EDIL3

EGF like repeats and discoidin domains 3

Basic information

Region (hg38): 5:83940553-84384880

Links

ENSG00000164176 ∙ NCBI:10085 ∙ OMIM:606018 ∙ HGNC:3173 ∙ Uniprot:O43854 ∙ 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 EDIL3 gene.

• Inborn genetic diseases (23 variants)
• not provided (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EDIL3 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	3	1	25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding					1	1
Total	0	0	21	3	2

Variants in EDIL3

This is a list of pathogenic ClinVar variants found in the EDIL3 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-83943496-T-C		not specified	Uncertain significance (Jan 09, 2024)
5-83963293-A-G		not specified	Uncertain significance (Feb 28, 2023)
5-83963336-C-T		not specified	Uncertain significance (Nov 09, 2023)
5-84060294-C-T			Likely benign (Mar 29, 2018)
5-84060407-G-A		not specified	Uncertain significance (Dec 20, 2021)
5-84060419-T-C		not specified	Likely benign (Mar 07, 2023)
5-84064741-T-C		not specified	Uncertain significance (Feb 16, 2023)
5-84064785-T-C		not specified	Uncertain significance (May 18, 2022)
5-84064787-T-C			Likely benign (Dec 17, 2018)
5-84064819-T-C		not specified	Uncertain significance (Jan 23, 2024)
5-84064826-C-T		not specified	Uncertain significance (Aug 02, 2021)
5-84064829-T-C		not specified	Likely benign (Oct 12, 2021)
5-84066493-C-G			Benign (Dec 31, 2019)
5-84066509-T-C		not specified	Uncertain significance (Jul 13, 2021)
5-84066539-G-A		not specified	Uncertain significance (May 26, 2023)
5-84106659-G-A		not specified	Uncertain significance (Jun 01, 2023)
5-84106737-T-G		not specified	Uncertain significance (Jul 09, 2021)
5-84106758-C-T		not specified	Uncertain significance (Jan 26, 2022)
5-84106804-C-T		not specified	Uncertain significance (Dec 15, 2023)
5-84137337-C-T		not specified	Uncertain significance (Dec 28, 2022)
5-84180485-G-A		not specified	Uncertain significance (Jul 08, 2021)
5-84229858-C-A		not specified	Uncertain significance (Aug 17, 2022)
5-84254086-A-G		not specified	Uncertain significance (Dec 28, 2022)
5-84254095-A-G		not specified	Uncertain significance (Nov 13, 2023)
5-84254102-A-C		not specified	Uncertain significance (Nov 21, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EDIL3	protein_coding	protein_coding	ENST00000296591	11	444239

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000146	1.00	125722	0	26	125748	0.000103

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.16	206	259	0.796	0.0000127	3140
Missense in Polyphen		82	126.72	0.64712		1524
Synonymous	0.476	82	87.7	0.935	0.00000433	877
Loss of Function	3.14	12	30.8	0.389	0.00000180	327

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000588	0.0000588
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.000758	0.000707
Finnish	0.00	0.00
European (Non-Finnish)	0.0000725	0.0000703
Middle Eastern	0.000758	0.000707
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Promotes adhesion of endothelial cells through interaction with the alpha-v/beta-3 integrin receptor. Inhibits formation of vascular-like structures. May be involved in regulation of vascular morphogenesis of remodeling in embryonic development.
• Pathway: Beta3 integrin cell surface interactions;Beta5 beta6 beta7 and beta8 integrin cell surface interactions;Integrins in angiogenesis (Consensus)

Recessive Scores

• pRec: 0.137

Intolerance Scores

• loftool: 0.270
• rvis_EVS: -0.43
• rvis_percentile_EVS: 25.37

Haploinsufficiency Scores

• pHI: 0.473
• hipred: Y
• hipred_score: 0.602
• ghis: 0.557

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.306

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Edil3
• Phenotype: craniofacial phenotype; muscle phenotype; cellular phenotype; homeostasis/metabolism phenotype; endocrine/exocrine gland phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); taste/olfaction phenotype; reproductive system phenotype; normal phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands 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); 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); hematopoietic system phenotype; growth/size/body region phenotype; vision/eye phenotype; limbs/digits/tail phenotype; hearing/vestibular/ear 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); digestive/alimentary phenotype; skeleton phenotype; renal/urinary system phenotype; immune system phenotype; liver/biliary system phenotype; respiratory system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); embryo phenotype

Gene ontology

• Biological process: cell adhesion;multicellular organism development;positive regulation of cell-substrate adhesion
• Cellular component: collagen-containing extracellular matrix;extracellular exosome;extracellular vesicle
• Molecular function: integrin binding;extracellular matrix structural constituent;calcium ion binding