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NM_000466.3(PEX1):c.1855A>T (p.Lys619Ter) AND Zellweger spectrum disorders

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Apr 9, 2023
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:
RCV003758675.1

Allele description

NM_000466.3(PEX1):c.1855A>T (p.Lys619Ter)

Gene:
PEX1:peroxisomal biogenesis factor 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
7q21.2
Genomic location:
Preferred name:
NM_000466.3(PEX1):c.1855A>T (p.Lys619Ter)
HGVS:
  • NC_000007.14:g.92506293T>A
  • NG_008341.2:g.27239A>T
  • NM_000466.3:c.1855A>TMANE SELECT
  • NM_001282677.2:c.1855A>T
  • NM_001282678.2:c.1231A>T
  • NP_000457.1:p.Lys619Ter
  • NP_001269606.1:p.Lys619Ter
  • NP_001269607.1:p.Lys411Ter
  • NC_000007.13:g.92135607T>A
Protein change:
K411*
Molecular consequence:
  • NM_000466.3:c.1855A>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001282677.2:c.1855A>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001282678.2:c.1231A>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:
Zellweger spectrum disorders (ZS)
Synonyms:
Zellweger syndrome; Zellweger Spectrum Disorder; Zellweger Spectrum
Identifiers:
MONDO: MONDO:0019609; MedGen: C0043459; Orphanet: 912

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004453656Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Apr 9, 2023) 		germlineclinical testing

PubMed (7)
[See all records that cite these PMIDs]

Help

Summary from all submissions

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

Citations

PubMed

Mutations in PEX1 are the most common cause of peroxisome biogenesis disorders.

Reuber BE, Germain-Lee E, Collins CS, Morrell JC, Ameritunga R, Moser HW, Valle D, Gould SJ.

Nat Genet. 1997 Dec;17(4):445-8.

PubMed [citation]
PMID:
9398847

PEX1 mutations in the Zellweger spectrum of the peroxisome biogenesis disorders.

Crane DI, Maxwell MA, Paton BC.

Hum Mutat. 2005 Sep;26(3):167-75. Review.

PubMed [citation]
PMID:
16086329
See all PubMed Citations (7)

Details of each submission

From Invitae, SCV004453656.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (7)

Description

For these reasons, this variant has been classified as Pathogenic. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. This variant has not been reported in the literature in individuals affected with PEX1-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Lys619*) in the PEX1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in PEX1 are known to be pathogenic (PMID: 9398847, 16086329, 16141001, 21031596, 26387595, 31831025).

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

Last Updated: Feb 28, 2024