MEGF11

protein-coding

multiple EGF like domains 11

Gene summary

Predicted to be an extracellular matrix structural constituent. Predicted to be involved in homotypic cell-cell adhesion; retina layer formation; and substrate adhesion-dependent cell spreading. Predicted to be located in basolateral plasma membrane. Predicted to be active in basement membrane and obsolete extracellular space. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_001385028.1

Inheritance

—

ClinVar variants

U:187B:8

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.89

Max pathogenic AF

—

Genomic locus

chr15:65,895,079-66,253,756

External References & Databases

Ensembl (ENSG00000157890)

Transcript & Mutation Effects

hg38 • Region Span ~358.7 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 MEGF11 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 189

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001385028.1. 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				2 clinvar		2
missense			185 clinvar	6 clinvar		191
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	187	8	0	195

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 34 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001385028.1	RefSeq	NP_001371957.1	25	MANE Select
ENST00000395614.6	Ensembl	ENSP00000378976.2	25	MANE Select
NM_001385029.1	RefSeq	NP_001371958.1	24	Standard
NM_001385030.1	RefSeq	NP_001371959.1	20	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

retina layer formation
homotypic cell-cell adhesion

Cellular Component

integral component of membrane
basolateral plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000409699
Coding exons: 22
Length: 358669
Individuals with no LoFs: 125430
Homozygous LoFs: 0
Heterozygous LoFs: 163
Defined: 125593
p: 0.000649

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.853	529	587	0.901	0.0000330	6766
Missense (PolyPhen)		162	180.12	0.89939		2069
Synonymous	1.81	201	236	0.850	0.0000147	1923
Loss of Function	0.746	49	55.0	0.891	0.00000287	633

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00070	0.00068	rare
Latino/Admixed American	0.00079	0.00078	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.00076	0.00076	rare
Finnish	0.000093	0.000092	rare
European (Non-Finnish)	0.00081	0.00079	rare
South Asian	0.00048	0.00046	rare
Other	0.00067	0.00065	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May regulate the mosaic spacing of specific neuron subtypes in the retina through homotypic retinal neuron repulsion. Mosaics provide a mechanism to distribute each cell type evenly across the retina, ensuring that all parts of the visual field have access to a full set of processing elements (By similarity). {ECO:0000250}.;

Recessive Scores

pRec: 0.0885

Intolerance Scores

LoFtool: 0.239
RVIS EVS: -0.64
RVIS percentile EVS: 16.76

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Indispensability pred.: N
Indispensability score: 0.270

Gene Damage Prediction

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