NM_001367916.1(MAGT1):c.462T>A (p.Tyr154Ter) AND X-linked immunodeficiency with magnesium defect, Epstein-Barr virus infection and neoplasia

This record was updated by the submitter. Please see the current version.

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Nov 3, 2022
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV003641422.1

Allele description

NM_001367916.1(MAGT1):c.462T>A (p.Tyr154Ter)

Gene:

MAGT1:magnesium transporter 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

Xq21.1

Genomic location:

Preferred name:

NM_001367916.1(MAGT1):c.462T>A (p.Tyr154Ter)

HGVS:

NC_000023.11:g.77857426A>T
NG_016390.1:g.43143T>A
NM_001367916.1:c.462T>AMANE SELECT
NM_032121.5:c.558T>A
NP_001354845.1:p.Tyr154Ter
NP_115497.4:p.Tyr186Ter
LRG_353t1:c.558T>A
LRG_353:g.43143T>A
LRG_353p1:p.Tyr186Ter
NC_000023.10:g.77112923A>T

Protein change:

Y154*

Molecular consequence:

NM_001367916.1:c.462T>A - nonsense - [Sequence Ontology: SO:0001587]
NM_032121.5:c.558T>A - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:: X-linked immunodeficiency with magnesium defect, Epstein-Barr virus infection and neoplasia
Identifiers:: MONDO: MONDO:0010455; MedGen: C3275445; Orphanet: 317476; OMIM: 300853

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004403770	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Nov 3, 2022)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 24550228, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004403770

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Nov 3, 2022)

germline

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

XMEN disease: a new primary immunodeficiency affecting Mg2+ regulation of immunity against Epstein-Barr virus.

Li FY, Chaigne-Delalande B, Su H, Uzel G, Matthews H, Lenardo MJ.

Blood. 2014 Apr 3;123(14):2148-52. doi: 10.1182/blood-2013-11-538686. Epub 2014 Feb 18. Review.

PubMed [citation]

PMID:: 24550228
PMCID:: PMC3975255

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Invitae, SCV004403770.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

For these reasons, this variant has been classified as Pathogenic. This variant has not been reported in the literature in individuals affected with MAGT1-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Tyr186*) in the MAGT1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in MAGT1 are known to be pathogenic (PMID: 24550228).

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Feb 28, 2024

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