NM_000286.3(PEX12):c.698dup (p.Asn233fs) AND Peroxisome biogenesis disorder 3A (Zellweger)

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jan 23, 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:: RCV003651186.1

Allele description [Variation Report for NM_000286.3(PEX12):c.698dup (p.Asn233fs)]

NM_000286.3(PEX12):c.698dup (p.Asn233fs)

Gene:

PEX12:peroxisomal biogenesis factor 12 [Gene - OMIM - HGNC]

Variant type:

Duplication

Cytogenetic location:

17q12

Genomic location:

Preferred name:

NM_000286.3(PEX12):c.698dup (p.Asn233fs)

HGVS:

NC_000017.11:g.35576166dup
NG_008447.1:g.7474dup
NM_000286.3:c.698dupMANE SELECT
NP_000277.1:p.Asn233fs
NC_000017.10:g.33903182_33903183insT
NC_000017.10:g.33903185dup

Protein change:

N233fs

Molecular consequence:

NM_000286.3:c.698dup - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:: Peroxisome biogenesis disorder 3A (Zellweger)
Synonyms:: PEROXISOMAL BIOGENESIS DISORDER 3A (ZELLWEGER); Peroxisome biogenesis disorder 3A
Identifiers:: MONDO: MONDO:0013927; MedGen: C3553929; Orphanet: 912; OMIM: 614859

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004435191	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jan 23, 2023)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 15542397, 21031596, 33123925, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004435191

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jan 23, 2023)

germline

clinical testing

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

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

The PEX Gene Screen: molecular diagnosis of peroxisome biogenesis disorders in the Zellweger syndrome spectrum.

Steinberg S, Chen L, Wei L, Moser A, Moser H, Cutting G, Braverman N.

Mol Genet Metab. 2004 Nov;83(3):252-63.

PubMed [citation]

PMID:: 15542397

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

See all PubMed Citations (4)

Details of each submission

From Invitae, SCV004435191.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

Description

For these reasons, this variant has been classified as Pathogenic. This variant disrupts a region of the PEX12 protein in which other variant(s) (p.Gln349del) have been determined to be pathogenic (PMID: 15542397, 21031596, 33123925). This suggests that this is a clinically significant region of the protein, and that variants that disrupt it are likely to be disease-causing. This variant has not been reported in the literature in individuals affected with PEX12-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Asn233Lysfs*30) in the PEX12 gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 127 amino acid(s) of the PEX12 protein.

#	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: Feb 28, 2024

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