MEGF6

protein-coding

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

Gene summary

Predicted to enable scavenger receptor activity. Predicted to be involved in vesicle-mediated transport. Predicted to be located in extracellular region. Predicted to be active in plasma membrane. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

EGFL3

MANE transcript

NM_001409.4

Inheritance

—

ClinVar variants

U:319B:54

Top phenotype

EBV-positive nodal T- and NK-cell lymphoma

gnomAD constraint

pLI —, LoF o/e 0.74

Max pathogenic AF

—

Genomic locus

chr1:3,487,951-3,611,508

External References & Databases

Ensembl (ENSG00000162591)

Transcript & Mutation Effects

hg38 • Region Span ~123.6 kb

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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 MEGF6 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 329

not providedTotal: 32

EBV-positive nodal T- and NK-cell lymphomaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001409.4. 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			3 clinvar	11 clinvar	8 clinvar	22
missense			309 clinvar	26 clinvar	9 clinvar	344
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			7 clinvar			7
Total	0	0	319	37	17	373

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 63 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001409.4	RefSeq	NP_001400.3	37	MANE Select
ENST00000356575.9	Ensembl	ENSP00000348982.4	37	MANE Select
NM_001410718.1	RefSeq	NP_001397647.1	34	Standard
ENST00000294599.8	Ensembl	ENSP00000294599.4	30	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

biological_process

Molecular Function

calcium ion binding
protein binding

Cellular Component

cellular_component
extracellular region

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000356575
Coding exons: 37
Length: 121576
Individuals with no LoFs: 124511
Homozygous LoFs: 1
Heterozygous LoFs: 281
Defined: 124793
p: 0.00113

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.458	923	963	0.958	0.0000651	9850
Missense (PolyPhen)		264	332.32	0.79441		3610
Synonymous	-2.15	479	423	1.13	0.0000337	2903
Loss of Function	2.27	65	88.0	0.739	0.00000480	947

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00029	0.00026	rare
Latino/Admixed American	0.0013	0.0012	notable
Ashkenazi Jewish	0.0010	0.00099	notable
East Asian	0.0019	0.0018	notable
Finnish	0.0022	0.0021	notable
European (Non-Finnish)	0.00096	0.00090	rare
South Asian	0.0013	0.0012	notable
Other	0.0010	0.00099	notable

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0988

Intolerance Scores

LoFtool: 0.187
RVIS EVS: 2.07
RVIS percentile EVS: 97.81

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.627

Gene Damage Prediction

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