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:
current
Accession:
RCV001008714.1

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)

Gene:
PEX1:peroxisomal biogenesis factor 1 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
7q21.2
Genomic location:
Preferred name:
NM_000466.3(PEX1):c.1886_1887del (p.Asp628_Cys629insTer)
HGVS:
  • 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
Links:
dbSNP: rs1398892633
NCBI 1000 Genomes Browser:
rs1398892633
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]

Condition(s)

Identifiers:
MedGen: CN517202

Recent activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...

Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
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

Description

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.

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

Last Updated: Jan 8, 2022

Support Center