EPN3

epsin 3

Basic information

Region (hg38): 17:50532682-50543750

Links

ENSG00000049283 ∙ NCBI:55040 ∙ OMIM:607264 ∙ HGNC:18235 ∙ Uniprot:Q9H201 ∙ 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 EPN3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EPN3 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			50	2		52
nonsense						0
start loss						0
frameshift					1	1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	50	2	1

Variants in EPN3

This is a list of pathogenic ClinVar variants found in the EPN3 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-50536561-C-A		not specified	Uncertain significance (Oct 05, 2023)
17-50536575-C-T		not specified	Uncertain significance (Feb 26, 2024)
17-50536576-G-A		not specified	Uncertain significance (Sep 26, 2023)
17-50536579-G-A		not specified	Uncertain significance (Mar 14, 2023)
17-50536589-G-T		not specified	Uncertain significance (Mar 04, 2024)
17-50536596-G-A		not specified	Uncertain significance (Oct 13, 2023)
17-50536606-A-G		not specified	Uncertain significance (Nov 07, 2022)
17-50536608-T-C		not specified	Uncertain significance (Mar 24, 2023)
17-50536629-C-T		not specified	Uncertain significance (Apr 18, 2023)
17-50536630-G-A		not specified	Uncertain significance (Feb 27, 2023)
17-50536633-A-G		not specified	Uncertain significance (Mar 01, 2023)
17-50536650-C-T		not specified	Uncertain significance (Apr 08, 2024)
17-50536727-G-A		not specified	Uncertain significance (Feb 27, 2024)
17-50536741-G-A		not specified	Uncertain significance (Jan 24, 2024)
17-50536800-G-C		not specified	Uncertain significance (Nov 21, 2022)
17-50536824-G-A		not specified	Uncertain significance (Feb 05, 2024)
17-50536828-G-A		not specified	Uncertain significance (Jun 24, 2022)
17-50536857-T-C		not specified	Uncertain significance (May 03, 2023)
17-50536895-C-A		not specified	Uncertain significance (Jul 13, 2022)
17-50536896-C-T		not specified	Uncertain significance (Jan 19, 2024)
17-50536971-C-T		not specified	Uncertain significance (Feb 22, 2023)
17-50536977-C-T		not specified	Uncertain significance (Mar 23, 2022)
17-50537022-C-G		not specified	Uncertain significance (May 26, 2022)
17-50537064-C-T		not specified	Uncertain significance (Sep 01, 2021)
17-50537073-G-A		not specified	Uncertain significance (Jan 03, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EPN3	protein_coding	protein_coding	ENST00000268933	9	11208

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.42e-17	0.00809	124908	11	829	125748	0.00335

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.584	424	392	1.08	0.0000245	3985
Missense in Polyphen		175	152.1	1.1506		1473
Synonymous	-1.57	203	176	1.15	0.0000112	1379
Loss of Function	0.0661	25	25.4	0.986	0.00000134	261

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0174	0.0174
Ashkenazi Jewish	0.00113	0.00109
East Asian	0.00142	0.00141
Finnish	0.000278	0.000277
European (Non-Finnish)	0.00164	0.00160
Middle Eastern	0.00142	0.00141
South Asian	0.000641	0.000621
Other	0.00313	0.00310

dbNSFP

Source: dbNSFP

• Pathway: Endocytosis - Homo sapiens (human);EGFR1 (Consensus)

Recessive Scores

• pRec: 0.0929

Intolerance Scores

• loftool: 0.816
• rvis_EVS: 1.14
• rvis_percentile_EVS: 92.37

Haploinsufficiency Scores

• pHI: 0.283
• hipred: N
• hipred_score: 0.251
• ghis: 0.417

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: H
• gene_indispensability_pred: N
• gene_indispensability_score: 0.137

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	High
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Epn3
• Phenotype: normal phenotype; hearing/vestibular/ear phenotype

Gene ontology

• Cellular component: nucleus;nucleoplasm;clathrin-coated pit;extrinsic component of plasma membrane;clathrin-coated vesicle;intracellular membrane-bounded organelle;perinuclear region of cytoplasm;extracellular exosome
• Molecular function: protein binding;lipid binding;EH domain binding