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

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Jun 9, 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:
RCV001174563.2

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 (PBD, ZSS)
Synonyms:
PEROXISOME BIOGENESIS DISORDER (NEONATAL ADRENOLEUKODYSTROPHY/INFANTILE REFSUM DISEASE); INFANTILE PHYTANIC ACID STORAGE DISEASE; PEROXISOME BIOGENESIS DISORDER (NALD/IRD); See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0019234; MedGen: C1832200; OMIM: PS214100

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001337725Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)		Pathogenic
(Jun 9, 2022) 		germlineclinical testing

PubMed (4)
[See all records that cite these PMIDs]

Citation Link

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Genetic classification and mutational spectrum of more than 600 patients with a Zellweger syndrome spectrum disorder.

Ebberink MS, Mooijer PA, Gootjes J, Koster J, Wanders RJ, Waterham HR.

Hum Mutat. 2011 Jan;32(1):59-69. doi: 10.1002/humu.21388.

PubMed [citation]
PMID:
21031596

A PEX10 defect in a patient with no detectable defect in peroxisome assembly or metabolism in cultured fibroblasts.

Steinberg SJ, Snowden A, Braverman NE, Chen L, Watkins PA, Clayton PT, Setchell KD, Heubi JE, Raymond GV, Moser AB, Moser HW.

J Inherit Metab Dis. 2009 Feb;32(1):109-19. doi: 10.1007/s10545-008-0969-8. Epub 2008 Dec 25.

PubMed [citation]
PMID:
19127411
See all PubMed Citations (4)

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV001337725.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (4)

Description

Variant summary: PEX10 c.600+1G>A is located in a canonical splice-site and is predicted to affect mRNA splicing resulting in a significantly altered protein due to either exon skipping, shortening, or inclusion of intronic material. Several computational tools predict a significant impact on normal splicing: Four predict that the variant abolishes a 5 prime splicing donor site. At least one publication reports experimental evidence that this variant affects mRNA splicing (Warren_1998). The variant allele was found at a frequency of 2.4e-05 in 248440 control chromosomes (gnomAD). c.600+1G>A has been reported in the literature in at least one individual affected with Zellweger Syndrome (Warren_1998, homozygous mutation) . These data indicate that the variant may be associated with disease. Sveral publications report experimental evidence evaluating an impact on protein function. The most pronounced variant effect results in <10% of normal activity (Warren_1998, Steinberg_2009). Four clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024