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NM_002085.5(GPX4):c.438_441del (p.Lys145_Trp146insTer) AND Spondylometaphyseal dysplasia, Sedaghatian type

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Feb 23, 2023
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:
RCV003152779.1

Allele description [Variation Report for NM_002085.5(GPX4):c.438_441del (p.Lys145_Trp146insTer)]

NM_002085.5(GPX4):c.438_441del (p.Lys145_Trp146insTer)

Gene:
GPX4:glutathione peroxidase 4 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
19p13.3
Genomic location:
Preferred name:
NM_002085.5(GPX4):c.438_441del (p.Lys145_Trp146insTer)
HGVS:
  • NC_000019.10:g.1105771_1105774del
  • NG_050621.1:g.6846_6849del
  • NM_001039847.3:c.438_441del
  • NM_001039848.4:c.549_552del
  • NM_001367832.1:c.357_360del
  • NM_002085.5:c.438_441delMANE SELECT
  • NP_001034936.1:p.Lys145_Trp146insTer
  • NP_001034937.1:p.Lys182_Trp183insTer
  • NP_001354761.1:p.Lys118_Trp119insTer
  • NP_002076.2:p.Lys145_Trp146insTer
  • NC_000019.9:g.1105768_1105771del
  • NC_000019.9:g.1105770_1105773del
Links:
dbSNP: rs772394824
NCBI 1000 Genomes Browser:
rs772394824
Molecular consequence:
  • NM_001039847.3:c.438_441del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001039848.4:c.549_552del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001367832.1:c.357_360del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_002085.5:c.438_441del - nonsense - [Sequence Ontology: SO:0001587]

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
SCV0038416503billion
criteria provided, single submitter

(ACMG Guidelines, 2015)		Likely pathogenic
(Feb 23, 2023) 		unknownclinical testing

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

Help

Summary from all submissions

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

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

Details of each submission

From 3billion, SCV003841650.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

The variant is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: 0.006%). This variant was predicted to result in a loss or disruption of normal protein function through nonsense-mediated decay (NMD) or protein truncation. Multiple pathogenic variants are reported downstream of the variant. Therefore, this variant is classified as Likely pathogenic according to the recommendation of ACMG/AMP guideline.

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

Last Updated: Sep 29, 2024