MEGF9

multiple EGF like domains 9

Basic information

Region (hg38): 9:120600811-120714470

Previous symbols: [ "EGFL5" ]

Links

ENSG00000106780 ∙ NCBI:1955 ∙ OMIM:604268 ∙ HGNC:3234 ∙ Uniprot:Q9H1U4 ∙ 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 MEGF9 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MEGF9 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						0
missense			35	3		38
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	35	3	0

Variants in MEGF9

This is a list of pathogenic ClinVar variants found in the MEGF9 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-120605236-T-C		not specified	Uncertain significance (Dec 13, 2022)
9-120605279-C-T		not specified	Uncertain significance (Oct 26, 2021)
9-120605377-T-C		not specified	Uncertain significance (Sep 11, 2024)
9-120605384-G-A		not specified	Uncertain significance (Mar 25, 2024)
9-120605390-T-C		not specified	Uncertain significance (Dec 27, 2023)
9-120605392-T-C		not specified	Uncertain significance (Jun 16, 2024)
9-120605483-C-G		not specified	Uncertain significance (Jun 05, 2024)
9-120605494-G-C		not specified	Uncertain significance (Jun 11, 2024)
9-120605525-T-A		not specified	Uncertain significance (Apr 01, 2024)
9-120605557-T-C		not specified	Uncertain significance (Jan 31, 2024)
9-120605573-G-A		not specified	Uncertain significance (Aug 04, 2023)
9-120605596-T-C		not specified	Uncertain significance (Jul 14, 2024)
9-120605605-A-G		not specified	Uncertain significance (Mar 31, 2024)
9-120605608-A-T		not specified	Uncertain significance (May 09, 2024)
9-120607746-T-C		not specified	Uncertain significance (May 30, 2024)
9-120607888-C-T		not specified	Uncertain significance (Aug 18, 2023)
9-120607914-C-T		not specified	Uncertain significance (Oct 12, 2022)
9-120607935-T-C		not specified	Uncertain significance (Dec 22, 2023)
9-120622633-C-T		not specified	Uncertain significance (Sep 16, 2021)
9-120622636-G-C		not specified	Uncertain significance (Sep 22, 2023)
9-120622639-G-A		not specified	Uncertain significance (Sep 29, 2022)
9-120622642-C-T		not specified	Uncertain significance (Nov 24, 2024)
9-120622679-T-G		not specified	Uncertain significance (Jun 29, 2023)
9-120622708-T-C		not specified	Uncertain significance (May 08, 2023)
9-120659383-G-A		not specified	Likely benign (Oct 26, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MEGF9	protein_coding	protein_coding	ENST00000373930	6	113658

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.988	0.0119	124630	0	3	124633	0.0000120

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.43	197	262	0.751	0.0000136	3848
Missense in Polyphen		67	113.89	0.5883		1531
Synonymous	2.45	73	105	0.696	0.00000576	1264
Loss of Function	3.69	1	17.8	0.0563	8.43e-7	254

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000646	0.0000646
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000177	0.0000177
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0749

Intolerance Scores

• loftool: 0.317
• rvis_EVS: -0.38
• rvis_percentile_EVS: 27.88

Haploinsufficiency Scores

• pHI: 0.0840
• hipred: Y
• hipred_score: 0.571
• ghis: 0.528

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0550

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Megf9

Gene ontology

• Biological process: biological_process
• Cellular component: cellular_component;basement membrane;integral component of membrane