NM_002617.4(PEX10):c.755_756del (p.His252fs) AND Peroxisome biogenesis disorder, complementation group 7

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Mar 26, 2024
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:: RCV002532039.4

Allele description [Variation Report for NM_002617.4(PEX10):c.755_756del (p.His252fs)]

NM_002617.4(PEX10):c.755_756del (p.His252fs)

Gene:

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

Variant type:

Deletion

Cytogenetic location:

1p36.32

Genomic location:

Preferred name:

NM_002617.4(PEX10):c.755_756del (p.His252fs)

HGVS:

NC_000001.11:g.2406741_2406742del
NG_008342.1:g.10831_10832del
NG_016128.1:g.19967_19968del
NM_001374425.1:c.812_813del
NM_001374426.1:c.380_381del
NM_001374427.1:c.323_324del
NM_002617.4:c.755_756delMANE SELECT
NM_153818.2:c.815_816del
NP_001361354.1:p.His271fs
NP_001361355.1:p.His127fs
NP_001361356.1:p.His108fs
NP_002608.1:p.His252fs
NP_722540.1:p.His272fs
NC_000001.10:g.2338179_2338180del
NC_000001.10:g.2338180_2338181del
NM_153818.1:c.815_816del
NM_153818.1:c.815_816delAC
NR_164636.1:n.870_871del

Protein change:

H108fs

Links:

dbSNP: rs1325771720

NCBI 1000 Genomes Browser:

rs1325771720

Molecular consequence:

NM_001374425.1:c.812_813del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001374426.1:c.380_381del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001374427.1:c.323_324del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_002617.4:c.755_756del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_153818.2:c.815_816del - frameshift variant - [Sequence Ontology: SO:0001589]
NR_164636.1:n.870_871del - non-coding transcript variant - [Sequence Ontology: SO:0001619]

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
SCV003485039	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Mar 26, 2024)	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

SCV003485039

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Mar 26, 2024)

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 Labcorp Genetics (formerly Invitae), Labcorp, SCV003485039.3

#	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 results in a frameshift in the PEX10 gene (p.His272Profs*86). While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 75 amino acid(s) of the PEX10 protein and extend the protein by 10 additional amino acid residues. 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. ClinVar contains an entry for this variant (Variation ID: 550383). 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 25, 2025

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