EEA1

early endosome antigen 1, the group of Zinc fingers FYVE-type

Basic information

Region (hg38): 12:92770637-92929331

Links

ENSG00000102189 ∙ NCBI:8411 ∙ OMIM:605070 ∙ HGNC:3185 ∙ Uniprot:Q15075 ∙ 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 EEA1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EEA1 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					1	1
missense			47	2	1	50
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	47	2	2

Variants in EEA1

This is a list of pathogenic ClinVar variants found in the EEA1 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-92776066-G-A		not specified	Uncertain significance (Apr 01, 2024)
12-92776085-T-G		not specified	Uncertain significance (Mar 27, 2023)
12-92776921-T-G		not specified	Uncertain significance (Aug 07, 2024)
12-92777652-C-T		not specified	Uncertain significance (Sep 04, 2024)
12-92778011-G-A		not specified	Uncertain significance (Oct 16, 2024)
12-92778082-C-T		not specified	Uncertain significance (May 21, 2024)
12-92778163-T-C		not specified	Uncertain significance (Feb 05, 2024)
12-92778173-C-T		not specified	Uncertain significance (Nov 21, 2022)
12-92779116-A-C		not specified	Uncertain significance (Apr 01, 2024)
12-92779218-G-A		not specified	Uncertain significance (Apr 08, 2024)
12-92779222-T-C		not specified	Uncertain significance (Dec 02, 2022)
12-92780288-T-G		not specified	Uncertain significance (Jun 11, 2021)
12-92780324-T-C		not specified	Uncertain significance (Jun 23, 2021)
12-92780347-C-T		not specified	Uncertain significance (May 20, 2024)
12-92780363-T-C		not specified	Uncertain significance (Aug 10, 2021)
12-92781964-T-C		not specified	Uncertain significance (May 07, 2024)
12-92782011-G-A		not specified	Uncertain significance (Jan 02, 2024)
12-92782065-T-C		not specified	Uncertain significance (Dec 05, 2024)
12-92782070-A-T		not specified	Benign (Mar 28, 2016)
12-92787941-C-G		not specified	Uncertain significance (Jun 16, 2023)
12-92798938-T-G		not specified	Uncertain significance (Jun 10, 2022)
12-92799037-A-G		not specified	Uncertain significance (Jul 08, 2021)
12-92799053-T-C		not specified	Uncertain significance (Jun 16, 2023)
12-92799058-T-C		not specified	Likely benign (May 23, 2024)
12-92801617-G-A		not specified	Uncertain significance (Jan 06, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EEA1	protein_coding	protein_coding	ENST00000322349	29	158695

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.929	0.0713	125702	0	42	125744	0.000167

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.38	536	634	0.846	0.0000305	9283
Missense in Polyphen		140	195.62	0.71566		2858
Synonymous	-0.0560	238	237	1.00	0.0000118	2418
Loss of Function	6.90	18	87.8	0.205	0.00000423	1145

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000155	0.000155
Ashkenazi Jewish	0.000422	0.000397
East Asian	0.000221	0.000163
Finnish	0.0000925	0.0000924
European (Non-Finnish)	0.000220	0.000211
Middle Eastern	0.000221	0.000163
South Asian	0.000106	0.0000980
Other	0.000165	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Binds phospholipid vesicles containing phosphatidylinositol 3-phosphate and participates in endosomal trafficking.
• Pathway: Endocytosis - Homo sapiens (human);Phagosome - Homo sapiens (human);Tuberculosis - Homo sapiens (human);VEGFA-VEGFR2 Signaling Pathway;phosphoinositides and their downstream targets;Toll Like Receptor 9 (TLR9) Cascade;Toll-Like Receptors Cascades;Innate Immune System;Immune System (Consensus)

Recessive Scores

• pRec: 0.355

Intolerance Scores

• loftool: 0.677
• rvis_EVS: -0.55
• rvis_percentile_EVS: 20

Haploinsufficiency Scores

• pHI: 0.646
• hipred: Y
• hipred_score: 0.706
• ghis: 0.584

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.334

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Eea1

Gene ontology

• Biological process: endocytosis;vesicle fusion;synaptic vesicle to endosome fusion;viral RNA genome replication;early endosome to late endosome transport
• Cellular component: cytoplasm;early endosome;cytosol;serine-pyruvate aminotransferase complex;membrane;extrinsic component of plasma membrane;early endosome membrane;axonal spine;recycling endosome;extracellular exosome;presynapse
• Molecular function: nucleic acid binding;protein binding;calmodulin binding;1-phosphatidylinositol binding;zinc ion binding;GTP-dependent protein binding;protein homodimerization activity