EPN2

epsin 2

Basic information

Region (hg38): 17:19215615-19336715

Links

ENSG00000072134 ∙ NCBI:22905 ∙ OMIM:607263 ∙ HGNC:18639 ∙ Uniprot:O95208 ∙ 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 EPN2 gene.

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	1		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: gnomAD

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: dbNSFP

• 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