MEGF11

multiple EGF like domains 11

Basic information

Region (hg38): 15:65895078-66253756

Links

ENSG00000157890 ∙ NCBI:84465 ∙ OMIM:612454 ∙ HGNC:29635 ∙ Uniprot:A6BM72 ∙ 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 MEGF11 gene.

• Inborn genetic diseases (58 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MEGF11 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				1		1
missense			55	3		58
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	55	4	0

Variants in MEGF11

This is a list of pathogenic ClinVar variants found in the MEGF11 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-65897939-A-G		not specified	Uncertain significance (Dec 20, 2023)
15-65897956-G-A		not specified	Uncertain significance (Jun 22, 2021)
15-65898023-G-A		not specified	Uncertain significance (Feb 06, 2024)
15-65898029-C-T		not specified	Uncertain significance (Sep 20, 2023)
15-65898053-A-C		not specified	Uncertain significance (Aug 09, 2021)
15-65898926-T-C		not specified	Uncertain significance (Dec 02, 2021)
15-65906132-C-T		not specified	Uncertain significance (Apr 25, 2022)
15-65913787-A-G		not specified	Uncertain significance (Apr 26, 2023)
15-65913791-G-A		not specified	Uncertain significance (Jan 27, 2022)
15-65913827-G-A		not specified	Uncertain significance (Dec 06, 2022)
15-65913829-C-T		not specified	Uncertain significance (Feb 10, 2022)
15-65913890-T-G		not specified	Uncertain significance (Sep 06, 2022)
15-65913916-G-A		not specified	Uncertain significance (Jul 15, 2021)
15-65913940-G-A		not specified	Uncertain significance (Oct 17, 2023)
15-65913956-C-T		not specified	Uncertain significance (Jun 21, 2023)
15-65913970-G-A		not specified	Uncertain significance (Dec 03, 2021)
15-65916241-G-A		not specified	Uncertain significance (Feb 10, 2022)
15-65916253-T-C		not specified	Uncertain significance (Jan 31, 2022)
15-65916896-G-A		not specified	Uncertain significance (Jun 09, 2022)
15-65916896-G-C		not specified	Uncertain significance (Oct 14, 2021)
15-65917971-G-A		not specified	Uncertain significance (Oct 10, 2023)
15-65918035-C-T		not specified	Uncertain significance (Jul 13, 2022)
15-65918038-T-C		not specified	Uncertain significance (Jan 20, 2023)
15-65918043-G-A		not specified	Uncertain significance (Oct 17, 2023)
15-65922377-C-G		not specified	Uncertain significance (Dec 15, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MEGF11	protein_coding	protein_coding	ENST00000409699	22	358669

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.37e-30	0.000618	125430	0	163	125593	0.000649

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.853	529	587	0.901	0.0000330	6766
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00148	0.00146
Ashkenazi Jewish	0.0000994	0.0000993
East Asian	0.000763	0.000761
Finnish	0.0000927	0.0000925
European (Non-Finnish)	0.000806	0.000793
Middle Eastern	0.000763	0.000761
South Asian	0.000480	0.000457
Other	0.000666	0.000653

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.356
• hipred: N
• hipred_score: 0.300
• ghis: 0.610

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.270

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Megf11
• Phenotype: vision/eye phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan)

Gene ontology

• Biological process: retina layer formation;homotypic cell-cell adhesion
• Cellular component: integral component of membrane;basolateral plasma membrane