EPN1
Basic information
Region (hg38): 19:55675226-55709858
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (97 variants)
- not_provided (2 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the EPN1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001130072.2. 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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 75 | 78 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 75 | 3 | 0 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| EPN1 | protein_coding | protein_coding | ENST00000411543 | 11 | 34633 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.786 | 0.214 | 125704 | 0 | 12 | 125716 | 0.0000477 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.34 | 342 | 419 | 0.815 | 0.0000286 | 4137 |
| Missense in Polyphen | 81 | 90.976 | 0.89035 | 939 | ||
| Synonymous | -1.12 | 217 | 197 | 1.10 | 0.0000160 | 1445 |
| Loss of Function | 3.93 | 5 | 27.1 | 0.185 | 0.00000139 | 291 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000308 | 0.0000308 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.000205 | 0.000185 |
| European (Non-Finnish) | 0.0000572 | 0.0000528 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.000175 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Binds to membranes enriched in phosphatidylinositol 4,5- bisphosphate (PtdIns(4,5)P2). Modifies membrane curvature and facilitates the formation of clathrin-coated invaginations (By similarity). Regulates receptor-mediated endocytosis. {ECO:0000250, ECO:0000269|PubMed:10557078}.;
- Pathway
- Endocytosis - Homo sapiens (human);VEGFA-VEGFR2 Signaling Pathway;EGF-EGFR Signaling Pathway;Signal Transduction;Vesicle-mediated transport;endocytotic role of ndk phosphins and dynamin;Membrane Trafficking;EGFR downregulation;Signaling by EGFR;Clathrin-mediated endocytosis;EGFR1;Cargo recognition for clathrin-mediated endocytosis;Signaling by Receptor Tyrosine Kinases;Internalization of ErbB1
(Consensus)
Recessive Scores
- pRec
- 0.174
Intolerance Scores
- loftool
- 0.442
- rvis_EVS
- -0.26
- rvis_percentile_EVS
- 34.93
Haploinsufficiency Scores
- pHI
- 0.294
- hipred
- Y
- hipred_score
- 0.774
- ghis
- 0.511
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.957
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Epn1
- Phenotype
- growth/size/body region phenotype; cellular phenotype; homeostasis/metabolism phenotype; embryo phenotype; neoplasm; reproductive system 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); normal phenotype; 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); 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);
Gene ontology
- Biological process
- in utero embryonic development;endocytosis;Notch signaling pathway;female pregnancy;negative regulation of epidermal growth factor receptor signaling pathway;embryonic organ development;membrane organization;negative regulation of sprouting angiogenesis
- Cellular component
- nucleus;cytosol;plasma membrane;clathrin-coated pit
- Molecular function
- protein binding;lipid binding