NM_002617.4(PEX10):c.363del (p.Asp122fs) AND Peroxisome biogenesis disorder, complementation group 7

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Dec 31, 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:: RCV003653991.2

Allele description [Variation Report for NM_002617.4(PEX10):c.363del (p.Asp122fs)]

NM_002617.4(PEX10):c.363del (p.Asp122fs)

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.363del (p.Asp122fs)

HGVS:

NC_000001.11:g.2408692del
NG_008342.1:g.8883del
NG_088790.1:g.111del
NM_001374425.1:c.363del
NM_001374426.1:c.-70del
NM_001374427.1:c.-70del
NM_002617.4:c.363delMANE SELECT
NM_153818.2:c.363del
NP_001361354.1:p.Asp122fs
NP_002608.1:p.Asp122fs
NP_722540.1:p.Asp122fs
NC_000001.10:g.2340128del
NC_000001.10:g.2340131del
NR_164636.1:n.482del

Protein change:

D122fs

Molecular consequence:

NM_001374426.1:c.-70del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001374427.1:c.-70del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001374425.1:c.363del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_002617.4:c.363del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_153818.2:c.363del - frameshift variant - [Sequence Ontology: SO:0001589]
NR_164636.1:n.482del - 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
SCV004472788	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Dec 31, 2022)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 9683594, 10862081, 21031596, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004472788

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Dec 31, 2022)

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

Identification of PEX10, the gene defective in complementation group 7 of the peroxisome-biogenesis disorders.

Warren DS, Morrell JC, Moser HW, Valle D, Gould SJ.

Am J Hum Genet. 1998 Aug;63(2):347-59.

PubMed [citation]

PMID:: 9683594
PMCID:: PMC1377304

Phenotype-genotype relationships in PEX10-deficient peroxisome biogenesis disorder patients.

Warren DS, Wolfe BD, Gould SJ.

Hum Mutat. 2000;15(6):509-21.

PubMed [citation]

PMID:: 10862081

See all PubMed Citations (4)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004472788.1

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

Description

This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Asp122Thrfs*31) in the PEX10 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in PEX10 are known to be pathogenic (PMID: 9683594, 10862081, 21031596). This variant has not been reported in the literature in individuals affected with PEX10-related conditions. 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: Sep 29, 2024

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