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NM_000466.3(PEX1):c.2071+1G>T

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Interpretation:
Pathogenic/Likely pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
2 (Most recent: Jan 7, 2021)
Last evaluated:
Mar 17, 2020
Accession:
VCV000928942.2
Variation ID:
928942
Description:
single nucleotide variant
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NM_000466.3(PEX1):c.2071+1G>T

Allele ID
917461
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
7q21.2
Genomic location
7: 92504731 (GRCh38) GRCh38 UCSC
7: 92134045 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000007.13:g.92134045C>A
NC_000007.14:g.92504731C>A
NG_008341.1:g.28801G>T
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000007.14:92504730:C:A
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
The Genome Aggregation Database (gnomAD), exomes 0.00000
The Genome Aggregation Database (gnomAD) 0.00001
Links
dbSNP: rs267608177
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic 1 criteria provided, single submitter May 31, 2019 RCV001193609.1
Likely pathogenic 1 criteria provided, single submitter Mar 17, 2020 RCV001377623.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
PEX1 - - GRCh38
GRCh37
554 793

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter More information
Pathogenic
(May 31, 2019)
criteria provided, single submitter
Method: clinical testing
Peroxisome biogenesis disorders, Zellweger syndrome spectrum
Affected status: unknown
Allele origin: germline
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV001362557.1
Submitted: (Mar 06, 2020)
Publications:
PubMed (4)
PubMed: 21031596262876552746951111389485
Comment:
Variant summary: PEX1 c.2071+1G>T is located in a canonical splice-site and is predicted to affect mRNA splicing resulting in a significantly altered protein due to … (more)
Likely pathogenic
(Mar 17, 2020)
criteria provided, single submitter
Method: clinical testing
Zellweger spectrum disorders
Affected status: unknown
Allele origin: germline
Invitae
Accession: SCV001575005.1
Submitted: (Jan 07, 2021)
Publications:
PubMed (6)
Comment:
This sequence change affects a donor splice site in intron 12 of the PEX1 gene. It is expected to disrupt RNA splicing and likely results … (more)

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
Cholic acid therapy in Zellweger spectrum disorders. Berendse K Journal of inherited metabolic disease 2016 PMID: 27469511
Zellweger spectrum disorders: clinical manifestations in patients surviving into adulthood. Berendse K Journal of inherited metabolic disease 2016 PMID: 26287655
Genetic classification and mutational spectrum of more than 600 patients with a Zellweger syndrome spectrum disorder. Ebberink MS Human mutation 2011 PMID: 21031596
Splicing in action: assessing disease causing sequence changes. Baralle D Journal of medical genetics 2005 PMID: 16199547
Genetic and clinical aspects of Zellweger spectrum patients with PEX1 mutations. Rosewich H Journal of medical genetics 2005 PMID: 16141001
PEX1 mutations in the Zellweger spectrum of the peroxisome biogenesis disorders. Crane DI Human mutation 2005 PMID: 16086329
Disorders of peroxisome biogenesis due to mutations in PEX1: phenotypes and PEX1 protein levels. Walter C American journal of human genetics 2001 PMID: 11389485
Mutations in PEX1 are the most common cause of peroxisome biogenesis disorders. Reuber BE Nature genetics 1997 PMID: 9398847

Text-mined citations for rs267608177...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Jan 08, 2022