NM_000318.3(PEX2):c.339_345del (p.Gly113_Arg114insTer) AND Peroxisome biogenesis disorder

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Apr 28, 2017
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:: RCV000587540.1

Allele description [Variation Report for NM_000318.3(PEX2):c.339_345del (p.Gly113_Arg114insTer)]

NM_000318.3(PEX2):c.339_345del (p.Gly113_Arg114insTer)

Gene:

PEX2:peroxisomal biogenesis factor 2 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

8q21.13

Genomic location:

Preferred name:

NM_000318.3(PEX2):c.339_345del (p.Gly113_Arg114insTer)

HGVS:

NC_000008.10:g.77896070_77896076del
NC_000008.11:g.76983839_76983845del
NG_008371.1:g.21449_21455del
NM_000318.3:c.339_345delMANE SELECT
NM_001079867.2:c.339_345del
NM_001172086.2:c.339_345del
NM_001172087.2:c.339_345del
NP_000309.2:p.Gly113_Arg114insTer
NP_001073336.2:p.Gly113_Arg114insTer
NP_001165557.2:p.Gly113_Arg114insTer
NP_001165558.2:p.Gly113_Arg114insTer
NC_000008.10:g.77896070_77896076del
NC_000008.10:g.77896070_77896076delCCACCTG
NC_000008.10:g.77896075_77896081del
NM_000318.2:c.339_345del
NM_000318.2:c.339_345delCAGGTGG
NM_000318.3:c.339_345delCAGGTGGMANE SELECT

Links:

dbSNP: rs764771123

NCBI 1000 Genomes Browser:

rs764771123

Molecular consequence:

NM_000318.3:c.339_345del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001079867.2:c.339_345del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001172086.2:c.339_345del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001172087.2:c.339_345del - frameshift variant - [Sequence Ontology: SO:0001589]

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
SCV000696557	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Pathogenic (Apr 28, 2017)	germline	clinical testing	PubMed (1) [See all records that cite this PMID] LabCorp Variant Classification Summary - May 2015.docx Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000696557

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

criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)

Pathogenic
(Apr 28, 2017)

germline

clinical testing

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

LabCorp Variant Classification Summary - May 2015.docx

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, SCV000696557.1

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

Description

Variant summary: The PEX2 c.339_345delCAGGTGG (p.Arg114fs) variant results in a premature termination codon, predicted to cause a truncated or absent PEX2 protein due to nonsense mediated decay, which are commonly known mechanisms for disease. LCA has classified another downstream truncation variant, c.355C>T (p.Arg119X) as pathogenic. This variant was found in 3/121458 control chromosomes at a frequency of 0.0000247, which does not exceed the estimated maximal expected allele frequency of a pathogenic PEX2 variant (0.001118). A publication has cited the variant in two individuals, one homozygous and one assumed compound heterozygous, diagnosed with ZS (Ebberink_2010). In addition, multiple clinical diagnostic laboratories classified this variant as "likely pathogenic/pathogenic. Taken together, this variant is classified as "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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