U.S. flag

An official website of the United States government

NM_002617.4(PEX10):c.335_338del (p.Pro112fs) AND Peroxisome biogenesis disorder

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Jun 28, 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:
RCV002271928.1

Allele description [Variation Report for NM_002617.4(PEX10):c.335_338del (p.Pro112fs)]

NM_002617.4(PEX10):c.335_338del (p.Pro112fs)

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.335_338del (p.Pro112fs)
HGVS:
  • NC_000001.11:g.2408714_2408717del
  • NG_008342.1:g.8855_8858del
  • NM_001374425.1:c.335_338del
  • NM_001374426.1:c.-98_-95del
  • NM_001374427.1:c.-98_-95del
  • NM_002617.4:c.335_338delMANE SELECT
  • NM_153818.2:c.335_338del
  • NP_001361354.1:p.Pro112fs
  • NP_002608.1:p.Pro112fs
  • NP_722540.1:p.Pro112fs
  • NC_000001.10:g.2340153_2340156del
  • NM_153818.1:c.335_338delCCCT
  • NR_164636.1:n.454_457del
Protein change:
P112fs
Links:
dbSNP: rs2100429450
NCBI 1000 Genomes Browser:
rs2100429450
Molecular consequence:
  • NM_001374426.1:c.-98_-95del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001374427.1:c.-98_-95del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001374425.1:c.335_338del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_002617.4:c.335_338del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_153818.2:c.335_338del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NR_164636.1:n.454_457del - non-coding transcript variant - [Sequence Ontology: SO:0001619]

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

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...

Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002556222Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)		Likely pathogenic
(Jun 28, 2022) 		germlineclinical testing

Citation Link

Help

Summary from all submissions

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

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV002556222.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

Variant summary: PEX10 c.335_338delCCCT (p.Pro112ArgfsX40) 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 248336 control chromosomes (gnomAD). To our knowledge, no occurrence of c.335_338delCCCT in individuals affected with Zellweger Syndrome and no experimental evidence demonstrating its impact on protein function have been reported. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014. 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: Dec 24, 2023