FEN1
flap structure-specific endonuclease 1
Basic information
Region (hg38): 11:61792911-61797238
Previous symbols: [ "RAD2" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the FEN1 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 | 13 | 13 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 13 | 0 | 0 |
Variants in FEN1
This is a list of pathogenic ClinVar variants found in the FEN1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 11-61795501-G-A | not specified | Uncertain significance (Oct 05, 2022) | ||
| 11-61795593-G-A | not specified | Uncertain significance (Feb 16, 2023) | ||
| 11-61795654-C-T | not specified | Uncertain significance (Mar 17, 2023) | ||
| 11-61795672-G-A | Hereditary breast ovarian cancer syndrome | Uncertain significance (Aug 01, 2020) | ||
| 11-61795747-G-A | not specified | Uncertain significance (Jan 24, 2024) | ||
| 11-61795930-T-C | Uncertain significance (Apr 08, 2021) | |||
| 11-61796034-G-T | not specified | Uncertain significance (Jun 03, 2024) | ||
| 11-61796065-G-A | Non-immune hydrops fetalis | Uncertain significance (Apr 29, 2021) | ||
| 11-61796077-G-A | not specified | Uncertain significance (Mar 11, 2024) | ||
| 11-61796217-C-G | not specified | Uncertain significance (Jun 16, 2024) | ||
| 11-61796257-G-A | not specified | Uncertain significance (Apr 18, 2023) | ||
| 11-61796308-T-A | not specified | Uncertain significance (Sep 07, 2022) | ||
| 11-61796325-C-T | not specified | Uncertain significance (Mar 22, 2022) | ||
| 11-61796356-G-A | not specified | Uncertain significance (Nov 13, 2023) | ||
| 11-61796403-G-A | not specified | Uncertain significance (Feb 28, 2024) | ||
| 11-61796463-G-A | not specified | Uncertain significance (Apr 07, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| FEN1 | protein_coding | protein_coding | ENST00000305885 | 1 | 4608 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0000477 | 0.673 | 125730 | 0 | 17 | 125747 | 0.0000676 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.36 | 169 | 227 | 0.745 | 0.0000139 | 2500 |
| Missense in Polyphen | 34 | 67.984 | 0.50012 | 670 | ||
| Synonymous | 1.78 | 67 | 88.3 | 0.759 | 0.00000491 | 766 |
| Loss of Function | 0.905 | 8 | 11.3 | 0.709 | 7.51e-7 | 124 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000904 | 0.0000904 |
| Ashkenazi Jewish | 0.0000996 | 0.0000992 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000528 | 0.0000527 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.000229 | 0.000229 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Structure-specific nuclease with 5'-flap endonuclease and 5'-3' exonuclease activities involved in DNA replication and repair. During DNA replication, cleaves the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. It enters the flap from the 5'-end and then tracks to cleave the flap base, leaving a nick for ligation. Also involved in the long patch base excision repair (LP-BER) pathway, by cleaving within the apurinic/apyrimidinic (AP) site-terminated flap. Acts as a genome stabilization factor that prevents flaps from equilibrating into structurs that lead to duplications and deletions. Also possesses 5'-3' exonuclease activity on nicked or gapped double- stranded DNA, and exhibits RNase H activity. Also involved in replication and repair of rDNA and in repairing mitochondrial DNA. {ECO:0000255|HAMAP-Rule:MF_03140, ECO:0000269|PubMed:10744741, ECO:0000269|PubMed:11986308, ECO:0000269|PubMed:18443037, ECO:0000269|PubMed:20729856, ECO:0000269|PubMed:7961795, ECO:0000269|PubMed:8621570}.;
- Pathway
- Base excision repair - Homo sapiens (human);DNA replication - Homo sapiens (human);Non-homologous end-joining - Homo sapiens (human);HDR through MMEJ (alt-NHEJ);DNA Repair;Disease;DNA Double-Strand Break Repair;HIV Life Cycle;HIV Infection;Homology Directed Repair;Infectious disease;DNA Replication;Removal of the Flap Intermediate;Processive synthesis on the lagging strand;Lagging Strand Synthesis;DNA strand elongation;Synthesis of DNA;POLB-Dependent Long Patch Base Excision Repair;S Phase;PCNA-Dependent Long Patch Base Excision Repair;Resolution of AP sites via the multiple-nucleotide patch replacement pathway;Resolution of Abasic Sites (AP sites);Base Excision Repair;Removal of the Flap Intermediate from the C-strand;Processive synthesis on the C-strand of the telomere;Telomere C-strand (Lagging Strand) Synthesis;Extension of Telomeres;Telomere Maintenance;Chromosome Maintenance;Cell Cycle;Cell Cycle, Mitotic;Early Phase of HIV Life Cycle
(Consensus)
Recessive Scores
- pRec
- 0.543
Intolerance Scores
- loftool
- 0.701
- rvis_EVS
- -0.12
- rvis_percentile_EVS
- 44.89
Haploinsufficiency Scores
- pHI
- 0.974
- hipred
- Y
- hipred_score
- 0.813
- ghis
- 0.696
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.976
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Fen1
- Phenotype
- neoplasm; hematopoietic system phenotype; reproductive system phenotype; normal 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); liver/biliary system phenotype; respiratory system phenotype; embryo phenotype; renal/urinary system phenotype; immune system phenotype; digestive/alimentary phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); endocrine/exocrine gland phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); growth/size/body region phenotype; homeostasis/metabolism phenotype; cellular phenotype;
Zebrafish Information Network
- Gene name
- fen1
- Affected structure
- anatomical system
- Phenotype tag
- abnormal
- Phenotype quality
- quality
Gene ontology
- Biological process
- double-strand break repair via homologous recombination;DNA replication;base-excision repair;double-strand break repair;UV protection;telomere maintenance via semi-conservative replication;DNA replication, removal of RNA primer;positive regulation of sister chromatid cohesion;nucleic acid phosphodiester bond hydrolysis;RNA phosphodiester bond hydrolysis, endonucleolytic
- Cellular component
- nuclear chromosome, telomeric region;nucleus;nucleoplasm;nucleolus;mitochondrion;membrane;protein-containing complex
- Molecular function
- magnesium ion binding;DNA binding;damaged DNA binding;double-stranded DNA binding;endonuclease activity;RNA-DNA hybrid ribonuclease activity;exonuclease activity;protein binding;double-stranded DNA exodeoxyribonuclease activity;5'-3' exonuclease activity;5'-flap endonuclease activity;manganese ion binding;flap endonuclease activity