NM_001367916.1(MAGT1):c.-2dup AND X-linked immunodeficiency with magnesium defect, Epstein-Barr virus infection and neoplasia

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Aug 31, 2021
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

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:: RCV001592784.3

Allele description [Variation Report for NM_001367916.1(MAGT1):c.-2dup]

NM_001367916.1(MAGT1):c.-2dup

Genes:

LOC130068460:ATAC-STARR-seq lymphoblastoid active region 29781 [Gene]
MAGT1:magnesium transporter 1 [Gene - OMIM - HGNC]

Variant type:

Duplication

Cytogenetic location:

Xq21.1

Genomic location:

Preferred name:

NM_001367916.1(MAGT1):c.-2dup

HGVS:

NC_000023.11:g.77895413dup
NG_016390.1:g.5157dup
NG_033027.2:g.950dup
NM_001367916.1:c.-2dupMANE SELECT
NM_032121.5:c.95dup
NP_115497.4:p.Asn32fs
LRG_353t1:c.95dup
LRG_1250:g.950dup
LRG_353:g.5157dup
LRG_353p1:p.Asn32fs
NC_000023.10:g.77150910dup
NM_032121.5:c.95dupA

Protein change:

N32fs

Links:

dbSNP: rs2149031468

NCBI 1000 Genomes Browser:

rs2149031468

Molecular consequence:

NM_001367916.1:c.-2dup - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_032121.5:c.95dup - frameshift variant - [Sequence Ontology: SO:0001589]

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
SCV001827203	Center for Molecular Medicine, Children’s Hospital of Fudan University	no assertion criteria provided	Likely pathogenic (Aug 31, 2021)	maternal	clinical testing

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001827203

Center for Molecular Medicine, Children’s Hospital of Fudan University

no assertion criteria provided

Likely pathogenic
(Aug 31, 2021)

maternal

clinical testing

Help

Summary from all submissions

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

Details of each submission

From Center for Molecular Medicine, Children’s Hospital of Fudan University, SCV001827203.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

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

Last Updated: Dec 24, 2023

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