MAGI1

membrane associated guanylate kinase, WW and PDZ domain containing 1, the group of PDZ domain containing|Membrane associated guanylate kinases

Basic information

Region (hg38): 3:65353524-66038918

Previous symbols: [ "BAIAP1" ]

Links

ENSG00000151276 ∙ NCBI:9223 ∙ OMIM:602625 ∙ HGNC:946 ∙ Uniprot:Q96QZ7 ∙ 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 MAGI1 gene.

• Inborn genetic diseases (48 variants)
• not provided (7 variants)
• not specified (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MAGI1 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	1	3
missense			44	4		48
nonsense						0
start loss						0
frameshift						0
inframe indel					1	1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			3			3
Total	0	0	47	6	2

Variants in MAGI1

This is a list of pathogenic ClinVar variants found in the MAGI1 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-65356662-G-A		not specified	Uncertain significance (Oct 26, 2021)
3-65357097-G-A		not specified	Uncertain significance (Jul 09, 2021)
3-65361249-C-T		not specified	Uncertain significance (Feb 05, 2024)
3-65361258-T-C		not specified	Uncertain significance (Jan 16, 2024)
3-65363509-G-A		not specified	Uncertain significance (Aug 10, 2021)
3-65364892-G-T		not specified	Uncertain significance (Dec 13, 2022)
3-65364931-G-T		not specified	Uncertain significance (Jan 23, 2023)
3-65375838-C-T		not specified	Uncertain significance (Nov 08, 2022)
3-65375945-C-A		not specified	Uncertain significance (Sep 12, 2023)
3-65379333-G-A		not specified	Uncertain significance (Apr 07, 2023)
3-65379345-C-T		not specified	Uncertain significance (Apr 22, 2022)
3-65379381-T-C		not specified	Uncertain significance (Feb 06, 2023)
3-65379399-T-G		not specified	Uncertain significance (Dec 18, 2023)
3-65379470-C-T		not specified	Uncertain significance (Mar 07, 2024)
3-65379477-C-G		not specified	Uncertain significance (Mar 31, 2023)
3-65379537-C-T		not specified	Uncertain significance (Apr 12, 2022)
3-65381879-G-A		not specified	Uncertain significance (Dec 17, 2021)
3-65382014-C-G		not specified	Uncertain significance (Dec 07, 2021)
3-65382021-G-A		not specified	Uncertain significance (May 24, 2023)
3-65382051-C-T		not specified	Uncertain significance (Jan 18, 2023)
3-65383605-T-A		not specified	Uncertain significance (Jan 10, 2022)
3-65391148-T-G		not specified	Uncertain significance (Feb 05, 2024)
3-65391149-T-G		not specified	Uncertain significance (Feb 05, 2024)
3-65391150-T-G		not specified	Uncertain significance (Feb 05, 2024)
3-65391165-G-C		not specified	Uncertain significance (Jun 12, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MAGI1	protein_coding	protein_coding	ENST00000402939	23	685310

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.560	0.440	125715	0	33	125748	0.000131

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.36	785	900	0.872	0.0000550	9535
Missense in Polyphen		293	383.19	0.76464		4240
Synonymous	-0.317	373	365	1.02	0.0000243	2937
Loss of Function	6.17	16	72.7	0.220	0.00000443	752

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000268	0.000268
Ashkenazi Jewish	0.00	0.00
East Asian	0.000164	0.000163
Finnish	0.0000978	0.0000924
European (Non-Finnish)	0.000134	0.000132
Middle Eastern	0.000164	0.000163
South Asian	0.000170	0.000163
Other	0.000170	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role as scaffolding protein at cell-cell junctions. May regulate acid-induced ASIC3 currents by modulating its expression at the cell surface (By similarity). {ECO:0000250}.
• Pathway: Tight junction - Homo sapiens (human);Rap1 signaling pathway - Homo sapiens (human);Human papillomavirus infection - Homo sapiens (human);Pathways Affected in Adenoid Cystic Carcinoma;EGFR1 (Consensus)

Recessive Scores

• pRec: 0.125

Intolerance Scores

• loftool: 0.519
• rvis_EVS: -1.38
• rvis_percentile_EVS: 4.36

Haploinsufficiency Scores

• pHI: 0.272
• hipred: Y
• hipred_score: 0.793
• ghis: 0.555

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.824

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Magi1

Gene ontology

• Biological process: cell adhesion;signal transduction;cell surface receptor signaling pathway;protein-containing complex assembly
• Cellular component: nucleoplasm;cytoplasm;plasma membrane;cell-cell junction;adherens junction;bicellular tight junction;cell junction;cell projection
• Molecular function: protein binding;ATP binding;protein C-terminus binding;protein-containing complex scaffold activity;alpha-actinin binding