EGFL6

EGF like domain multiple 6, the group of MicroRNA protein coding host genes

Basic information

Region (hg38): X:13569601-13633575

Previous symbols: [ "MAEG" ]

Links

ENSG00000198759 ∙ NCBI:25975 ∙ OMIM:300239 ∙ HGNC:3235 ∙ Uniprot:Q8IUX8 ∙ 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 EGFL6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EGFL6 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				3	3	6
missense			25	2	3	30
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	25	5	6

Variants in EGFL6

This is a list of pathogenic ClinVar variants found in the EGFL6 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-13569921-C-T			Likely benign (Mar 01, 2023)
X-13589567-A-G		not specified	Uncertain significance (Jan 19, 2022)
X-13589615-C-T		not specified	Uncertain significance (Dec 16, 2023)
X-13589624-C-T		not specified	Uncertain significance (Oct 16, 2023)
X-13594844-G-A			Benign (May 15, 2018)
X-13594871-G-A			Likely benign (Mar 05, 2018)
X-13594880-A-G		not specified	Uncertain significance (Dec 20, 2023)
X-13594910-G-A		not specified	Uncertain significance (Dec 21, 2022)
X-13599992-A-C		not specified	Uncertain significance (Sep 14, 2022)
X-13600001-C-T			Likely benign (Nov 24, 2017)
X-13600018-A-G			Benign (Apr 11, 2018)
X-13600031-C-T		not specified	Uncertain significance (Oct 27, 2023)
X-13600042-C-T			Benign (Feb 25, 2018)
X-13600045-G-A			Benign (Apr 11, 2018)
X-13600087-G-A			Likely benign (Sep 01, 2022)
X-13603347-A-G		not specified	Uncertain significance (Dec 16, 2023)
X-13603356-G-A		not specified	Uncertain significance (May 28, 2024)
X-13603357-T-G		not specified	Uncertain significance (May 16, 2022)
X-13603403-C-T		not specified	Uncertain significance (Nov 22, 2022)
X-13603406-C-T			Benign (May 15, 2018)
X-13606382-T-C		not specified	Uncertain significance (Dec 01, 2022)
X-13606482-G-T			Likely benign (Mar 01, 2022)
X-13606493-G-A		not specified	Uncertain significance (Jun 17, 2024)
X-13608342-T-C		not specified	Uncertain significance (Sep 25, 2023)
X-13608441-G-A		not specified	Uncertain significance (Mar 07, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EGFL6	protein_coding	protein_coding	ENST00000380602	12	63971

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.98e-13	0.0802	125679	22	45	125746	0.000266

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.637	189	215	0.878	0.0000162	3667
Missense in Polyphen		65	77.886	0.83455		1332
Synonymous	-0.936	96	85.0	1.13	0.00000695	1007
Loss of Function	0.507	20	22.6	0.885	0.00000198	350

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000680	0.000603
Ashkenazi Jewish	0.00	0.00
East Asian	0.000514	0.000381
Finnish	0.0000626	0.0000462
European (Non-Finnish)	0.000259	0.000185
Middle Eastern	0.000514	0.000381
South Asian	0.00134	0.000817
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May bind integrin alpha-8/beta-1 and play a role in hair follicle morphogenesis. Promotes matrix assembly (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.0927

Intolerance Scores

• loftool: 0.296
• rvis_EVS: 1.11
• rvis_percentile_EVS: 92.06

Haploinsufficiency Scores

• pHI: 0.102
• hipred: N
• hipred_score: 0.196

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.567

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Egfl6
• Phenotype: normal phenotype

Zebrafish Information Network

• Gene name: egfl6
• Affected structure: endothelial tip cell
• Phenotype tag: abnormal
• Phenotype quality: decreased occurrence

Gene ontology

• Biological process: cell adhesion;multicellular organism development;positive regulation of cell-substrate adhesion;cell differentiation;extracellular matrix organization
• Cellular component: basement membrane;extracellular space;membrane
• Molecular function: integrin binding;calcium ion binding