MEGF6

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

Basic information

Region (hg38): 1:3487951-3611508

Previous symbols: [ "EGFL3" ]

Links

ENSG00000162591 ∙ NCBI:1953 ∙ OMIM:604266 ∙ HGNC:3232 ∙ Uniprot:O75095 ∙ 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 MEGF6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MEGF6 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				8	8	16
missense			183	20	10	213
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				2		2
non coding						0
Total	0	0	183	28	18

Variants in MEGF6

This is a list of pathogenic ClinVar variants found in the MEGF6 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-3490548-C-T			Benign (Dec 31, 2019)
1-3490553-C-T		not specified	Uncertain significance (Mar 01, 2025)
1-3490554-G-A		not specified	Uncertain significance (Sep 12, 2023)
1-3490567-G-A			Likely benign (Oct 01, 2024)
1-3490571-G-A		not specified	Uncertain significance (May 30, 2024)
1-3490939-C-T		not specified	Uncertain significance (Oct 22, 2024)
1-3490947-C-T		not specified	Likely benign (May 30, 2023)
1-3490948-G-A		not specified	Uncertain significance (Sep 03, 2024)
1-3490959-C-A		not specified	Uncertain significance (May 31, 2023)
1-3492689-C-A		not specified	Uncertain significance (Aug 10, 2024)
1-3492699-C-T		not specified	Uncertain significance (Nov 18, 2022)
1-3492713-C-A		not specified	Uncertain significance (Nov 20, 2024)
1-3492717-C-T		not specified	Uncertain significance (Sep 25, 2024)
1-3492751-C-A		not specified	Likely benign (Aug 27, 2024)
1-3493785-G-C		not specified	Uncertain significance (Apr 01, 2024)
1-3493810-G-A		not specified	Uncertain significance (Nov 24, 2024)
1-3493862-C-G		not specified	Uncertain significance (Feb 19, 2025)
1-3493887-C-G		not specified	Uncertain significance (Dec 15, 2023)
1-3494004-C-T		not specified	Uncertain significance (Nov 21, 2024)
1-3494014-C-T		not specified	Uncertain significance (Nov 15, 2021)
1-3494023-C-T		not specified	Uncertain significance (Jul 08, 2022)
1-3494040-C-T		not specified	Likely benign (Apr 12, 2023)
1-3494064-G-A		not specified	Uncertain significance (Sep 02, 2024)
1-3494399-G-A		not specified	Likely benign (Jul 27, 2024)
1-3494421-G-A		not specified	Uncertain significance (Jan 02, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MEGF6	protein_coding	protein_coding	ENST00000356575	37	121576

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.80e-34	0.123	124511	1	281	124793	0.00113

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.458	923	963	0.958	0.0000651	9850
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00160	0.00157
Ashkenazi Jewish	0.00104	0.000994
East Asian	0.00190	0.00184
Finnish	0.00218	0.00214
European (Non-Finnish)	0.000960	0.000901
Middle Eastern	0.00190	0.00184
South Asian	0.00130	0.00124
Other	0.00103	0.000989

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0988

Intolerance Scores

• loftool: 0.187
• rvis_EVS: 2.07
• rvis_percentile_EVS: 97.81

Haploinsufficiency Scores

• pHI: 0.110
• hipred: N
• hipred_score: 0.475
• ghis: 0.406

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.627

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Megf6

Gene ontology

• Biological process: biological_process
• Cellular component: cellular_component;extracellular region
• Molecular function: calcium ion binding;protein binding