EGFL6

protein-coding

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

Gene summary

This gene encodes a member of the epidermal growth factor (EGF) repeat superfamily. Members of this superfamily are characterized by the presence of EGF-like repeats and are often involved in the regulation of cell cycle, proliferation, and developmental processes. The gene product contains a signal peptide, suggesting that it is secreted; an EGF repeat region consisting of 4 complete EGF-like repeats and 1 partial EGF-like repeat, 3 of which have a calcium-binding consensus sequence; an arg-gly-asp integrin association motif; and a MAM domain, which is believed to have an adhesive function. This gene is expressed early during development, and its expression has been detected in lung and meningioma tumors. [provided by RefSeq, Jul 2008]

Previous symbols:

MAEG

MANE transcript

NM_015507.4

Inheritance

—

ClinVar variants

U:102B:12

Top phenotype

Exstrophy-epispadias complex

gnomAD constraint

pLI —, LoF o/e 0.88

Max pathogenic AF

—

Genomic locus

chrX:13,569,601-13,633,575

External References & Databases

Ensembl (ENSG00000198759)

Transcript & Mutation Effects

hg38 • Region Span ~64.0 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to EGFL6 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 63

not providedTotal: 11

Exstrophy-epispadias complexTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_015507.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			4 clinvar	3 clinvar	3 clinvar	10
missense			85 clinvar	3 clinvar	3 clinvar	91
nonsense			5 clinvar			5
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			8 clinvar			8
Total	0	0	102	6	6	114

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 11 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_015507.4	RefSeq	NP_056322.2	12	MANE Select
ENST00000361306.6	Ensembl	ENSP00000355126.1	12	MANE Select
NM_001167890.2	RefSeq	NP_001161362.1	12	Standard
ENST00000380602.3	Ensembl	ENSP00000369976.3	12	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
egfl6	Danio rerio	Structure: endothelial tip cell Quality: decreased occurrence abnormal

Gene / Model

Organism

Observed Phenotype

egfl6

Danio rerio

Structure: endothelial tip cell

Quality: decreased occurrence

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

cell adhesion
multicellular organism development
positive regulation of cell-substrate adhesion
cell differentiation
extracellular matrix organization

Molecular Function

integrin binding
calcium ion binding

Cellular Component

basement membrane
extracellular space
membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000380602
Coding exons: 12
Length: 63971
Individuals with no LoFs: 125679
Homozygous LoFs: 22
Heterozygous LoFs: 45
Defined: 125746
p: 0.000266

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.637	189	215	0.878	0.0000162	3667
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00038	0.00031	rare
Latino/Admixed American	0.00030	0.00023	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00051	0.00038	rare
Finnish	0.000063	0.000046	rare
European (Non-Finnish)	0.00026	0.00018	rare
South Asian	0.0013	0.00082	notable
Other	0	0.0	absent

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.567

Gene Damage Prediction

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