NM_000288.4(PEX7):c.277C>T (p.Gln93Ter) AND Peroxisome biogenesis disorder 9B

Clinical significance:Pathogenic (Last evaluated: Oct 2, 2020)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV001387967.1

Allele description [Variation Report for NM_000288.4(PEX7):c.277C>T (p.Gln93Ter)]

NM_000288.4(PEX7):c.277C>T (p.Gln93Ter)

Gene:
PEX7:peroxisomal biogenesis factor 7 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
6q23.3
Genomic location:
Preferred name:
NM_000288.4(PEX7):c.277C>T (p.Gln93Ter)
HGVS:
  • NC_000006.12:g.136826407C>T
  • NG_008462.1:g.8828C>T
  • NM_000288.4:c.277C>TMANE SELECT
  • NP_000279.1:p.Gln93Ter
  • NC_000006.11:g.137147545C>T
  • NM_000288.3:c.277C>T
Protein change:
Q93*
Links:
dbSNP: rs763514968
NCBI 1000 Genomes Browser:
rs763514968
Molecular consequence:
  • NM_000288.4:c.277C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:
Peroxisome biogenesis disorder 9B (PBD9B)
Synonyms:
PEROXISOME BIOGENESIS DISORDER, PEX7-RELATED, ATYPICAL
Identifiers:
MONDO: MONDO:0013945; MedGen: CN159238; Orphanet: 773; OMIM: 614879

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001588747Invitaecriteria provided, single submitter
Pathogenic
(Oct 2, 2020)
germlineclinical testing

PubMed (4)
[See all records that cite these PMIDs]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Mutation analysis of PEX7 in 60 probands with rhizomelic chondrodysplasia punctata and functional correlations of genotype with phenotype.

Braverman N, Chen L, Lin P, Obie C, Steel G, Douglas P, Chakraborty PK, Clarke JT, Boneh A, Moser A, Moser H, Valle D.

Hum Mutat. 2002 Oct;20(4):284-97.

PubMed [citation]
PMID:
12325024

Identification of PEX7 as the second gene involved in Refsum disease.

van den Brink DM, Brites P, Haasjes J, Wierzbicki AS, Mitchell J, Lambert-Hamill M, de Belleroche J, Jansen GA, Waterham HR, Wanders RJ.

Am J Hum Genet. 2003 Feb;72(2):471-7. Epub 2003 Jan 9.

PubMed [citation]
PMID:
12522768
PMCID:
PMC379239
See all PubMed Citations (4)

Details of each submission

From Invitae, SCV001588747.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (4)

Description

This sequence change creates a premature translational stop signal (p.Gln93*) in the PEX7 gene. It is expected to result in an absent or disrupted protein product. This variant is present in population databases (rs763514968, ExAC 0.001%). This variant has not been reported in the literature in individuals with PEX7-related conditions. ClinVar contains an entry for this variant (Variation ID: 370682). Loss-of-function variants in PEX7 are known to be pathogenic (PMID: 12325024, 12522768, 20301447). For these reasons, this variant has been classified as Pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Oct 7, 2021

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