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NM_003630.3(PEX3):c.745C>T (p.Gln249Ter) AND not provided

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Aug 14, 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:
RCV003571287.2

Allele description [Variation Report for NM_003630.3(PEX3):c.745C>T (p.Gln249Ter)]

NM_003630.3(PEX3):c.745C>T (p.Gln249Ter)

Gene:
PEX3:peroxisomal biogenesis factor 3 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
6q24.2
Genomic location:
Preferred name:
NM_003630.3(PEX3):c.745C>T (p.Gln249Ter)
HGVS:
  • NC_000006.12:g.143472326C>T
  • NG_008459.1:g.26546C>T
  • NM_003630.3:c.745C>TMANE SELECT
  • NP_003621.1:p.Gln249Ter
  • NC_000006.11:g.143793463C>T
Protein change:
Q249*
Molecular consequence:
  • NM_003630.3:c.745C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004316715Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Aug 14, 2023) 		germlineclinical testing

PubMed (3)
[See all records that cite these PMIDs]

Help

Summary from all submissions

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

Citations

PubMed

Identification of PEX3 as the gene mutated in a Zellweger syndrome patient lacking peroxisomal remnant structures.

Shimozawa N, Suzuki Y, Zhang Z, Imamura A, Ghaedi K, Fujiki Y, Kondo N.

Hum Mol Genet. 2000 Aug 12;9(13):1995-9.

PubMed [citation]
PMID:
10942428

Genetic classification and mutational spectrum of more than 600 patients with a Zellweger syndrome spectrum disorder.

Ebberink MS, Mooijer PA, Gootjes J, Koster J, Wanders RJ, Waterham HR.

Hum Mutat. 2011 Jan;32(1):59-69. doi: 10.1002/humu.21388.

PubMed [citation]
PMID:
21031596
See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004316715.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)

Description

For these reasons, this variant has been classified as Pathogenic. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. This variant has not been reported in the literature in individuals affected with PEX3-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Gln249*) in the PEX3 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in PEX3 are known to be pathogenic (PMID: 10942428, 21031596).

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

Last Updated: Sep 29, 2024