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NM_002085.5(GPX4):c.477-8_477-4del AND Spondylometaphyseal dysplasia, Sedaghatian type

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Jul 1, 2014
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:
RCV000128832.4

Allele description [Variation Report for NM_002085.5(GPX4):c.477-8_477-4del]

NM_002085.5(GPX4):c.477-8_477-4del

Gene:
GPX4:glutathione peroxidase 4 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
19p13.3
Genomic location:
Preferred name:
NM_002085.5(GPX4):c.477-8_477-4del
HGVS:
  • NC_000019.10:g.1106234_1106238del
  • NG_050621.1:g.7309_7313del
  • NM_001039847.3:c.477-8_477-4del
  • NM_001039848.4:c.588-8_588-4del
  • NM_001367832.1:c.396-8_396-4del
  • NM_002085.5:c.477-8_477-4delMANE SELECT
  • NC_000019.9:g.1106233_1106237del
  • NM_001039848.2:c.588-8_588-4del
Links:
OMIM: 138322.0002; dbSNP: rs1599810980
NCBI 1000 Genomes Browser:
rs1599810980
Molecular consequence:
  • NM_001039847.3:c.477-8_477-4del - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001039848.4:c.588-8_588-4del - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001367832.1:c.396-8_396-4del - intron variant - [Sequence Ontology: SO:0001627]
  • NM_002085.5:c.477-8_477-4del - intron variant - [Sequence Ontology: SO:0001627]
Functional consequence:
exon loss [PubMedVariation Ontology: 0381]

Condition(s)

Name:
Spondylometaphyseal dysplasia, Sedaghatian type
Synonyms:
METAPHYSEAL CHONDRODYSPLASIA, CONGENITAL LETHAL; SEDAGHATIAN CHONDRODYSPLASIA; Lethal metaphyseal dysplasia
Identifiers:
MONDO: MONDO:0009593; MedGen: C1855229; Orphanet: 93317; OMIM: 250220

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000172488OMIM
no assertion criteria provided
Pathogenic
(Jul 1, 2014) 		germlineliterature only

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only

Citations

PubMed

Mutations in the enzyme glutathione peroxidase 4 cause Sedaghatian-type spondylometaphyseal dysplasia.

Smith AC, Mears AJ, Bunker R, Ahmed A, MacKenzie M, Schwartzentruber JA, Beaulieu CL, Ferretti E; FORGE Canada Consortium., Majewski J, Bulman DE, Celik FC, Boycott KM, Graham GE.

J Med Genet. 2014 Jul;51(7):470-4. doi: 10.1136/jmedgenet-2013-102218. Epub 2014 Apr 4.

PubMed [citation]
PMID:
24706940

Details of each submission

From OMIM, SCV000172488.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (1)

Description

For discussion of the 5-bp deletion in the GPX4 gene (c.588-8_588-4del) that was found in compound heterozygous state in a deceased female infant with the Sedaghatian type of spondylometaphyseal dysplasia (SMDS; 250220) by Smith et al. (2014), see 138322.0001.

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

Last Updated: Apr 23, 2022