NM_002617.4(PEX10):c.600+1G>A AND Peroxisome biogenesis disorder, complementation group 7

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jan 24, 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:: RCV000817369.6

Allele description [Variation Report for NM_002617.4(PEX10):c.600+1G>A]

NM_002617.4(PEX10):c.600+1G>A

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.600+1G>A

HGVS:

NC_000001.11:g.2408451C>T
NG_008342.1:g.9121G>A
NM_001374425.1:c.600+1G>A
NM_001374426.1:c.168+1G>A
NM_001374427.1:c.168+1G>A
NM_002617.4:c.600+1G>AMANE SELECT
NM_153818.2:c.600+1G>A
NC_000001.10:g.2339890C>T
NM_002617.3:c.600+1G>A
NM_153818.1:c.600+1G>A

Note:

NCBI staff reviewed the sequence information reported in PubMed 9683594 to determine the location of this allele on the current reference sequence.

Nucleotide change:

IVS, G-A, +1

Links:

OMIM: 602859.0001; dbSNP: rs267608183

NCBI 1000 Genomes Browser:

rs267608183

Molecular consequence:

NM_001374425.1:c.600+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001374426.1:c.168+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001374427.1:c.168+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_002617.4:c.600+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_153818.2:c.600+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]

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
SCV000957924	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jan 24, 2024)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 9683594, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000957924

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jan 24, 2024)

germline

clinical testing

PubMed (2)
[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

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000957924.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

This sequence change affects a donor splice site in intron 3 of the PEX10 gene. RNA analysis indicates that disruption of this splice site induces altered splicing and may result in an absent or disrupted protein product. This variant is present in population databases (rs267608183, gnomAD 0.009%). Disruption of this splice site has been observed in individual(s) with Zellweger syndrome (PMID: 9683594). ClinVar contains an entry for this variant (Variation ID: 6770). Studies have shown that disruption of this splice site results in skipping of exon 3 and introduces a premature termination codon (PMID: 9683594). The resulting mRNA is expected to undergo nonsense-mediated decay. 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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