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NM_000466.3(PEX1):c.2992C>T (p.Arg998Ter)

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Interpretation:
Pathogenic/Likely pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
6 (Most recent: Nov 19, 2021)
Last evaluated:
Oct 11, 2018
Accession:
VCV000495880.4
Variation ID:
495880
Description:
single nucleotide variant
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NM_000466.3(PEX1):c.2992C>T (p.Arg998Ter)

Allele ID
487227
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
7q21.2
Genomic location
7: 92494331 (GRCh38) GRCh38 UCSC
7: 92123645 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000007.13:g.92123645G>A
NC_000007.14:g.92494331G>A
NG_008341.1:g.39201C>T
... more HGVS
Protein change
R998*, R941*, R790*
Other names
-
Canonical SPDI
NC_000007.14:92494330:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00001
Links
ClinGen: CA4340941
dbSNP: rs61750428
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 Nov 18, 2016 RCV000590014.1
Pathogenic 2 criteria provided, single submitter Oct 11, 2018 RCV000818703.2
Likely pathogenic 1 no assertion criteria provided Sep 11, 2015 RCV000984291.1
Likely pathogenic 1 no assertion criteria provided Sep 11, 2015 RCV000984292.1
Pathogenic 1 no assertion criteria provided Aug 17, 2020 RCV001783092.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
GATAD1 - - GRCh38
GRCh37
95 332
PEX1 - - GRCh38
GRCh37
547 786

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely pathogenic
(Nov 18, 2016)
criteria provided, single submitter
Method: clinical testing
Peroxisome biogenesis disorders, Zellweger syndrome spectrum
Allele origin: germline
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV000696796.1
Submitted: (Jan 25, 2018)
Evidence details
Publications
PubMed (2)
Comment:
Variant summary: The PEX1 c.2992C>T (p.Arg998X) variant results in a premature termination codon, predicted to cause a truncated or absent PEX1 protein due to nonsense … (more)
Pathogenic
(Oct 11, 2018)
criteria provided, single submitter
Method: clinical testing
Zellweger syndrome
Allele origin: germline
Invitae
Accession: SCV000959329.1
Submitted: (Mar 28, 2019)
Evidence details
Publications
PubMed (2)
Comment:
This sequence change creates a premature translational stop signal (p.Arg998*) in the PEX1 gene. It is expected to result in an absent or disrupted protein … (more)
Likely pathogenic
(Sep 11, 2015)
no assertion criteria provided
Method: clinical testing
Heimler syndrome 1
Allele origin: unknown
Counsyl
Accession: SCV001132456.1
Submitted: (Aug 05, 2019)
Evidence details
Publications
PubMed (3)
Likely pathogenic
(Sep 11, 2015)
no assertion criteria provided
Method: clinical testing
Peroxisome biogenesis disorder 1A (Zellweger)
Allele origin: unknown
Counsyl
Accession: SCV001132457.1
Submitted: (Aug 05, 2019)
Evidence details
Publications
PubMed (3)
Likely pathogenic
(Sep 11, 2015)
no assertion criteria provided
Method: clinical testing
Peroxisome biogenesis disorder 1B
Allele origin: unknown
Counsyl
Accession: SCV001132458.1
Submitted: (Aug 05, 2019)
Evidence details
Publications
PubMed (3)
Pathogenic
(Aug 17, 2020)
no assertion criteria provided
Method: clinical testing
not provided
Allele origin: germline
PerkinElmer Genomics
Accession: SCV002016574.1
Submitted: (Nov 19, 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
RNA splicing. The human splicing code reveals new insights into the genetic determinants of disease. Xiong HY Science (New York, N.Y.) 2015 PMID: 25525159
Identification of novel mutations and sequence variation in the Zellweger syndrome spectrum of peroxisome biogenesis disorders. Yik WY Human mutation 2009 PMID: 19105186
Novel PEX1 mutations and genotype-phenotype correlations in Australasian peroxisome biogenesis disorder patients. Maxwell MA Human mutation 2002 PMID: 12402331

Text-mined citations for rs61750428...

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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 28, 2021