EPN2
Basic information
Region (hg38): 17:19215615-19336715
Links
Phenotypes
GenCC
Source:
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 EPN2 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 | 21 | 22 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 0 | |||||
Total | 0 | 0 | 21 | 1 | 0 |
Variants in EPN2
This is a list of pathogenic ClinVar variants found in the EPN2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
17-19283124-C-G | not specified | Uncertain significance (Aug 13, 2021) | ||
17-19283130-C-T | not specified | Uncertain significance (Oct 06, 2021) | ||
17-19283141-C-T | not specified | Uncertain significance (May 05, 2023) | ||
17-19283159-G-A | not specified | Uncertain significance (Dec 21, 2023) | ||
17-19283234-C-A | not specified | Uncertain significance (Jun 16, 2023) | ||
17-19283289-T-C | not specified | Uncertain significance (Nov 09, 2023) | ||
17-19283423-G-A | not specified | Uncertain significance (Nov 17, 2022) | ||
17-19283473-C-G | not specified | Uncertain significance (Nov 08, 2021) | ||
17-19283489-C-T | not specified | Uncertain significance (Mar 08, 2024) | ||
17-19285620-C-T | not specified | Uncertain significance (Jun 10, 2022) | ||
17-19285748-G-T | not specified | Uncertain significance (Sep 25, 2023) | ||
17-19312122-T-C | not specified | Uncertain significance (Oct 30, 2023) | ||
17-19313112-C-G | not specified | Uncertain significance (Dec 28, 2023) | ||
17-19313199-C-T | not specified | Uncertain significance (Apr 11, 2023) | ||
17-19313253-G-A | not specified | Uncertain significance (Mar 29, 2023) | ||
17-19313265-C-T | not specified | Uncertain significance (Jan 10, 2022) | ||
17-19328743-G-T | not specified | Uncertain significance (Dec 19, 2023) | ||
17-19328846-C-T | not specified | Uncertain significance (Sep 06, 2022) | ||
17-19329561-G-C | not specified | Uncertain significance (Apr 01, 2024) | ||
17-19331862-T-A | not specified | Uncertain significance (Apr 09, 2024) | ||
17-19331981-G-T | not specified | Uncertain significance (Jan 10, 2023) | ||
17-19334091-T-C | not specified | Uncertain significance (Feb 23, 2023) | ||
17-19334093-G-A | not specified | Uncertain significance (Jan 07, 2022) | ||
17-19334114-G-A | not specified | Likely benign (Apr 04, 2023) | ||
17-19334168-C-T | not specified | Uncertain significance (Mar 25, 2024) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
EPN2 | protein_coding | protein_coding | ENST00000314728 | 9 | 121101 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.748 | 0.252 | 125726 | 0 | 22 | 125748 | 0.0000875 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 1.39 | 301 | 377 | 0.799 | 0.0000230 | 4078 |
Missense in Polyphen | 69 | 117.95 | 0.58499 | 1254 | ||
Synonymous | 1.45 | 141 | 165 | 0.857 | 0.0000107 | 1380 |
Loss of Function | 3.87 | 5 | 26.5 | 0.189 | 0.00000139 | 277 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.0000618 | 0.0000615 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.0000585 | 0.0000544 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.000108 | 0.000105 |
Middle Eastern | 0.0000585 | 0.0000544 |
South Asian | 0.000230 | 0.000229 |
Other | 0.000164 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Plays a role in the formation of clathrin-coated invaginations and endocytosis. {ECO:0000269|PubMed:10567358}.;
- Pathway
- Endocytosis - Homo sapiens (human);Vesicle-mediated transport;Membrane Trafficking;Clathrin-mediated endocytosis;EGFR1;Cargo recognition for clathrin-mediated endocytosis
(Consensus)
Recessive Scores
- pRec
- 0.102
Intolerance Scores
- loftool
- 0.521
- rvis_EVS
- -0.38
- rvis_percentile_EVS
- 28.11
Haploinsufficiency Scores
- pHI
- 0.218
- hipred
- Y
- hipred_score
- 0.651
- ghis
- 0.505
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.756
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Epn2
- Phenotype
- homeostasis/metabolism phenotype; cellular phenotype; growth/size/body region 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); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); 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); normal phenotype; reproductive system phenotype; neoplasm; embryo phenotype;
Gene ontology
- Biological process
- endocytosis;negative regulation of vascular endothelial growth factor receptor signaling pathway;positive regulation of Notch signaling pathway;membrane organization;negative regulation of sprouting angiogenesis
- Cellular component
- cytosol;clathrin coat of endocytic vesicle;intracellular membrane-bounded organelle
- Molecular function
- protein binding;lipid binding;cadherin binding