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NM_000466.3(PEX1):c.1239+1G>T AND PEX1-related disorder

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Jun 25, 2024
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:
RCV003422106.5

Allele description [Variation Report for NM_000466.3(PEX1):c.1239+1G>T]

NM_000466.3(PEX1):c.1239+1G>T

Gene:
PEX1:peroxisomal biogenesis factor 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
7q21.2
Genomic location:
Preferred name:
NM_000466.3(PEX1):c.1239+1G>T
HGVS:
  • NC_000007.14:g.92517275C>A
  • NG_008341.2:g.16257G>T
  • NM_000466.3:c.1239+1G>TMANE SELECT
  • NM_001282677.2:c.1239+1G>T
  • NM_001282678.2:c.615+1G>T
  • NC_000007.13:g.92146589C>A
  • NM_000466.2:c.1239+1G>T
Nucleotide change:
IVS5, G-T, +1
Links:
OMIM: 602136.0008; dbSNP: rs756876301
NCBI 1000 Genomes Browser:
rs756876301
Molecular consequence:
  • NM_000466.3:c.1239+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001282677.2:c.1239+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001282678.2:c.615+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]

Condition(s)

Name:
PEX1-related disorder
Synonyms:
PEX1-related condition
Identifiers:

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004117013PreventionGenetics, part of Exact Sciences
no assertion criteria provided
Pathogenic
(Jun 25, 2024) 		germlineclinical testing

Help

Summary from all submissions

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

Details of each submission

From PreventionGenetics, part of Exact Sciences, SCV004117013.2

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

Description

The PEX1 c.1239+1G>T variant is predicted to disrupt the GT donor site and interfere with normal splicing. This variant has been reported in multiple patients with peroxisomal biogenesis disorders, including Zellweger syndrome and Heimler syndrome (referred to as c.1240+1G>T in Yik et al. 2009. PubMed ID: 19105186; Ebberink et al. 2011. PubMed ID: 21031596; Ratbi et al. 2015. PubMed ID: 26387595; Gao et al. 2019. PubMed ID: 31831025). This variant is reported in 0.0058% of alleles in individuals of Latino descent in gnomAD. Variants that disrupt the consensus splice donor site in PEX1 are expected to be pathogenic. This variant is interpreted as pathogenic.

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

Last Updated: Nov 24, 2024