ClinVar Genomic variation as it relates to human health
NM_000288.4(PEX7):c.875T>A (p.Leu292Ter)
The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.
Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.
No data submitted for somatic clinical impact
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_000288.4(PEX7):c.875T>A (p.Leu292Ter)
Variation ID: 7780 Accession: VCV000007780.70
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 6q23.3 6: 136898213 (GRCh38) [ NCBI UCSC ] 6: 137219351 (GRCh37) [ NCBI UCSC ]
- Timeline in ClinVar
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First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.
Last submission Help The date of the most recent submission for each type of classification for this variant.
Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline Apr 4, 2013 May 12, 2024 Jan 30, 2024 - HGVS
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Nucleotide Protein Molecular
consequenceNM_000288.4:c.875T>A MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000279.1:p.Leu292Ter nonsense NC_000006.12:g.136898213T>A NC_000006.11:g.137219351T>A NG_008462.1:g.80634T>A - Protein change
- L292*
- Other names
- -
- Canonical SPDI
- NC_000006.12:136898212:T:A
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Functional
consequence HelpThe effect of the variant on RNA or protein function, based on experimental evidence from submitters.
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Global minor allele
frequency (GMAF) HelpThe global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.
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-
Allele frequency
Help
The frequency of the allele represented by this VCV record.
Exome Aggregation Consortium (ExAC) 0.00025
The Genome Aggregation Database (gnomAD), exomes 0.00033
Trans-Omics for Precision Medicine (TOPMed) 0.00037
The Genome Aggregation Database (gnomAD) 0.00048
Genes
Gene | OMIM | ClinGen Gene Dosage Sensitivity Curation |
Variation Viewer
Help
Links to Variation Viewer, a genome browser to view variation data from NCBI databases. |
Related variants | ||
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HI score
Help
The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
TS score
Help
The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
Within gene
Help
The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants. |
All
Help
The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene. |
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PEX7 | - | - |
GRCh38 GRCh37 |
649 | 670 |
Conditions - Germline
Condition
Help
The condition for this variant-condition (RCV) record in ClinVar. |
Classification
Help
The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions) |
Review status
Help
The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. |
Last evaluated
Help
The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
Help
The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page. |
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Pathogenic (9) |
criteria provided, multiple submitters, no conflicts
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Oct 19, 2020 | RCV000008222.26 | |
Pathogenic (12) |
criteria provided, multiple submitters, no conflicts
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May 9, 2022 | RCV000339271.46 | |
Pathogenic (2) |
criteria provided, multiple submitters, no conflicts
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Oct 27, 2023 | RCV000352824.14 | |
Pathogenic (2) |
criteria provided, multiple submitters, no conflicts
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Jan 30, 2024 | RCV000380952.20 | |
Pathogenic (1) |
no assertion criteria provided
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Aug 16, 2016 | RCV000477898.10 | |
Pathogenic (1) |
criteria provided, single submitter
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Mar 3, 2022 | RCV000515356.11 |
Submissions - Germline
Classification
Help
The submitted germline classification for each SCV record. (Last evaluated) |
Review status
Help
Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria) |
Condition
Help
The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant. |
Submitter
Help
The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar. |
More information
Help
This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter. |
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Pathogenic
(Oct 10, 2014)
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criteria provided, single submitter
Method: clinical testing
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Rhizomelic chondrodysplasia punctata, type 1
Affected status: yes
Allele origin:
germline
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Genetic Services Laboratory, University of Chicago
Accession: SCV000248509.1
First in ClinVar: Oct 05, 2015 Last updated: Oct 05, 2015 |
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Pathogenic
(Dec 08, 2016)
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criteria provided, single submitter
Method: clinical testing
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Rhizomelic chondrodysplasia punctata type 1
Affected status: unknown
Allele origin:
germline
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Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV000696493.1
First in ClinVar: Oct 11, 2015 Last updated: Oct 11, 2015 |
Comment:
Variant summary: The PEX7 c.875T>A (p.Leu292X) variant results in a premature termination codon, predicted to cause a truncated or absent PEX7 protein due to nonsense … (more)
Variant summary: The PEX7 c.875T>A (p.Leu292X) variant results in a premature termination codon, predicted to cause a truncated or absent PEX7 protein due to nonsense mediated decay, which are commonly known mechanisms for disease. The variant of interest has been indicated to be a known founder mutation arising from an ancestral chromosome in the Caucasian population per Braverman_2000. The variant of interest was observed in the large, broad control population, ExAC, with an allele frequency of 30/121346 (1/4045), which does not exceed the estimated maximal expected allele frequency for a pathogenic PEX7 variant of 1/534. The variant of interest has been reported in multiple affected individuals in a homozygous and compound heterozygous state. In addition, multiple reputable clinical diagnostic laboratories/databases cite the variant as "pathogenic." Therefore, the variant of interest has been classified as "pathogenic." (less)
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Pathogenic
(May 25, 2018)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: unknown
Allele origin:
germline
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Eurofins Ntd Llc (ga)
Accession: SCV000331429.4
First in ClinVar: Dec 06, 2016 Last updated: May 30, 2018 |
Number of individuals with the variant: 5
Sex: mixed
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Pathogenic
(Apr 27, 2017)
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criteria provided, single submitter
Method: clinical testing
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PEX7-Related Disorders
Affected status: unknown
Allele origin:
germline
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Illumina Laboratory Services, Illumina
Accession: SCV000460548.3
First in ClinVar: Dec 06, 2016 Last updated: May 24, 2019 |
Comment:
The PEX7 c.875T>A (p.Leu292Ter) variant is a stop-gained variant that is well described as a pathogenic variant, accounting for 51% of disease alleles in individuals … (more)
The PEX7 c.875T>A (p.Leu292Ter) variant is a stop-gained variant that is well described as a pathogenic variant, accounting for 51% of disease alleles in individuals with rhizomelic chondrodysplasia punctata (Bravermann et al. 2012). The p.Leu292Ter variant is described in at least ten studies and found in a total of at least 187 individuals including 107 in a homozygous state, 47 in a compound heterozygous state, and 33 individuals in a heterozygous state (Braverman et al. 1997; Motley et al. 1997; Purdue et al. 1997; Brites et al. 1998; Shimozawa et al. 1999; Braverman et al. 2000; Motley et al. 2002; Braverman et al. 2002; Huffnagel et al. 2013; Jacobsen et al. 2016). The variant was absent from 41 controls but is reported at a frequency of 0.00058 in the European American population of the Exome Sequencing Project. The high frequency of the p.Leu292Ter allele is secondary to a founder effect in individuals of Northern European descent. Functional studies showed that the p.Leu292Ter variant protein is localized to the peroxisomes in contrast to the cystolic location of the wild type protein (Bravermann et al. 2012). The variant protein was also shown to be inactive in restoring defective PTS2 import in fibroblasts from patients and Chinese hamster ovary cells and to be impaired in binding both PST2 and PEX5 (Motley et al. 1997; Purdue et al. 1997; Mukai et al. 2002). Based on the collective evidence and the potential impact of stop-gained variants, the p.Leu292Ter variant is classified as pathogenic for PEX7-related disorders. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population. (less)
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Pathogenic
(Apr 19, 2022)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: unknown
Allele origin:
germline
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Revvity Omics, Revvity
Accession: SCV003824888.2
First in ClinVar: Mar 04, 2023 Last updated: Feb 04, 2024 |
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Pathogenic
(Dec 01, 2019)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: yes
Allele origin:
germline
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CeGaT Center for Human Genetics Tuebingen
Accession: SCV000493517.28
First in ClinVar: Dec 06, 2016 Last updated: May 12, 2024 |
Number of individuals with the variant: 3
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Pathogenic
(Nov 11, 2014)
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criteria provided, single submitter
Method: clinical testing
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Rhizomelic chondrodysplasia punctata, type 1
Affected status: unknown
Allele origin:
germline
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Courtagen Diagnostics Laboratory, Courtagen Life Sciences
Accession: SCV000236510.2
First in ClinVar: Jul 02, 2015 Last updated: Jul 12, 2015 |
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Pathogenic
(-)
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criteria provided, single submitter
Method: clinical testing
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Rhizomelic chondrodysplasia punctata type 1
Affected status: unknown
Allele origin:
germline
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Baylor Genetics
Accession: SCV001163004.1
First in ClinVar: Feb 28, 2020 Last updated: Feb 28, 2020 |
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Pathogenic
(Nov 12, 2019)
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criteria provided, single submitter
Method: clinical testing
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Rhizomelic chondrodysplasia punctata type 1
Affected status: unknown
Allele origin:
unknown
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Myriad Genetics, Inc.
Accession: SCV001194024.2
First in ClinVar: Apr 06, 2020 Last updated: Jul 03, 2020 |
Comment:
NM_000288.3(PEX7):c.875T>A(L292*) is classified as pathogenic in the context of type 1 rhizomelic chondrodysplasia punctata. Sources cited for classification include the following: PMID 9090383, 21465523, 10673331, … (more)
NM_000288.3(PEX7):c.875T>A(L292*) is classified as pathogenic in the context of type 1 rhizomelic chondrodysplasia punctata. Sources cited for classification include the following: PMID 9090383, 21465523, 10673331, 12325024, 11781871 and 9090381. Classification of NM_000288.3(PEX7):c.875T>A(L292*) is based on the following criteria: The variant causes a premature termination codon that is not expected to be targeted by nonsense-mediated mRNA decay; however, literature evidence strongly supports pathogenicity. Please note: this variant was assessed in the context of healthy population screening. (less)
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Pathogenic
(Oct 07, 2019)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: unknown
Allele origin:
germline
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ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
Accession: SCV001471931.1
First in ClinVar: Jan 26, 2021 Last updated: Jan 26, 2021 |
Comment:
The PEX7 c.875T>A; p.Leu292Ter variant (rs1805137) accounts for about 50% of disease alleles in individuals affected with rhizomelic chondrodysplasia punctata type 1, and is reported … (more)
The PEX7 c.875T>A; p.Leu292Ter variant (rs1805137) accounts for about 50% of disease alleles in individuals affected with rhizomelic chondrodysplasia punctata type 1, and is reported in the literature in many affected individuals in the homozygous and compound heterozygous state (Braverman 1997, Braverman 2000, Jacobsen 2015, Motley 2002). This variant is reported in ClinVar (Variation ID: 7780), and is found in the general population with an overall allele frequency of 0.034% (96/282696 alleles) in the Genome Aggregation Database. This variant induces an early termination codon and is predicted to result in a truncated protein, since functional analyses of the variant protein show normal expression but a loss of function due to an inability to bind to the PTS2 ligand (Braverman 1997, Mukai 2002). Based on available information, this variant is considered to be pathogenic. References: Braverman et al. Human PEX7 encodes the peroxisomal PTS2 receptor and is responsible for rhizomelic chondrodysplasia punctata. Nat Genet. 1997 Apr;15(4):369-76. Braverman N et al. PEX7 gene structure, alternative transcripts, and evidence for a founder haplotype for the frequent RCDP allele, L292ter. Genomics. 2000 Jan 15;63(2):181-92. Jacobsen JC et al. Whole Exome Sequencing Reveals Compound Heterozygosity for Ethnically Distinct PEX7 Mutations Responsible for Rhizomelic Chondrodysplasia Punctata, Type 1. Case Rep Genet. 2015;2015:454526. Motley AM et al. Mutational spectrum in the PEX7 gene and functional analysis of mutant alleles in 78 patients with rhizomelic chondrodysplasia punctata type 1. Am J Hum Genet. 2002 Mar;70(3):612-24. Mukai S et al. Intracellular localization, function, and dysfunction of the peroxisome-targeting signal type 2 receptor, Pex7p, in mammalian cells. J Biol Chem. 2002 Mar 15;277(11):9548-61. (less)
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Pathogenic
(Mar 16, 2021)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: yes
Allele origin:
germline
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Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center
Accession: SCV002051645.2
First in ClinVar: Jan 08, 2022 Last updated: Feb 05, 2022 |
Comment:
PVS1, PS3, PM3
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Pathogenic
(Oct 19, 2020)
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criteria provided, single submitter
Method: clinical testing
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Rhizomelic chondrodysplasia punctata type 1
(Autosomal recessive inheritance)
Affected status: yes
Allele origin:
germline
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Victorian Clinical Genetics Services, Murdoch Childrens Research Institute
Additional submitter:
Shariant Australia, Australian Genomics
Accession: SCV002767878.1
First in ClinVar: Dec 24, 2022 Last updated: Dec 24, 2022 |
Comment:
Based on the classification scheme VCGS_Germline_v1.3.2, this variant is classified as Pathogenic. Following criteria are met: 0102 - Loss of function is a known mechanism … (more)
Based on the classification scheme VCGS_Germline_v1.3.2, this variant is classified as Pathogenic. Following criteria are met: 0102 - Loss of function is a known mechanism of disease in this gene and is associated with rhizomelic chondrodysplasia punctata, type 1. (I) 0106 - This gene is associated with autosomal recessive disease. (I) 0205 - Variant is predicted to result in a truncated protein (premature termination codon is NOT located at least 54 nucleotides upstream of the final exon-exon junction) with less than 1/3 of the protein sequence affected. (SP) 0252 - This variant is homozygous. (I) 0304 - Variant is present in gnomAD (v2) <0.01 for a recessive condition (96 heterozygotes, 0 homozygotes). (SP) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals. The variant has previously been reported as pathogenic in many patients with rhizomelic chondrodysplasia punctata, and is considered to be a founder variant in the European population (ClinVar, HGMD, PMID: 9090381, PMID: 20301447). (SP) 1002 - This variant has moderate functional evidence supporting abnormal protein function. Functional studies in transfected cells showed impaired protein function (PMID: 9090381). (SP) 1209 - This variant has been shown to be both maternally and paternally inherited (biallelic) (VCGS #20G001699 and 20G001700). (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign (less)
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Pathogenic
(Mar 03, 2022)
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criteria provided, single submitter
Method: clinical testing
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Rhizomelic chondrodysplasia punctata type 1
Phytanic acid storage disease Peroxisome biogenesis disorder 9B
Affected status: unknown
Allele origin:
unknown
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Fulgent Genetics, Fulgent Genetics
Accession: SCV000611237.2
First in ClinVar: Nov 11, 2017 Last updated: Dec 31, 2022 |
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Pathogenic
(May 09, 2022)
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criteria provided, single submitter
Method: clinical testing
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Not Provided
Affected status: yes
Allele origin:
germline
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GeneDx
Accession: SCV000329459.10
First in ClinVar: Dec 06, 2016 Last updated: Mar 04, 2023 |
Comment:
Nonsense variant in the C-terminus predicted to result in protein truncation of the last 32 amino acids; In vitro functional studies of p.(L292*) demonstrate impaired … (more)
Nonsense variant in the C-terminus predicted to result in protein truncation of the last 32 amino acids; In vitro functional studies of p.(L292*) demonstrate impaired binding of essential protein and reduced protein function (Mukai et al., 2002); This variant is associated with the following publications: (PMID: 30487145, 10083738, 25525159, 9090381, 28555434, 26587300, 11781871, 31980526, 31589614, 23572185, 21990100, 9090382, 11756410, 35055178) (less)
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Pathogenic
(Oct 23, 2023)
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criteria provided, single submitter
Method: clinical testing
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Peroxisome biogenesis disorder 9B
Affected status: unknown
Allele origin:
unknown
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Baylor Genetics
Accession: SCV004201629.1
First in ClinVar: Dec 30, 2023 Last updated: Dec 30, 2023 |
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Pathogenic
(Jan 30, 2024)
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criteria provided, single submitter
Method: clinical testing
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Peroxisome biogenesis disorder 9B
Affected status: unknown
Allele origin:
germline
|
Invitae
Accession: SCV000776820.8
First in ClinVar: Dec 06, 2016 Last updated: Feb 20, 2024 |
Comment:
This sequence change creates a premature translational stop signal (p.Leu292*) in the PEX7 gene. While this is not anticipated to result in nonsense mediated decay, … (more)
This sequence change creates a premature translational stop signal (p.Leu292*) in the PEX7 gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 32 amino acid(s) of the PEX7 protein. This variant is present in population databases (rs1805137, gnomAD 0.07%). This premature translational stop signal has been observed in individuals with rhizomelic chondrodysplasia punctata (PMID: 9090381, 9090382, 10083738, 21990100, 22008564, 23572185, 25800479). It is commonly reported in individuals of Northern European ancestry (PMID: 9090381, 9090382, 10083738, 21990100, 22008564, 23572185, 25800479). ClinVar contains an entry for this variant (Variation ID: 7780). Algorithms developed to predict the effect of variants on protein structure and function are not available or were not evaluated for this variant. Experimental studies have shown that this premature translational stop signal affects PEX7 function (PMID: 9090381, 9090382, 11756410). For these reasons, this variant has been classified as Pathogenic. (less)
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Pathogenic
(Oct 27, 2023)
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criteria provided, single submitter
Method: clinical testing
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PEX7-related condition
Affected status: unknown
Allele origin:
germline
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PreventionGenetics, part of Exact Sciences
Accession: SCV004779062.1
First in ClinVar: Mar 16, 2024 Last updated: Mar 16, 2024 |
Comment:
The PEX7 c.875T>A variant is predicted to result in premature protein termination (p.Leu292*). This variant is reported to be one of the most common pathogenic … (more)
The PEX7 c.875T>A variant is predicted to result in premature protein termination (p.Leu292*). This variant is reported to be one of the most common pathogenic variants identified in rhizomelic chondrodysplasia punctata patients (Braverman et al. 1997. PubMed ID: 9090381; Motley et al. 2002. PubMed ID: 11781871; Shimozawa et al. 1999. PubMed ID: 10083738). This variant is reported in 0.068% of alleles in individuals of European (Non-Finnish) descent in gnomAD (http://gnomad.broadinstitute.org/variant/6-137219351-T-A). Nonsense variants in PEX7 are expected to be pathogenic. This variant is interpreted as pathogenic. (less)
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Pathogenic
(Mar 01, 2002)
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no assertion criteria provided
Method: literature only
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RHIZOMELIC CHONDRODYSPLASIA PUNCTATA, TYPE 1
Affected status: not provided
Allele origin:
germline
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OMIM
Accession: SCV000028429.3
First in ClinVar: Apr 04, 2013 Last updated: Jul 25, 2015 |
Comment on evidence:
In 26 of 36 probands with rhizomelic chondrodysplasia punctata (RCDP1; 215100), Braverman et al. (1997) found a nonsense mutation, leu292 to ter (L292X). All these … (more)
In 26 of 36 probands with rhizomelic chondrodysplasia punctata (RCDP1; 215100), Braverman et al. (1997) found a nonsense mutation, leu292 to ter (L292X). All these probands had a severe phenotype. The same mutation, resulting from an A-to-T transversion at nucleotide 875, was identified by Purdue et al. (1997) and Motley et al. (1997). Braverman et al. (1997) suggested that founder effect may account for the high frequency of L292X in northern Europeans; none of the 26 patients either heterozygous or homozygous for L292X were of African or Asian descent. In a Chilean boy with a typical RCDP phenotype and an inversion of chromosome 8 reported by Castillo-Taucher et al. (1991), Shimozawa et al. (1999) found the L292X mutation in compound heterozygous state with A218V (601757.0002). The inversion was also present in the child's unaffected mother. Motley et al. (2002) found the L292X mutation to be by far the most common mutation causing RCDP type 1, followed by the A218V missense mutation (601757.0002). In their large series, these 2 mutations were approximately 52% and 12%, respectively, which is similar to the frequencies of 49% and 6% reported by Braverman et al. (2000), who analyzed 36 patients with RCDP type 1. (less)
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Pathogenic
(-)
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no assertion criteria provided
Method: clinical testing
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not provided
Affected status: yes
Allele origin:
germline
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Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001740180.3 First in ClinVar: Jul 07, 2021 Last updated: Sep 08, 2021 |
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Pathogenic
(Aug 16, 2016)
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no assertion criteria provided
Method: research
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Peroxisome biogenesis disorder 9B
Rhizomelic chondrodysplasia punctata type 1
Affected status: unknown
Allele origin:
germline
|
Division of Human Genetics, Children's Hospital of Philadelphia
Study: CSER-PediSeq
Accession: SCV000536707.1 First in ClinVar: Apr 23, 2017 Last updated: Apr 23, 2017 |
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Pathogenic
(Sep 16, 2020)
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no assertion criteria provided
Method: clinical testing
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Rhizomelic chondrodysplasia punctata type 1
Affected status: unknown
Allele origin:
germline
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Natera, Inc.
Accession: SCV001459669.1
First in ClinVar: Jan 02, 2021 Last updated: Jan 02, 2021 |
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Pathogenic
(-)
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no assertion criteria provided
Method: clinical testing
|
not provided
Affected status: yes
Allele origin:
germline
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Genome Diagnostics Laboratory, Amsterdam University Medical Center
Study: VKGL Data-share Consensus
Accession: SCV001807310.1 First in ClinVar: Aug 27, 2021 Last updated: Aug 27, 2021 |
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Pathogenic
(-)
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no assertion criteria provided
Method: clinical testing
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not provided
Affected status: yes
Allele origin:
germline
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Clinical Genetics, Academic Medical Center
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001917885.1 First in ClinVar: Sep 24, 2021 Last updated: Sep 24, 2021 |
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Pathogenic
(-)
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no assertion criteria provided
Method: clinical testing
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not provided
Affected status: yes
Allele origin:
germline
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Genome Diagnostics Laboratory, University Medical Center Utrecht
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001928571.1 First in ClinVar: Sep 24, 2021 Last updated: Sep 24, 2021 |
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Pathogenic
(-)
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no assertion criteria provided
Method: clinical testing
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not provided
Affected status: yes
Allele origin:
germline
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Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001959535.1 First in ClinVar: Oct 02, 2021 Last updated: Oct 02, 2021 |
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Pathogenic
(-)
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no assertion criteria provided
Method: clinical testing
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not provided
Affected status: yes
Allele origin:
germline
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Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001972932.1 First in ClinVar: Oct 07, 2021 Last updated: Oct 07, 2021 |
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not provided
(-)
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no classification provided
Method: literature only
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Rhizomelic chondrodysplasia punctata type 1
Affected status: not provided
Allele origin:
unknown
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GeneReviews
Accession: SCV000055662.2
First in ClinVar: Apr 04, 2013 Last updated: Oct 01, 2022 |
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Germline Functional Evidence
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 germline classification of this variant
HelpTitle | Author | Journal | Year | Link |
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Rhizomelic Chondrodysplasia Punctata Type 1. | Adam MP | - | 2020 | PMID: 20301447 |
Whole Exome Sequencing Reveals Compound Heterozygosity for Ethnically Distinct PEX7 Mutations Responsible for Rhizomelic Chondrodysplasia Punctata, Type 1. | Jacobsen JC | Case reports in genetics | 2015 | PMID: 26587300 |
Rhizomelic Chondrodysplasia Punctata Type 1 Caused by a Novel Mutation in the PEX7 Gene. | Çim A | Journal of clinical research in pediatric endocrinology | 2015 | PMID: 25800479 |
Rhizomelic chondrodysplasia punctata and cardiac pathology. | Huffnagel IC | Journal of medical genetics | 2013 | PMID: 23572185 |
Functional characterization of novel mutations in GNPAT and AGPS, causing rhizomelic chondrodysplasia punctata (RCDP) types 2 and 3. | Itzkovitz B | Human mutation | 2012 | PMID: 21990100 |
In vitro and in vivo plasmalogen replacement evaluations in rhizomelic chrondrodysplasia punctata and Pelizaeus-Merzbacher disease using PPI-1011, an ether lipid plasmalogen precursor. | Wood PL | Lipids in health and disease | 2011 | PMID: 22008564 |
Nonsense suppressor therapies rescue peroxisome lipid metabolism and assembly in cells from patients with specific PEX gene mutations. | Dranchak PK | Journal of cellular biochemistry | 2011 | PMID: 21465523 |
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 |
Mutational spectrum in the PEX7 gene and functional analysis of mutant alleles in 78 patients with rhizomelic chondrodysplasia punctata type 1. | Motley AM | American journal of human genetics | 2002 | PMID: 11781871 |
Intracellular localization, function, and dysfunction of the peroxisome-targeting signal type 2 receptor, Pex7p, in mammalian cells. | Mukai S | The Journal of biological chemistry | 2002 | PMID: 11756410 |
PEX7 gene structure, alternative transcripts, and evidence for a founder haplotype for the frequent RCDP allele, L292ter. | Braverman N | Genomics | 2000 | PMID: 10673331 |
A novel nonsense mutation of the PEX7 gene in a patient with rhizomelic chondrodysplasia punctata. | Shimozawa N | Journal of human genetics | 1999 | PMID: 10083738 |
Molecular basis of rhizomelic chondrodysplasia punctata type I: high frequency of the Leu-292 stop mutation in 38 patients. | Brites P | Journal of inherited metabolic disease | 1998 | PMID: 9686382 |
Rhizomelic chondrodysplasia punctata is caused by deficiency of human PEX7, a homologue of the yeast PTS2 receptor. | Purdue PE | Nature genetics | 1997 | PMID: 9090383 |
Rhizomelic chondrodysplasia punctata is a peroxisomal protein targeting disease caused by a non-functional PTS2 receptor. | Motley AM | Nature genetics | 1997 | PMID: 9090382 |
Human PEX7 encodes the peroxisomal PTS2 receptor and is responsible for rhizomelic chondrodysplasia punctata. | Braverman N | Nature genetics | 1997 | PMID: 9090381 |
Balanced pericentric inversion 8(p23q13) in a child with rhizomelic chondrodysplasia punctata and his mother. | Castillo-Taucher S | Clinical genetics | 1991 | PMID: 1773541 |
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=PEX7 | - | - | - | - |
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Text-mined citations for rs1805137 ...
HelpRecord last updated May 27, 2024
This date represents the last time this VCV record was updated. The update may be due to an update to one of the included submitted records (SCVs), or due to an update that ClinVar made to the variant such as adding HGVS expressions or a rs number. So this date may be different from the date of the “most recent submission” reported at the top of this page.