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NM_002617.4(PEX10):c.352C>T (p.Gln118Ter) AND Peroxisome biogenesis disorder

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Apr 21, 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:
RCV001290646.2

Allele description [Variation Report for NM_002617.4(PEX10):c.352C>T (p.Gln118Ter)]

NM_002617.4(PEX10):c.352C>T (p.Gln118Ter)

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.352C>T (p.Gln118Ter)
HGVS:
  • NC_000001.11:g.2408700G>A
  • NG_008342.1:g.8872C>T
  • NM_001374425.1:c.352C>T
  • NM_001374426.1:c.-81C>T
  • NM_001374427.1:c.-81C>T
  • NM_002617.4:c.352C>TMANE SELECT
  • NM_153818.2:c.352C>T
  • NP_001361354.1:p.Gln118Ter
  • NP_002608.1:p.Gln118Ter
  • NP_722540.1:p.Gln118Ter
  • NP_722540.1:p.Gln118Ter
  • NC_000001.10:g.2340139G>A
  • NM_153818.1:c.352C>T
  • NR_164636.1:n.471C>T
Protein change:
Q118*
Links:
dbSNP: rs369965266
NCBI 1000 Genomes Browser:
rs369965266
Molecular consequence:
  • NM_001374426.1:c.-81C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001374427.1:c.-81C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NR_164636.1:n.471C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NM_001374425.1:c.352C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_002617.4:c.352C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_153818.2:c.352C>T - nonsense - [Sequence Ontology: SO:0001587]

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
SCV001478768Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)		Likely pathogenic
(Apr 21, 2022) 		germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

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

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV001478768.2

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

Description

Variant summary: PEX10 c.352C>T (p.Gln118X) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay, which are commonly known mechanisms for disease. Truncations downstream of this position have been classified as pathogenic by our laboratory. The variant was absent in 247864 control chromosomes (gnomAD). c.352C>T has been reported in the literature in an individual (homozygous) affected with Zellweger Syndrome Spectrum disorder (Ebberink_2010). These data indicate that the variant may be associated with disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. One ClinVar submitter (evaluation after 2014) cite the variant as likely pathogenic. Based on the evidence outlined above, the variant was classified as likely pathogenic.

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

Last Updated: Sep 29, 2024