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NM_000466.3(PEX1):c.1587+1G>A

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Interpretation:
Likely pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
3 (Most recent: Feb 6, 2020)
Last evaluated:
Jun 24, 2019
Accession:
VCV000371701.2
Variation ID:
371701
Description:
single nucleotide variant
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NM_000466.3(PEX1):c.1587+1G>A

Allele ID
357610
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
7q21.2
Genomic location
7: 92510943 (GRCh38) GRCh38 UCSC
7: 92140257 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000007.13:g.92140257C>T
NC_000007.14:g.92510943C>T
NG_008341.1:g.22589G>A
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000007.14:92510942:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
-
Links
ClinGen: CA16041164
dbSNP: rs1057517469
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely pathogenic 1 criteria provided, single submitter Jan 18, 2016 RCV000409309.1
Likely pathogenic 1 criteria provided, single submitter Jan 18, 2016 RCV000411742.1
Likely pathogenic 1 criteria provided, single submitter Jun 24, 2019 RCV001212702.1
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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 Supporting information
Likely pathogenic
(Jan 18, 2016)
criteria provided, single submitter
Method: clinical testing
Peroxisome biogenesis disorder 1A (Zellweger)
Allele origin: unknown
Counsyl
Accession: SCV000487488.1
Submitted: (Nov 23, 2016)
Evidence details
Likely pathogenic
(Jan 18, 2016)
criteria provided, single submitter
Method: clinical testing
Peroxisome biogenesis disorder 1B
Allele origin: unknown
Counsyl
Accession: SCV000487489.1
Submitted: (Nov 23, 2016)
Evidence details
Likely pathogenic
(Jun 24, 2019)
criteria provided, single submitter
Method: clinical testing
Zellweger syndrome
Allele origin: germline
Invitae
Accession: SCV001384295.1
Submitted: (Feb 06, 2020)
Evidence details
Publications
PubMed (4)
Comment:
This sequence change affects a donor splice site in intron 8 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
Genetic classification and mutational spectrum of more than 600 patients with a Zellweger syndrome spectrum disorder. Ebberink MS Human mutation 2011 PMID: 21031596
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
Mutations in PEX1 are the most common cause of peroxisome biogenesis disorders. Reuber BE Nature genetics 1997 PMID: 9398847

Text-mined citations for rs1057517469...

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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 Nov 27, 2021