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NM_000466.3(PEX1):c.1239+1G>T AND not provided

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Dec 3, 2021
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:
RCV001795328.2

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)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002032659GeneDx
criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)		Pathogenic
(Dec 3, 2021) 		germlineclinical testing

Citation Link

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Summary from all submissions

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

Details of each submission

From GeneDx, SCV002032659.2

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

Description

Identified with a frameshift variant in an individual suspected of having a peroxisomal biogenesis disorder (Yik et al., 2009); Canonical splice site variant predicted to result in a null allele in a gene for which loss-of-function is a known mechanism of disease; Not observed at a significant frequency in large population cohorts (Lek et al., 2016); This variant is associated with the following publications: (PMID: 26387595, 19105186)

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

Last Updated: Nov 24, 2024