MAGI3

membrane associated guanylate kinase, WW and PDZ domain containing 3, the group of PDZ domain containing|Membrane associated guanylate kinases

Basic information

Region (hg38): 1:113390514-113685923

Links

ENSG00000081026 ∙ NCBI:260425 ∙ OMIM:615943 ∙ HGNC:29647 ∙ Uniprot:Q5TCQ9 ∙ 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 MAGI3 gene.

• Inborn genetic diseases (40 variants)
• not provided (3 variants)
• Arthrogryposis multiplex congenita;Fetal akinesia deformation sequence 1 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MAGI3 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					2	2
missense			41	1		42
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	41	1	2

Variants in MAGI3

This is a list of pathogenic ClinVar variants found in the MAGI3 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-113391113-G-T		not specified	Uncertain significance (Feb 28, 2024)
1-113391173-G-A		not specified	Uncertain significance (Jan 29, 2024)
1-113391215-C-G		not specified	Uncertain significance (Jul 12, 2023)
1-113391292-A-G		not specified	Uncertain significance (Mar 07, 2024)
1-113549539-G-A		not specified	Uncertain significance (Aug 30, 2022)
1-113549574-A-G		not specified	Uncertain significance (Dec 19, 2023)
1-113585502-G-A			Benign (Dec 31, 2019)
1-113590558-A-G		not specified	Uncertain significance (Dec 01, 2022)
1-113590628-A-G		not specified	Uncertain significance (Apr 18, 2023)
1-113590642-A-T		not specified	Uncertain significance (Jun 24, 2022)
1-113594552-A-C		not specified	Uncertain significance (Feb 16, 2023)
1-113594554-G-A		not specified	Uncertain significance (Feb 05, 2024)
1-113619780-C-G		not specified	Uncertain significance (Aug 13, 2021)
1-113622850-G-A		not specified	Uncertain significance (Nov 18, 2022)
1-113622863-G-A		not specified	Uncertain significance (Jan 04, 2024)
1-113622884-C-T		not specified	Uncertain significance (Dec 01, 2022)
1-113622886-A-G		not specified	Uncertain significance (May 01, 2022)
1-113641950-G-C		not specified	Uncertain significance (Jan 04, 2024)
1-113641975-G-T		not specified	Uncertain significance (Jul 12, 2023)
1-113642138-G-T		not specified	Uncertain significance (Jan 23, 2023)
1-113642181-C-T		not specified	Uncertain significance (May 23, 2023)
1-113642462-G-A		not specified	Uncertain significance (Aug 08, 2022)
1-113642472-A-G		not specified	Uncertain significance (Dec 20, 2021)
1-113643746-C-T		not specified	Uncertain significance (Sep 25, 2023)
1-113646531-G-C		not specified	Uncertain significance (Jul 06, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MAGI3	protein_coding	protein_coding	ENST00000307546	21	295175

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0298	0.970	125665	0	83	125748	0.000330

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.33	595	778	0.765	0.0000385	9687
Missense in Polyphen		237	350.26	0.67665		4295
Synonymous	2.12	237	282	0.839	0.0000142	2862
Loss of Function	5.47	16	62.8	0.255	0.00000334	808

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00146	0.00139
Ashkenazi Jewish	0.0000994	0.0000992
East Asian	0.000223	0.000217
Finnish	0.0000464	0.0000462
European (Non-Finnish)	0.000263	0.000255
Middle Eastern	0.000223	0.000217
South Asian	0.000642	0.000621
Other	0.000346	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as a scaffolding protein at cell-cell junctions, thereby regulating various cellular and signaling processes. Cooperates with PTEN to modulate the kinase activity of AKT1. Its interaction with PTPRB and tyrosine phosphorylated proteins suggests that it may link receptor tyrosine phosphatase with its substrates at the plasma membrane. In polarized epithelial cells, involved in efficient trafficking of TGFA to the cell surface. Regulates the ability of LPAR2 to activate ERK and RhoA pathways. Regulates the JNK signaling cascade via its interaction with FZD4 and VANGL2. {ECO:0000269|PubMed:10748157}.
• Pathway: Rap1 signaling pathway - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.109

Intolerance Scores

• loftool: 0.744
• rvis_EVS: -0.93
• rvis_percentile_EVS: 9.75

Haploinsufficiency Scores

• pHI: 0.931
• hipred: Y
• hipred_score: 0.652
• ghis: 0.553

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.589

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Magi3

Zebrafish Information Network

• Gene name: magi3b
• Affected structure: otolith
• Phenotype tag: abnormal
• Phenotype quality: morphology

Gene ontology

• Biological process: apoptotic process;signal transduction;viral process;intracellular signal transduction;GMP metabolic process;regulation of JNK cascade;GDP metabolic process
• Cellular component: nucleus;cytoplasm;plasma membrane;cell-cell junction;bicellular tight junction;membrane;cell junction
• Molecular function: guanylate kinase activity;protein binding;ATP binding;protein-containing complex scaffold activity