NM_002617.4(PEX10):c.475del (p.Ala159fs) 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:: Aug 30, 2021
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:: RCV001967792.3

Allele description

NM_002617.4(PEX10):c.475del (p.Ala159fs)

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.475del (p.Ala159fs)

HGVS:

NC_000001.11:g.2408579del
NG_008342.1:g.8995del
NM_001374425.1:c.475del
NM_001374426.1:c.43del
NM_001374427.1:c.43del
NM_002617.4:c.475delMANE SELECT
NM_153818.2:c.475del
NP_001361354.1:p.Ala159fs
NP_001361355.1:p.Ala15fs
NP_001361356.1:p.Ala15fs
NP_002608.1:p.Ala159fs
NP_722540.1:p.Ala159fs
NC_000001.10:g.2340016del
NC_000001.10:g.2340018del
NR_164636.1:n.594del

Protein change:

A159fs

Links:

dbSNP: rs2100428583

NCBI 1000 Genomes Browser:

rs2100428583

Molecular consequence:

NM_001374425.1:c.475del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001374426.1:c.43del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001374427.1:c.43del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_002617.4:c.475del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_153818.2:c.475del - frameshift variant - [Sequence Ontology: SO:0001589]
NR_164636.1:n.594del - 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
SCV002218885	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Aug 30, 2021)	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

SCV002218885

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Aug 30, 2021)

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 Invitae, SCV002218885.3

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

Description

This sequence change creates a premature translational stop signal (p.Ala159Argfs*45) 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). For these reasons, this variant has been classified as Pathogenic. This variant has not been reported in the literature in individuals affected with PEX10-related conditions. This variant is not present in population databases (ExAC no frequency).

#	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 20, 2024

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