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NM_000466.3(PEX1):c.1A>T (p.Met1Leu)

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Interpretation:
Pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
4 (Most recent: Jan 7, 2021)
Last evaluated:
Feb 2, 2020
Accession:
VCV000371744.4
Variation ID:
371744
Description:
single nucleotide variant
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NM_000466.3(PEX1):c.1A>T (p.Met1Leu)

Allele ID
357628
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
7q21.2
Genomic location
7: 92528435 (GRCh38) GRCh38 UCSC
7: 92157749 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000007.13:g.92157749T>A
NC_000007.14:g.92528435T>A
NG_008341.1:g.5097A>T
... more HGVS
Protein change
M1L
Other names
-
Canonical SPDI
NC_000007.14:92528434:T:A
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
The Genome Aggregation Database (gnomAD), exomes 0.00000
Links
ClinGen: CA16041178
dbSNP: rs1057517501
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 Jan 17, 2019 RCV000598681.1
Pathogenic 1 criteria provided, single submitter Feb 2, 2020 RCV001384497.1
Likely pathogenic 1 no assertion criteria provided May 24, 2016 RCV000409502.1
Likely pathogenic 1 no assertion criteria provided May 24, 2016 RCV000411873.1
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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
543 782

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Pathogenic
(Jan 17, 2019)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000710574.1
Submitted: (Jan 29, 2019)
Evidence details
Comment:
The c.1 A>T variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The … (more)
Pathogenic
(Feb 02, 2020)
criteria provided, single submitter
Method: clinical testing
Zellweger syndrome
Allele origin: germline
Invitae
Accession: SCV001584007.1
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (2)
Comment:
This sequence change affects the initiator methionine of the PEX1 mRNA. The next in-frame methionine is located at codon 209. This variant is not present … (more)
Likely pathogenic
(May 24, 2016)
no assertion criteria provided
Method: clinical testing
Peroxisome biogenesis disorder 1A (Zellweger)
Allele origin: unknown
Counsyl
Accession: SCV000487617.2
Submitted: (Aug 05, 2019)
Evidence details
Likely pathogenic
(May 24, 2016)
no assertion criteria provided
Method: clinical testing
Peroxisome biogenesis disorder 1B
Allele origin: unknown
Counsyl
Accession: SCV000487618.2
Submitted: (Aug 05, 2019)
Evidence details

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

Text-mined citations for rs1057517501...

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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 Oct 08, 2021