand break ends;Presynaptic phase of homologous DNA pairing and strand exchange;Homologous DNA Pairing and Strand Exchange;Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha);Resolution of D-loop Structures through Holliday Junction Intermediates;Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA);Resolution of D-Loop Structures;HDR through Homologous Recombination (HRR) (Consensus)

Recessive Scores

pRec
0.261

Intolerance Scores

loftool
0.974
rvis_EVS
3.14
rvis_percentile_EVS
99.3

Haploinsufficiency Scores

pHI
0.363
hipred
Y
hipred_score
0.531
ghis
0.515

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.699

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyHighMediumHigh
CancerHighMediumHigh

Mouse Genome Informatics

Gene name
Exo1
Phenotype
mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); reproductive system phenotype; hematopoietic system phenotype; neoplasm; immune system phenotype; endocrine/exocrine gland phenotype; cellular phenotype; homeostasis/metabolism phenotype;

Gene ontology

Biological process
DNA replication;DNA repair;mismatch repair;DNA recombination;RNA phosphodiester bond hydrolysis, endonucleolytic;t-circle formation
Cellular component
nucleus;nucleoplasm;plasma membrane;nuclear body
Molecular function
DNA binding;RNA-DNA hybrid ribonuclease activity;exonuclease activity;protein binding;5'-3' exonuclease activity;5'-flap endonuclease activity;5'-3' exodeoxyribonuclease activity;single-stranded DNA 5'-3' exodeoxyribonuclease activity;metal ion binding;flap endonuclease activity;double-stranded DNA 5'-3' exodeoxyribonuclease activity