NM_000466.3(PEX1):c.1886_1887del (p.Asp628_Cys629insTer) AND not provided

Clinical significance:Likely pathogenic (Last evaluated: Dec 6, 2018)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:

Allele description [Variation Report for NM_000466.3(PEX1):c.1886_1887del (p.Asp628_Cys629insTer)]

NM_000466.3(PEX1):c.1886_1887del (p.Asp628_Cys629insTer)

PEX1:peroxisomal biogenesis factor 1 [Gene - OMIM - HGNC]
Variant type:
Cytogenetic location:
Genomic location:
Preferred name:
NM_000466.3(PEX1):c.1886_1887del (p.Asp628_Cys629insTer)
  • NC_000007.14:g.92506262_92506263del
  • NG_008341.1:g.27270_27271del
  • NG_008341.2:g.27270_27271del
  • NM_000466.3:c.1886_1887delMANE SELECT
  • NM_001282677.2:c.1886_1887del
  • NM_001282678.2:c.1262_1263del
  • NP_000457.1:p.Asp628_Cys629insTer
  • NP_001269606.1:p.Asp628_Cys629insTer
  • NP_001269607.1:p.Asp420_Cys421insTer
  • NC_000007.13:g.92135576_92135577del
  • NM_000466.2:c.1886_1887delGT
  • NM_000466.3:c.1886_1887delGTMANE SELECT
dbSNP: rs1398892633
NCBI 1000 Genomes Browser:
Molecular consequence:
  • NM_000466.3:c.1886_1887del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001282677.2:c.1886_1887del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001282678.2:c.1262_1263del - nonsense - [Sequence Ontology: SO:0001587]


MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
SCV001168494GeneDxcriteria provided, single submitter
Likely pathogenic
(Dec 6, 2018)
germlineclinical testing

Citation Link

Summary from all submissions

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

Details of each submission

From GeneDx, SCV001168494.1

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


The c.1886_1887delGT variant in the PEX1 gene has been reported previously in the heterozygous state in a fibroblast cell line derived from a patient with Zellweger syndrome spectrum (Ebberink et al., 2011); it is unclear if this cell line harbored a second PEX1 variant. The c.1886_1887delGT variant causes a frameshift start at codon Cysteine 629, changing this amino acid to a premature stop codon, denoted p.C629Ter. This variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. The c.1886_1887delGT variant is not observed at a significant frequency in large population cohorts (Lek et al., 2016). We interpret c.1886_1887delGT as a likely pathogenic variant.

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

Last Updated: Jan 8, 2022

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