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NM_000288.4(PEX7):c.592C>T (p.Gln198Ter)

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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:
Sep 9, 2019
Accession:
VCV000813366.3
Variation ID:
813366
Description:
single nucleotide variant
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NM_000288.4(PEX7):c.592C>T (p.Gln198Ter)

Allele ID
801613
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
6q23.3
Genomic location
6: 136866692 (GRCh38) GRCh38 UCSC
6: 137187830 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000006.11:g.137187830C>T
NC_000006.12:g.136866692C>T
NG_008462.1:g.49113C>T
NM_000288.4:c.592C>T MANE Select NP_000279.1:p.Gln198Ter nonsense
Protein change
Q198*
Other names
-
Canonical SPDI
NC_000006.12:136866691:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
Exome Aggregation Consortium (ExAC) 0.00002
Trans-Omics for Precision Medicine (TOPMed) 0.00002
The Genome Aggregation Database (gnomAD), exomes 0.00001
Links
dbSNP: rs764924345
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 - RCV001004180.1
Pathogenic 1 criteria provided, single submitter Sep 9, 2019 RCV001234064.2
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
PEX7 - - GRCh38
GRCh37
291 310

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely pathogenic
(-)
criteria provided, single submitter
Method: clinical testing
Rhizomelic chondrodysplasia punctata type 1
Allele origin: germline
Baylor Genetics
Accession: SCV001162998.1
Submitted: (Sep 27, 2019)
Evidence details
Pathogenic
(Sep 09, 2019)
criteria provided, single submitter
Method: clinical testing
Peroxisome biogenesis disorder 9B
Allele origin: germline
Invitae
Accession: SCV001406690.2
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (3)
Comment:
This sequence change creates a premature translational stop signal (p.Gln198*) in the PEX7 gene. It is expected to result in an absent or disrupted protein … (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
Rhizomelic Chondrodysplasia Punctata Type 1 Braverman NE - 2020 PMID: 20301447
Identification of PEX7 as the second gene involved in Refsum disease. van den Brink DM American journal of human genetics 2003 PMID: 12522768
Mutation analysis of PEX7 in 60 probands with rhizomelic chondrodysplasia punctata and functional correlations of genotype with phenotype. Braverman N Human mutation 2002 PMID: 12325024

Text-mined citations for rs764924345...

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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