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NM_000466.3(PEX1):c.2088A>G (p.Ile696Met)

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Interpretation:
Benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
9 (Most recent: Sep 3, 2021)
Last evaluated:
Jul 1, 2021
Accession:
VCV000129882.8
Variation ID:
129882
Description:
single nucleotide variant
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NM_000466.3(PEX1):c.2088A>G (p.Ile696Met)

Allele ID
135328
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
7q21.2
Genomic location
7: 92503179 (GRCh38) GRCh38 UCSC
7: 92132493 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
O43933:p.Ile696Met
NC_000007.13:g.92132493T>C
NG_008341.1:g.30353A>G
... more HGVS
Protein change
I696M, I639M, I488M
Other names
NM_000466.2(PEX1):c.2088A>G(p.Ile696Met)
NM_001282677.1(PEX1):c.1917A>G(p.Ile639Met)
NM_001282678.1(PEX1):c.1464A>G(p.Ile488Met)
Canonical SPDI
NC_000007.14:92503178:T:C
Functional consequence
-
Global minor allele frequency (GMAF)
0.01757 (C)

Allele frequency
The Genome Aggregation Database (gnomAD) 0.02322
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.02937
Trans-Omics for Precision Medicine (TOPMed) 0.02600
Exome Aggregation Consortium (ExAC) 0.02698
The Genome Aggregation Database (gnomAD), exomes 0.02710
1000 Genomes Project 0.01757
Links
ClinGen: CA154229
UniProtKB: O43933#VAR_034376
dbSNP: rs35996821
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign 3 criteria provided, multiple submitters, no conflicts Jul 1, 2021 RCV000288096.3
Benign 3 criteria provided, single submitter - RCV000117900.6
Benign 2 criteria provided, single submitter Nov 1, 2018 RCV000992519.2
Benign 1 criteria provided, single submitter Dec 5, 2020 RCV001513794.1
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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
538 776

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(-)
criteria provided, single submitter
Method: clinical testing
NOT SPECIFIED
Allele origin: germline
PreventionGenetics,PreventionGenetics
Accession: SCV000304419.1
Submitted: (Apr 28, 2016)
Evidence details
Benign
(May 31, 2018)
criteria provided, single submitter
Method: curation
Peroxisome biogenesis disorder 1A (Zellweger)
Allele origin: unknown
SIB Swiss Institute of Bioinformatics
Accession: SCV000803438.1
Submitted: (Jun 13, 2018)
Evidence details
Comment:
This variant is interpreted as a Benign - Stand Alone, for Peroxisome biogenesis disorder 1A (Zellweger), in Autosomal Recessive manner. The following ACMG Tag(s) were … (more)
Benign
(Nov 01, 2018)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Athena Diagnostics Inc
Accession: SCV001144899.1
Submitted: (Sep 25, 2019)
Evidence details
Publications
PubMed (4)
Benign
(Jan 13, 2018)
criteria provided, single submitter
Method: clinical testing
Peroxisome biogenesis disorder 1A (Zellweger)
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000470514.3
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated … (more)
Benign
(Dec 05, 2020)
criteria provided, single submitter
Method: clinical testing
Zellweger syndrome
Allele origin: germline
Invitae
Accession: SCV001721477.1
Submitted: (Jan 07, 2021)
Evidence details
Benign
(Jul 01, 2021)
criteria provided, single submitter
Method: clinical testing
Peroxisome biogenesis disorder 1A (Zellweger)
Allele origin: germline
Nilou-Genome Lab
Accession: SCV001748551.1
Submitted: (Jul 07, 2021)
Evidence details
Likely benign
(-)
no assertion criteria provided
Method: clinical testing
AllHighlyPenetrant
(Autosomal recessive inheritance)
Allele origin: germline
Genetic Services Laboratory, University of Chicago
Accession: SCV000152174.2
Submitted: (Jun 27, 2014)
Evidence details
Comment:
Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated … (more)
Benign
(-)
no assertion criteria provided
Method: clinical testing
not specified
Allele origin: germline
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001742320.3
Submitted: (Sep 02, 2021)
Evidence details
Likely benign
(Apr 03, 2021)
no assertion criteria provided
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV001829571.1
Submitted: (Sep 03, 2021)
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
Identification of novel mutations and sequence variation in the Zellweger syndrome spectrum of peroxisome biogenesis disorders. Yik WY Human mutation 2009 PMID: 19105186
PEX1 mutations in the Zellweger spectrum of the peroxisome biogenesis disorders. Crane DI Human mutation 2005 PMID: 16086329
The PEX Gene Screen: molecular diagnosis of peroxisome biogenesis disorders in the Zellweger syndrome spectrum. Steinberg S Molecular genetics and metabolism 2004 PMID: 15542397
Disorders of peroxisome biogenesis due to mutations in PEX1: phenotypes and PEX1 protein levels. Walter C American journal of human genetics 2001 PMID: 11389485

Text-mined citations for rs35996821...

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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 Sep 07, 2021