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NM_001367916.1(MAGT1):c.14G>A (p.Trp5Ter) AND not provided

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Jul 14, 2015
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:
RCV000479226.1

Allele description [Variation Report for NM_001367916.1(MAGT1):c.14G>A (p.Trp5Ter)]

NM_001367916.1(MAGT1):c.14G>A (p.Trp5Ter)

Genes:
LOC130068460:ATAC-STARR-seq lymphoblastoid active region 29781 [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.14G>A (p.Trp5Ter)
HGVS:
  • NC_000023.11:g.77895397C>T
  • NG_016390.1:g.5172G>A
  • NG_033027.2:g.934C>T
  • NM_001367916.1:c.14G>AMANE SELECT
  • NM_032121.5:c.110G>A
  • NP_001354845.1:p.Trp5Ter
  • NP_115497.4:p.Trp37Ter
  • LRG_353t1:c.110G>A
  • LRG_1250:g.934C>T
  • LRG_353:g.5172G>A
  • LRG_353p1:p.Trp37Ter
  • NC_000023.10:g.77150894C>T
  • NG_033027.1:g.934C>T
Protein change:
W37*; TRP37TER
Links:
OMIM: 300715.0004; dbSNP: rs200934080
NCBI 1000 Genomes Browser:
rs200934080
Molecular consequence:
  • NM_001367916.1:c.14G>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_032121.5:c.110G>A - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: CN517202

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000567010GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))		Pathogenic
(Jul 14, 2015) 		germlineclinical testing

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From GeneDx, SCV000567010.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The W37X variant in the MAGT1 gene has not been reported previously as a pathogenic variant nor as a benign polymorphism, to our knowledge. This variant is predicted to cause loss ofnormal protein function either through protein truncation or nonsense-mediated mRNA decay. TheW37X variant was not observed in approximately 6,500 individuals of European and AfricanAmerican ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benignvariant in these populations. We interpret W37X as a pathogenic variant.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Oct 14, 2023