NM_001127649.3(PEX26):c.185G>A (p.Trp62Ter) AND Peroxisome biogenesis disorder

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Aug 11, 2022
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:: RCV000589459.2

Allele description [Variation Report for NM_001127649.3(PEX26):c.185G>A (p.Trp62Ter)]

NM_001127649.3(PEX26):c.185G>A (p.Trp62Ter)

Gene:

PEX26:peroxisomal biogenesis factor 26 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

22q11.21

Genomic location:

Preferred name:

NM_001127649.3(PEX26):c.185G>A (p.Trp62Ter)

HGVS:

NC_000022.11:g.18078561G>A
NG_008339.1:g.5642G>A
NM_001127649.3:c.185G>AMANE SELECT
NM_001199319.2:c.185G>A
NM_017929.6:c.185G>A
NP_001121121.1:p.Trp62Ter
NP_001186248.1:p.Trp62Ter
NP_060399.1:p.Trp62Ter
NC_000022.10:g.18561327G>A
NM_017929.5:c.185G>A

Protein change:

W62*

Links:

dbSNP: rs1556586479

NCBI 1000 Genomes Browser:

rs1556586479

Molecular consequence:

NM_001127649.3:c.185G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001199319.2:c.185G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_017929.6:c.185G>A - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:: Peroxisome biogenesis disorder (PBD, ZSS)
Synonyms:: PEROXISOME BIOGENESIS DISORDER (NEONATAL ADRENOLEUKODYSTROPHY/INFANTILE REFSUM DISEASE); INFANTILE PHYTANIC ACID STORAGE DISEASE; PEROXISOME BIOGENESIS DISORDER (NALD/IRD); See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0019234; MedGen: C1832200; OMIM: PS214100

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000699449	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Likely pathogenic (Aug 11, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID] Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000699449

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)

Likely pathogenic
(Aug 11, 2022)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Genetic classification and mutational spectrum of more than 600 patients with a Zellweger syndrome spectrum disorder.

Ebberink MS, Mooijer PA, Gootjes J, Koster J, Wanders RJ, Waterham HR.

Hum Mutat. 2011 Jan;32(1):59-69. doi: 10.1002/humu.21388.

PubMed [citation]

PMID:: 21031596

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000699449.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

Variant summary: PEX26 c.185G>A (p.Trp62X) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay, which are commonly known mechanisms for disease. Truncations downstream of this position have been classified as pathogenic by our laboratory. The variant was absent in 212352 control chromosomes (gnomAD). c.185G>A has been reported in the literature in at least one homozygous individual affected with Zellweger Syndrome (e.g. Ebberink_2011). These data indicate that the variant is likely associated with disease. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014. Based on the evidence outlined above, the variant was classified as likely pathogenic.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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