NM_002617.4(PEX10):c.899G>A (p.Trp300Ter) AND Peroxisome biogenesis disorder, complementation group 7

This record was updated by the submitter. Please see the current version.

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Oct 9, 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:: RCV003649501.1

Allele description

NM_002617.4(PEX10):c.899G>A (p.Trp300Ter)

Gene:

PEX10:peroxisomal biogenesis factor 10 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

1p36.32

Genomic location:

Preferred name:

NM_002617.4(PEX10):c.899G>A (p.Trp300Ter)

HGVS:

NC_000001.11:g.2406497C>T
NG_008342.1:g.11075G>A
NG_016128.1:g.19723C>T
NM_001374425.1:c.956G>A
NM_001374426.1:c.524G>A
NM_001374427.1:c.467G>A
NM_002617.4:c.899G>AMANE SELECT
NM_153818.2:c.959G>A
NP_001361354.1:p.Trp319Ter
NP_001361355.1:p.Trp175Ter
NP_001361356.1:p.Trp156Ter
NP_002608.1:p.Trp300Ter
NP_722540.1:p.Trp320Ter
NC_000001.10:g.2337936C>T
NR_164636.1:n.1014G>A

Protein change:

W156*

Molecular consequence:

NR_164636.1:n.1014G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NM_001374425.1:c.956G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001374426.1:c.524G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001374427.1:c.467G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_002617.4:c.899G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_153818.2:c.959G>A - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:: Peroxisome biogenesis disorder, complementation group 7 (CG7)
Synonyms:: Peroxisome biogenesis disorder, complementation group B
Identifiers:: MedGen: C1864399

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004377503	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Oct 9, 2023)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 20695019, 27230853, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004377503

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Oct 9, 2023)

germline

clinical testing

PubMed (3)
[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

Mutations in PEX10 are a cause of autosomal recessive ataxia.

Régal L, Ebberink MS, Goemans N, Wanders RJ, De Meirleir L, Jaeken J, Schrooten M, Van Coster R, Waterham HR.

Ann Neurol. 2010 Aug;68(2):259-63. doi: 10.1002/ana.22035. Review.

PubMed [citation]

PMID:: 20695019

Expanding the spectrum of PEX10-related peroxisomal biogenesis disorders: slowly progressive recessive ataxia.

Renaud M, Guissart C, Mallaret M, Ferdinandusse S, Cheillan D, Drouot N, Muller J, Claustres M, Tranchant C, Anheim M, Koenig M.

J Neurol. 2016 Aug;263(8):1552-8. doi: 10.1007/s00415-016-8167-3. Epub 2016 May 26.

PubMed [citation]

PMID:: 27230853

See all PubMed Citations (3)

Details of each submission

From Invitae, SCV004377503.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

This sequence change creates a premature translational stop signal (p.Trp320*) in the PEX10 gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 27 amino acid(s) of the PEX10 protein. This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with PEX10-related conditions. This variant disrupts a region of the PEX10 protein in which other variant(s) (p.Arg331Gln) have been determined to be pathogenic (PMID: 20695019, 27230853). This suggests that this is a clinically significant region of the protein, and that variants that disrupt it are likely to be disease-causing. For these reasons, this variant has been 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: Feb 28, 2024

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