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NM_000288.4(PEX7):c.12del (p.Cys5fs) AND Peroxisome biogenesis disorder 9B

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Dec 14, 2023
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV003536317.2

Allele description [Variation Report for NM_000288.4(PEX7):c.12del (p.Cys5fs)]

NM_000288.4(PEX7):c.12del (p.Cys5fs)

Gene:
PEX7:peroxisomal biogenesis factor 7 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
6q23.3
Genomic location:
Preferred name:
NM_000288.4(PEX7):c.12del (p.Cys5fs)
HGVS:
  • NC_000006.12:g.136822677del
  • NG_008462.1:g.5098del
  • NG_109276.1:g.582del
  • NG_109276.2:g.615del
  • NM_000288.4:c.12delMANE SELECT
  • NP_000279.1:p.Cys5fs
  • NC_000006.11:g.137143815del
Protein change:
C5fs
Molecular consequence:
  • NM_000288.4:c.12del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:
Peroxisome biogenesis disorder 9B
Synonyms:
PEROXISOME BIOGENESIS DISORDER, PEX7-RELATED, ATYPICAL; Refsum disease, adult, 2
Identifiers:
MONDO: MONDO:0013945; MedGen: C2749346; Orphanet: 773; OMIM: 614879

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004364032Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Dec 14, 2023) 		germlineclinical testing

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

Help

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 Labcorp Genetics (formerly Invitae), Labcorp, SCV004364032.1

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

Description

This sequence change creates a premature translational stop signal (p.Cys5Alafs*45) in the PEX7 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in PEX7 are known to be pathogenic (PMID: 12325024, 12522768, 20301447). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with PEX7-related conditions. 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: Sep 29, 2024