MAGI1

protein-coding

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

Gene summary

The protein encoded by this gene is a member of the membrane-associated guanylate kinase homologue (MAGUK) family. MAGUK proteins participate in the assembly of multiprotein complexes on the inner surface of the plasma membrane at regions of cell-cell contact. The product of this gene may play a role as scaffolding protein at cell-cell junctions. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2008]

Previous symbols:

BAIAP1

MANE transcript

NM_001033057.2

Inheritance

—

ClinVar variants

U:158B:20

Top phenotype

EBV-positive nodal T- and NK-cell lymphoma

gnomAD constraint

pLI —, LoF o/e 0.22

Max pathogenic AF

—

Genomic locus

chr3:65,353,525-66,038,918

External References & Databases

Ensembl (ENSG00000151276)

Transcript & Mutation Effects

hg38 • Region Span ~685.4 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to MAGI1 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 154

not providedTotal: 11

EBV-positive nodal T- and NK-cell lymphomaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001033057.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			7 clinvar	11 clinvar	1 clinvar	19
missense			145 clinvar	6 clinvar	1 clinvar	152
nonsense			1 clinvar	1 clinvar		2
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	0	158	18	2	178

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 22 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001033057.2	RefSeq	NP_001028229.1	23	MANE Select
ENST00000402939.7	Ensembl	ENSP00000385450.2	23	MANE Select
NM_001365903.2	RefSeq	NP_001352832.1	25	Standard
NM_001365904.2	RefSeq	NP_001352833.1	25	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Tight junction - Homo sapiens (human)
Rap1 signaling pathway - Homo sapiens (human)
Human papillomavirus infection - Homo sapiens (human)
Pathways Affected in Adenoid Cystic Carcinoma
EGFR1

Biological Process

cell adhesion
signal transduction
cell surface receptor signaling pathway
protein-containing complex assembly

Molecular Function

protein binding
ATP binding
protein C-terminus binding
protein-containing complex scaffold activity
alpha-actinin binding

Cellular Component

nucleoplasm
cytoplasm
plasma membrane
cell-cell junction
adherens junction

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000402939
Coding exons: 23
Length: 685310
Individuals with no LoFs: 125715
Homozygous LoFs: 0
Heterozygous LoFs: 33
Defined: 125748
p: 0.000131

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.36	785	900	0.872	0.0000550	9535
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00012	0.00012	rare
Latino/Admixed American	0.00014	0.00014	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00016	0.00016	rare
Finnish	0.000098	0.000092	rare
European (Non-Finnish)	0.00013	0.00013	rare
South Asian	0.00017	0.00016	rare
Other	0.00017	0.00016	rare

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.125

Intolerance Scores

LoFtool: 0.519
RVIS EVS: -1.38
RVIS percentile EVS: 4.36

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.824

Gene Damage Prediction

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