MFGE8

milk fat globule EGF and factor V/VIII domain containing

Basic information

Region (hg38): 15:88898683-88913468

Previous symbols: [ "SPAG10" ]

Links

ENSG00000140545 ∙ NCBI:4240 ∙ OMIM:602281 ∙ HGNC:7036 ∙ Uniprot:Q08431 ∙ 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 MFGE8 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MFGE8 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				3	4	7
missense			29	3	2	34
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	29	6	7

Variants in MFGE8

This is a list of pathogenic ClinVar variants found in the MFGE8 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-88899404-C-T			Benign (Dec 31, 2019)
15-88899466-G-A		not specified	Uncertain significance (Jan 30, 2024)
15-88899480-G-A		not specified	Uncertain significance (Feb 05, 2024)
15-88899492-T-A		not specified	Uncertain significance (Dec 21, 2023)
15-88899507-T-C		not specified	Uncertain significance (Nov 10, 2022)
15-88899520-T-C		not specified	Uncertain significance (Jan 19, 2024)
15-88899706-C-T		not specified	Uncertain significance (Apr 28, 2023)
15-88899768-T-G		not specified	Uncertain significance (Jun 12, 2023)
15-88901561-T-A		not specified	Uncertain significance (Jul 05, 2023)
15-88901592-C-G		not specified	Uncertain significance (Jan 29, 2024)
15-88901673-T-A		not specified	Uncertain significance (Jun 04, 2024)
15-88901681-G-A		not specified	Uncertain significance (Nov 30, 2022)
15-88901700-T-G			Uncertain significance (Nov 23, 2022)
15-88901726-T-C		not specified	Uncertain significance (Nov 30, 2022)
15-88901730-C-T		not specified	Uncertain significance (Aug 12, 2021)
15-88905757-C-T			Likely benign (Apr 26, 2018)
15-88905779-C-T			Benign (Aug 20, 2018)
15-88905783-A-G		not specified	Uncertain significance (Jun 17, 2024)
15-88905787-G-A		not specified	Uncertain significance (Aug 08, 2023)
15-88905801-G-A		not specified	Uncertain significance (May 24, 2023)
15-88905805-G-A		not specified	Uncertain significance (Jul 14, 2021)
15-88905829-C-T		not specified	Uncertain significance (Dec 22, 2023)
15-88905884-C-G		not specified	Uncertain significance (Apr 11, 2023)
15-88906664-C-T		not specified	Likely benign (Aug 16, 2021)
15-88906694-A-C		not specified	Uncertain significance (Aug 30, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MFGE8	protein_coding	protein_coding	ENST00000268150	8	14727

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000440	0.964	125543	1	204	125748	0.000815

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.365	237	222	1.07	0.0000150	2530
Missense in Polyphen		107	96.761	1.1058		1103
Synonymous	-0.919	107	95.6	1.12	0.00000691	756
Loss of Function	1.90	10	18.9	0.529	9.19e-7	209

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000294	0.000294
Ashkenazi Jewish	0.00	0.00
East Asian	0.000381	0.000381
Finnish	0.00592	0.00588
European (Non-Finnish)	0.000291	0.000290
Middle Eastern	0.000381	0.000381
South Asian	0.000817	0.000817
Other	0.00114	0.00114

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays an important role in the maintenance of intestinal epithelial homeostasis and the promotion of mucosal healing. Promotes VEGF-dependent neovascularization (By similarity). Contributes to phagocytic removal of apoptotic cells in many tissues. Specific ligand for the alpha-v/beta-3 and alpha-v/beta-5 receptors. Also binds to phosphatidylserine-enriched cell surfaces in a receptor-independent manner. Zona pellucida-binding protein which may play a role in gamete interaction. {ECO:0000250, ECO:0000269|PubMed:19204935}.
• Pathway: Extracellular vesicle-mediated signaling in recipient cells;Glucocorticoid Receptor Pathway;Nuclear Receptors Meta-Pathway;Ebola Virus Pathway on Host;Ebola Virus Pathway on Host;Post-translational protein phosphorylation;Post-translational protein modification;Metabolism of proteins;Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs);Validated transcriptional targets of TAp63 isoforms;Integrins in angiogenesis (Consensus)

Intolerance Scores

• loftool: 0.0884
• rvis_EVS: -0.53
• rvis_percentile_EVS: 20.78

Haploinsufficiency Scores

• pHI: 0.337
• hipred: N
• hipred_score: 0.170
• ghis: 0.609

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.657

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mfge8
• Phenotype: immune system phenotype; renal/urinary system phenotype; reproductive system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype; endocrine/exocrine gland phenotype; neoplasm; cellular phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan)

Gene ontology

• Biological process: angiogenesis;phagocytosis, recognition;phagocytosis, engulfment;cell adhesion;single fertilization;apoptotic cell clearance;post-translational protein modification;cellular protein metabolic process;positive regulation of phagocytosis
• Cellular component: extracellular region;extracellular space;endoplasmic reticulum lumen;external side of plasma membrane;membrane;extrinsic component of plasma membrane;collagen-containing extracellular matrix;extracellular exosome;extracellular vesicle
• Molecular function: phosphatidylserine binding;integrin binding;extracellular matrix structural constituent;phosphatidylethanolamine binding