EPS15L1

epidermal growth factor receptor pathway substrate 15 like 1, the group of EF-hand domain containing

Basic information

Region (hg38): 19:16355225-16472085

Links

ENSG00000127527

∙ NCBI:58513 ∙ OMIM:616826 ∙ HGNC:24634 ∙ Uniprot:Q9UBC2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

split hand-foot malformation (Supportive), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the EPS15L1 gene.

not_specified (87 variants)
not_provided (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EPS15L1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001258374.3. 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			82 clinvar	5 clinvar		87
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)						0
Total	0	0	83	5	0

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EPS15L1	protein_coding	protein_coding	ENST00000455140	24	116847

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.000363	125734	0	14	125748	0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.90	417	542	0.770	0.0000322	6002
Missense in Polyphen		111	182.89	0.60691		2116
Synonymous	0.746	220	235	0.938	0.0000164	1739
Loss of Function	5.90	7	53.6	0.131	0.00000293	579

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000973	0.0000879
Middle Eastern	0.000109	0.000109
South Asian	0.0000328	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Seems to be a constitutive component of clathrin-coated pits that is required for receptor-mediated endocytosis. Involved in endocytosis of integrin beta-1 (ITGB1) and transferrin receptor (TFR); internalization of ITGB1 as DAB2-dependent cargo but not TFR seems to require association with DAB2. {ECO:0000269|PubMed:22648170, ECO:0000269|PubMed:9407958}.;
Pathway: Endocytosis - Homo sapiens (human);EGF-EGFR Signaling Pathway;Signal Transduction;Vesicle-mediated transport;Membrane Trafficking;EGFR downregulation;Signaling by EGFR;Clathrin-mediated endocytosis;Cargo recognition for clathrin-mediated endocytosis;Signaling by Receptor Tyrosine Kinases (Consensus)

Recessive Scores

pRec: 0.127

Intolerance Scores

loftool: 0.269
rvis_EVS: -2.13
rvis_percentile_EVS: 1.51

Haploinsufficiency Scores

pHI: 0.146
hipred: Y
hipred_score: 0.756
ghis: 0.654

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: S
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.603

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Eps15l1
Phenotype

Zebrafish Information Network

Gene name: eps15l1b
Affected structure: T cell differentiation in thymus
Phenotype tag: abnormal
Phenotype quality: disrupted

Gene ontology

Biological process: endocytosis;negative regulation of epidermal growth factor receptor signaling pathway;membrane organization
Cellular component: nucleus;cytosol;plasma membrane;membrane;clathrin coat of coated pit
Molecular function: calcium ion binding;protein binding;cadherin binding