NM_001367916.1(MAGT1):c.895C>T (p.Arg299Ter) AND Congenital disorder of glycosylation

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jul 1, 2018
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:: RCV000767845.1

Allele description [Variation Report for NM_001367916.1(MAGT1):c.895C>T (p.Arg299Ter)]

NM_001367916.1(MAGT1):c.895C>T (p.Arg299Ter)

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.895C>T (p.Arg299Ter)

HGVS:

NC_000023.11:g.77841252G>A
NG_016390.1:g.59317C>T
NM_001367916.1:c.895C>TMANE SELECT
NM_032121.5:c.991C>T
NP_001354845.1:p.Arg299Ter
NP_115497.4:p.Arg331Ter
LRG_353t1:c.991C>T
LRG_353:g.59317C>T
LRG_353p1:p.Arg331Ter
NC_000023.10:g.77096749G>A

Protein change:

R299*; ARG331TER

Links:

OMIM: 300715.0009; dbSNP: rs1569547876

NCBI 1000 Genomes Browser:

rs1569547876

Molecular consequence:

NM_001367916.1:c.895C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_032121.5:c.991C>T - nonsense - [Sequence Ontology: SO:0001587]

Observations:

Condition(s)

Name:: Congenital disorder of glycosylation (CDG)
Synonyms:: Carbohydrate-deficient glycoprotein syndrome; Congenital disorders of glycosylation
Identifiers:: MONDO: MONDO:0015286; MedGen: C0282577; Orphanet: 137

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000898468	Center for Human Genetics, University of Leuven	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Jul 1, 2018)	de novo	clinical testing, research	PubMed (2) [See all records that cite these PMIDs] 25741868, 25135935

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000898468

Center for Human Genetics, University of Leuven

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Jul 1, 2018)

de novo

clinical testing, research

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	de novo	yes	1	not provided	not provided	1	not provided	clinical testing, research

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Oxidoreductase activity is necessary for N-glycosylation of cysteine-proximal acceptor sites in glycoproteins.

Cherepanova NA, Shrimal S, Gilmore R.

J Cell Biol. 2014 Aug 18;206(4):525-39. doi: 10.1083/jcb.201404083.

PubMed [citation]

PMID:: 25135935
PMCID:: PMC4137057

Details of each submission

From Center for Human Genetics, University of Leuven, SCV000898468.1

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

Description

LOF mutation, Functional assays were performed to assess the functionality of the protein

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	de novo	yes	1	not provided	not provided		1	not provided	not provided	not provided
2	de novo	yes	not provided	not provided	assert pathogenicity		not provided	not provided	not provided	not provided

Last Updated: Feb 28, 2024

ClinVar

Relating variation to medicine