NM_000466.3(PEX1):c.1A>T (p.Met1Leu) AND not provided

Clinical significance:Pathogenic (Last evaluated: Jan 17, 2019)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV000598681.1

Allele description [Variation Report for NM_000466.3(PEX1):c.1A>T (p.Met1Leu)]

NM_000466.3(PEX1):c.1A>T (p.Met1Leu)

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.1A>T (p.Met1Leu)
HGVS:
  • NC_000007.14:g.92528435T>A
  • NG_008341.1:g.5097A>T
  • NG_008341.2:g.5097A>T
  • NM_000466.3:c.1A>TMANE SELECT
  • NM_001282677.2:c.1A>T
  • NM_001282678.2:c.-659A>T
  • NP_000457.1:p.Met1Leu
  • NP_001269606.1:p.Met1Leu
  • NC_000007.13:g.92157749T>A
  • NM_000466.2:c.1A>T
Protein change:
M1L
Links:
dbSNP: rs1057517501
NCBI 1000 Genomes Browser:
rs1057517501
Molecular consequence:
  • NM_001282678.2:c.-659A>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_000466.3:c.1A>T - initiatior codon variant - [Sequence Ontology: SO:0001582]
  • NM_001282677.2:c.1A>T - initiatior codon variant - [Sequence Ontology: SO:0001582]
  • NM_000466.3:c.1A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001282677.2:c.1A>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000710574GeneDxcriteria provided, single submitter
Pathogenic
(Jan 17, 2019)
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, SCV000710574.1

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

Description

The c.1 A>T variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The c.1 A>T variant is not observed in large population cohorts (Lek et al., 2016). The c.1 A>T variant alters the initiator Methionine codon, and the resultant protein would be described as p.Met1?" using a question mark to signify that it is not known if the loss of Met1 means that all protein translation is completely prevented or if an abnormal protein is produced using an alternate Met. In summary, we interpret this variant as pathogenic."

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

Last Updated: Oct 8, 2021

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