MAGT1

magnesium transporter 1, the group of Oligosaccharyltransferase complex subunits|Solute carrier family 58

Basic information

Region (hg38): X:77825747-77899271

Links

ENSG00000102158 ∙ NCBI:84061 ∙ OMIM:300715 ∙ HGNC:28880 ∙ Uniprot:Q9H0U3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• intellectual disability, X-linked 95 (Limited), mode of inheritance: XLR
• X-linked immunodeficiency with magnesium defect, Epstein-Barr virus infection and neoplasia (Supportive), mode of inheritance: Unknown
• intellectual disability, X-linked 95 (Limited), mode of inheritance: XL
• X-linked immunodeficiency with magnesium defect, Epstein-Barr virus infection and neoplasia (Strong), mode of inheritance: XL
• X-linked intellectual disability (Disputed Evidence), mode of inheritance: XL

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Immunodeficiency, X-linked, with magnesium defect, Epstein-Barr virus infection and neoplasia	XL	Allergy/Immunology/Infectious	Antiinfectious prophylaxis and early and aggressive treatment of infections may be beneficial	Allergy/Immunology/Infectious; Craniofacial; Neurologic	18455129; 21796205; 23871722; 25504528; 25956530; 31036665
For Mental retardation, X-linked 95, the evidence of variants as being related to disease causation has been questioned due to subsequent population-based studies

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the MAGT1 gene.

• X-linked immunodeficiency with magnesium defect, Epstein-Barr virus infection and neoplasia (18 variants)
• not provided (2 variants)
• Congenital disorder of glycosylation, type ICC (2 variants)
• Congenital disorder of glycosylation (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MAGT1 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			1	24	5	30
missense	1		56	6	3	66
nonsense	11		1			12
start loss			1			1
frameshift	6	4				10
inframe indel			2			2
splice donor/acceptor (+/-2bp)	1	3				4
splice region			4	4	2	10
non coding			23	28	18	69
Total	19	7	84	58	26

Variants in MAGT1

This is a list of pathogenic ClinVar variants found in the MAGT1 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-77830760-C-T			Likely benign (Aug 31, 2020)
X-77830802-T-C		X-linked immunodeficiency with magnesium defect, Epstein-Barr virus infection and neoplasia	Uncertain significance (Nov 28, 2023)
X-77830804-C-T		X-linked immunodeficiency with magnesium defect, Epstein-Barr virus infection and neoplasia • Inherited Immunodeficiency Diseases	Conflicting classifications of pathogenicity (Sep 06, 2022)
X-77830820-T-C		X-linked immunodeficiency with magnesium defect, Epstein-Barr virus infection and neoplasia	Uncertain significance (Mar 26, 2022)
X-77830825-T-G		Congenital disorder of glycosylation, type ICC • Congenital disorder of glycosylation	Pathogenic (Jul 01, 2018)
X-77830839-T-C		X-linked immunodeficiency with magnesium defect, Epstein-Barr virus infection and neoplasia	Uncertain significance (Sep 21, 2019)
X-77830846-C-A		X-linked immunodeficiency with magnesium defect, Epstein-Barr virus infection and neoplasia	Uncertain significance (Jul 13, 2022)
X-77830848-T-C		X-linked immunodeficiency with magnesium defect, Epstein-Barr virus infection and neoplasia	Uncertain significance (Jul 14, 2023)
X-77830849-C-T		X-linked immunodeficiency with magnesium defect, Epstein-Barr virus infection and neoplasia	Pathogenic (Aug 06, 2019)
X-77830852-A-G		X-linked immunodeficiency with magnesium defect, Epstein-Barr virus infection and neoplasia	Likely benign (Aug 03, 2023)
X-77830864-TACA-T		X-linked immunodeficiency with magnesium defect, Epstein-Barr virus infection and neoplasia	Uncertain significance (Jun 23, 2021)
X-77830865-A-C		not specified • X-linked immunodeficiency with magnesium defect, Epstein-Barr virus infection and neoplasia • MAGT1-related disorder • Congenital disorder of glycosylation, type ICC;X-linked immunodeficiency with magnesium defect, Epstein-Barr virus infection and neoplasia	Benign/Likely benign (Jan 09, 2024)
X-77830888-A-T		X-linked immunodeficiency with magnesium defect, Epstein-Barr virus infection and neoplasia	Pathogenic (Aug 09, 2022)
X-77830890-A-G			Uncertain significance (Feb 14, 2024)
X-77830893-T-C		X-linked immunodeficiency with magnesium defect, Epstein-Barr virus infection and neoplasia	Uncertain significance (Nov 25, 2022)
X-77830901-G-C		X-linked immunodeficiency with magnesium defect, Epstein-Barr virus infection and neoplasia	Uncertain significance (Apr 17, 2020)
X-77830970-TTTTTA-T			Benign (Nov 26, 2019)
X-77830970-TTTTTATTTTA-T			Benign (Mar 07, 2020)
X-77830970-TTTTTATTTTATTTTA-T			Benign (Jun 06, 2020)
X-77830970-TTTTTATTTTATTTTATTTTA-T			Benign (Nov 22, 2019)
X-77830970-T-TTTTTA			Likely benign (Aug 28, 2020)
X-77830970-T-TTTTTATTTTA			Likely benign (Oct 03, 2020)
X-77831066-G-A			Benign (Jun 08, 2021)
X-77841235-A-C		X-linked immunodeficiency with magnesium defect, Epstein-Barr virus infection and neoplasia	Likely benign (Oct 29, 2023)
X-77841238-T-C		X-linked immunodeficiency with magnesium defect, Epstein-Barr virus infection and neoplasia	Likely benign (Apr 12, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MAGT1	protein_coding	protein_coding	ENST00000358075	10	69230

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.961	0.0386	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.06	109	145	0.752	0.0000107	2412
Missense in Polyphen		10	34.177	0.29259		594
Synonymous	-0.456	54	49.9	1.08	0.00000364	706
Loss of Function	3.29	1	14.6	0.0687	0.00000112	239

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as accessory component of the N-oligosaccharyl transferase (OST) complex which catalyzes the transfer of a high mannose oligosaccharide from a lipid-linked oligosaccharide donor to an asparagine residue within an Asn-X-Ser/Thr consensus motif in nascent polypeptide chains. Involved in N-glycosylation of STT3B-dependent substrates. Specifically required for the glycosylation of a subset of acceptor sites that are near cysteine residues; in this function seems to act redundantly with TUSC3. In its oxidized form proposed to form transient mixed disulfides with a glycoprotein substrate to facilitate access of STT3B to the unmodified acceptor site. Has also oxidoreductase-independent functions in the STT3B-containing OST complex possibly involving substrate recognition. {ECO:0000269|PubMed:25135935, ECO:0000269|PubMed:26864433, ECO:0000305}.
• Disease: DISEASE: Immunodeficiency, X-linked, with magnesium defect, Epstein-Barr virus infection and neoplasia (XMEN) [MIM:300853]: A disease characterized by CD4 lymphopenia, severe chronic viral infections, and defective T-lymphocyte activation. {ECO:0000269|PubMed:21796205}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: miR-targeted genes in epithelium - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;miR-targeted genes in squamous cell - TarBase;Neutrophil degranulation;Post-translational protein modification;Metabolism of proteins;Innate Immune System;Immune System;Transport of small molecules;Asparagine N-linked glycosylation;Miscellaneous transport and binding events (Consensus)

Recessive Scores

• pRec: 0.0789

Intolerance Scores

• loftool: 0.338
• rvis_EVS: 0.1
• rvis_percentile_EVS: 61.49

Haploinsufficiency Scores

• pHI: 0.118
• hipred: Y
• hipred_score: 0.662
• ghis: 0.504

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.645

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Magt1
• Phenotype: normal phenotype; hematopoietic system phenotype; immune system phenotype

Gene ontology

• Biological process: protein N-linked glycosylation;magnesium ion transport;protein N-linked glycosylation via asparagine;neutrophil degranulation;cognition;transmembrane transport;magnesium ion transmembrane transport
• Cellular component: endoplasmic reticulum;plasma membrane;integral component of plasma membrane;oligosaccharyltransferase complex;membrane;azurophil granule membrane
• Molecular function: dolichyl-diphosphooligosaccharide-protein glycotransferase activity;magnesium ion transmembrane transporter activity