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NM_003630.3(PEX3):c.144C>A (p.Tyr48Ter) AND Peroxisome biogenesis disorder 10A (Zellweger)

Germline classification:
Likely pathogenic (1 submission)
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:
RCV003388694.2

Allele description [Variation Report for NM_003630.3(PEX3):c.144C>A (p.Tyr48Ter)]

NM_003630.3(PEX3):c.144C>A (p.Tyr48Ter)

Gene:
PEX3:peroxisomal biogenesis factor 3 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
6q24.2
Genomic location:
Preferred name:
NM_003630.3(PEX3):c.144C>A (p.Tyr48Ter)
HGVS:
  • NC_000006.12:g.143459155C>A
  • NG_008459.1:g.13375C>A
  • NM_003630.3:c.144C>AMANE SELECT
  • NP_003621.1:p.Tyr48Ter
  • NC_000006.11:g.143780292C>A
  • NM_003630.2:c.144C>A
Protein change:
Y48*
Molecular consequence:
  • NM_003630.3:c.144C>A - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:
Peroxisome biogenesis disorder 10A (Zellweger)
Synonyms:
Peroxisome biogenesis disorder 10A
Identifiers:
MONDO: MONDO:0013948; MedGen: C3553999; Orphanet: 912; OMIM: 614882

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004100407Neuberg Centre For Genomic Medicine, NCGM
criteria provided, single submitter

(ACMG Guidelines, 2015)		Likely pathogenicgermlineclinical testing

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

Help

Summary from all submissions

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

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From Neuberg Centre For Genomic Medicine, NCGM, SCV004100407.1

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

Description

The stop gained p.Y48* in PEX3 (NM_003630.3) has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. The p.Y48* variant is novel (not in any individuals) in gnomAD Exomes and is novel (not in any individuals) in 1000 Genomes. The p.Y48* variant is a loss of function variant in the gene PEX3, which is intolerant of Loss of Function variants, as indicated by the presence of existing pathogenic loss of function variant NP_003621.1:p.S98Rfs*43 and 3 others. This variant is predicted to cause loss of normal protein function through protein truncation. For these reasons, this variant has been classified as Likely Pathogenic. No reportable variant in the PEX3 gene has been detected in the spouse.

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

Last Updated: Apr 6, 2024