EPN1

epsin 1

Basic information

Region (hg38): 19:55675225-55709858

Links

ENSG00000063245 ∙ NCBI:29924 ∙ OMIM:607262 ∙ HGNC:21604 ∙ Uniprot:Q9Y6I3 ∙ 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 EPN1 gene.

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.

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				2		2
missense			48	4		52
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			2	1		3
Total	0	0	50	7	0

Variants in EPN1

This is a list of pathogenic ClinVar variants found in the EPN1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
19-55677187-T-C		not specified	Uncertain significance (May 09, 2022)
19-55677191-T-C		not specified	Uncertain significance (Oct 06, 2021)
19-55677585-A-G		not specified	Uncertain significance (Apr 07, 2023)
19-55677604-C-G		not specified	Uncertain significance (Jul 22, 2022)
19-55677604-C-T			Likely benign (Jun 01, 2022)
19-55677626-G-A		not specified	Uncertain significance (Dec 22, 2023)
19-55677653-C-G		not specified	Uncertain significance (Aug 02, 2021)
19-55677653-C-T		not specified	Uncertain significance (Jan 17, 2024)
19-55677683-A-G		not specified	Likely benign (Jul 11, 2023)
19-55677693-C-T		not specified	Uncertain significance (Oct 17, 2023)
19-55677714-C-T		not specified	Uncertain significance (Apr 07, 2022)
19-55678552-G-A			Likely benign (Apr 01, 2023)
19-55678586-C-T		not specified	Uncertain significance (Jan 09, 2024)
19-55678686-C-G		not specified	Uncertain significance (Feb 21, 2024)
19-55685573-G-A		not specified	Uncertain significance (Dec 13, 2023)
19-55685583-G-T		not specified	Uncertain significance (Sep 26, 2023)
19-55685601-C-T		not specified	Uncertain significance (Jan 19, 2024)
19-55685643-C-T		not specified	Uncertain significance (Jun 05, 2023)
19-55688933-G-T		not specified	Uncertain significance (Mar 29, 2024)
19-55689301-C-T			Likely benign (Mar 01, 2023)
19-55689943-A-G		not specified	Uncertain significance (Mar 01, 2023)
19-55691785-C-T		not specified	Uncertain significance (Mar 06, 2023)
19-55691799-G-C		not specified	Likely benign (Jul 12, 2022)
19-55691803-C-T		not specified	Uncertain significance (Apr 07, 2022)
19-55691809-C-T		not specified	Uncertain significance (Jan 23, 2023)

GnomAD

Source: gnomAD

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: dbNSFP

• 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